Methods for fragmenting and labeling DNA
Abstract
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Expired 17 February 2025, 1.6 years ago.
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14 claims: 2 independent, 12 dependent
- 1A method for fragmenting and labeling DNA comprising:mixing the DNA in a reaction comprising a buffer that has a pH between 6 and 9 at a first temperature, wherein said first temperature is between 16 and 37°C, and less than 6 at a second temperature, wherein said second temperature is between 65 and 105°C, wherein the reaction is mixed at said first temperature;incubating the reaction at the second temperature to generate a plurality of abasic sites in the DNA;incubating the reaction under conditions that promote cleavage of abasic sites and optionally with a nuclease that has 3' phosphatase activity, wherein the condition that promotes cleavage of abasic sites comprises incubation with an apurinic/apyrimidinic (AP) endonuclease;and, labeling the fragments in a reaction comprising TdT;wherein the buffer comprises a buffer selected from the group consisting of Tris, imidazole and colamine.
- 8A method for fragmenting and labeling a nucleic acid sample comprising DNA comprising:generating a plurality of abasic sites in the DNA by a chemical method;cleaving the phosphate backbone at a plurality of the abasic sites;optionally removing modifications at the 3' ends of the fragments, wherein said modifications are moieties other than a 3' hydroxyl group;and labeling the fragments with a detectable label;wherein the nucleic acid sample is in a buffer solution comprising a buffer selected from the group consisting of Tris, imidazole and colamine and wherein said buffer solution has a pH between 6 and 9 at a temperature between 20 and 30°C and a pH less than 6 at a temperature greater than 85°C and wherein said chemical method comprises incubating the sample at a temperature greater than 85°C for at least 15 minutes.
Independent claims2
122 paragraphs in 8 sections, as filed
RELATED APPLICATIONS
0001This application claims priority to <patcit id="pcit0001" dnum="US54541704P" dnum-type="L"><text>U.S. Provisional Patent Application Nos. 60/545,417 filed February 17, 2004</text></patcit>, <patcit id="pcit0002" dnum="US60639193P" dnum-type="L"><text>60/639,193 filed December 22, 2004</text></patcit>, <patcit id="pcit0003" dnum="US60616652P" dnum-type="L"><text>60/616,652 filed October 6, 2004</text></patcit> and <patcit id="pcit0004" dnum="US60589648P" dnum-type="L"><text>60/589,648 filed July 20, 2004</text></patcit>.
FIELD OF THE INVENTION
0002Methods for fragmenting DNA using a chemical nuclease are disclosed. Methods for labelling the fragmented samples are also disclosed. Methods for detection of nucleic acids on a nucleic acid array are also disclosed.
BACKGROUND OF THE INVENTION
0003Nucleic acid sample preparation methods have greatly transformed laboratory research that utilize molecular biology and recombinant DNA techniques and have also impacted the fields of diagnostics, forensics, nucleic acid analysis and gene expression monitoring, to name a few. There remains a need in the art for methods for reproducibly and efficiently fragmenting nucleic acids used for hybridization to oligonucleotide arrays.
SUMMARY OF THE INVENTION
0004Methods and compositions are provided for fragmenting nucleic acid samples. In one aspect the invention provides a method for fragmenting and labeling DNA comprising: mixing the DNA in a reaction comprising a buffer that has a pH between 6 and 9 at a first temperature, wherein said first temperature is between 16 and 37°C and less than 6 at a second temperature, wherein said second temperature is between 65 and 105°C, wherein the reaction is mixed at said first temperature; incubating the reaction at the second temperature to generate a plurality of abasic sites in the DNA; incubating the reaction under conditions that promote cleavage of abasic sites and optionally with a nuclease that has 3' phosphatase activity, wherein the condition that promotes cleavage of abasic sites comprises incubation with an apurinic/apyrimidinic (AP) endonuclease; and, labeling the fragments in a reaction comprising TdT; wherein the buffer comprises a buffer selected from the group consisting of Tris, imidazole and colamine. In another aspect the invention provides a method for fragmenting and labeling a nucleic acid sample comprising DNA comprising: generating a plurality of abasic sites in the DNA by a chemical method; cleaving the phosphate backbone at a plurality of the abasic sites; optionally removing modifications at the 3' ends of the fragments, wherein said modifications are moieties other than a 3' hydroxyl group; and labeling the fragments with a detectable label; wherein the nucleic acid sample is in a buffer solution comprising a buffer selected from the group consisting of Tris, imidazole and colamine and wherein said buffer solution has a pH between 6 and 9 at a temperature between 20 and 30°C and a pH less than 6 at a temperature greater than 85°C and wherein said chemical method comprises incubating the sample at a temperature greater than 85°C for at least 15 minutes. In preferred embodiments, the methods and compositions are used to fragment DNA samples for labeling and hybridization to oligonucleotide arrays. The methods may be used, for example, for gene expression monitoring and for genotyping.
0005In some aspects the DNA that is to be fragmented is an amplification product. In a preferred embodiment the DNA is cDNA that is an amplification product of a sample containing RNA transcripts. RNA transcript samples may be used as templates for reverse transcription to synthesize single stranded cDNA or double stranded cDNA. Methods for cDNA synthesis are well known in the art. The resulting cDNA may be used as template for in vitro transcription to synthesize cRNA and the cRNA may then be used as template for additional cDNA synthesis as described in <patcit id="pcit0005" dnum="US917643A" dnum-type="L"><text>U.S. Patent Application No. 10/917,643</text></patcit>. The resulting cDNA may be single or double stranded.
0006In one aspect the DNA sample to be fragmented is in an aqueous solution containing a buffer that is neutral (pH greater than or equal to 6.0) at a temperature between 20 and 37°C but becomes acidic (pH less than 6.0) at a temperature between 80 and 105°C. The buffer is a Tris (Tris(hydroyxmethyl)aminomethane) buffer solution, an imidazole buffer solution or a colamine buffer solution. The heating results in acidic conditions that generate abasic sites in the DNA by acid catalyzed depurination. The abasic sites can subsequently be cleaved thermally, by base treatment or by the use of an endonuclease that recognizes and cleaves abasic sites, for example Endo IV or Ape 1. Following cleavage at the abasic sites the fragments may be end labeled by terminal transferase to incorporate a detectable label into the 3' end of the fragments. In some aspects the abasic fragments are cleaved thermally or chemically and the 3' ends may be blocked from enzymatic labeling and the fragments may be treated with an AP endonuclease to remove blocking modifications prior to TdT labeling. The detectable label may include, for example, one or more biotins.
0007In another aspect the depurinated DNA is fragmented by chemical or thermal treatment and the fragments are chemically labeled. Chemical labeling may be by reaction with RNH<sub>2</sub> where R is the detectable label. In a preferred aspect R is biotin.
BRIEF DESCRIPTION OF THE FIGURES
0008<ul id="ul0001" list-style="none" compact="compact"><li><figref idref="f0001">Figure 1</figref> shows a schematic of a whole transcript amplification, fragmentation and labeling method.</li><li><figref idref="f0002">Figure 2</figref> shows a schematic of a method of amplifying and reducing the complexity of a genomic DNA sample followed by fragmentation and labeling of the amplification products.</li><li><figref idref="f0003">Figure 3</figref> shows fragmentation by acid-catalzyed depurination. Abasic sites and 3' modified fragments are generated.</li><li><figref idref="f0005">Figure 5</figref> shows propose mechanisms and distribution of products for oxidative scission. Oxidation at different sites of the deoxyribose leads to different 3' modified ends that may require further treatment to generate ends suitable for TdT end labeling.</li><li><figref idref="f0005">Figure 5</figref> shows chemical labeling of oxidative scission products by reductive amination with RNH2.</li><li><figref idref="f0006">Figure 6</figref> shows a method of cleaving depurinated DNA using a β-lyase followed by labeling with a biotin-amine.</li><li><figref idref="f0007">Figure 7</figref> shows a 2'-deoxypseudouriding analog (i-DLR) which can be used for internal labeling of cDNA.</li><li><figref idref="f0008">Figure 8</figref> shows the hybridization results of Tris/Endo IV or APE 1 fragmentation and TdT labeling in percent present and also shows average fragment size.</li><li><figref idref="f0009">Figure 9</figref> shows scaled intensity data for hybridization of samples fragmented with Tris/Endo IV or APE 1 labeled with DLR using TdT.</li><li><figref idref="f0010">Figure 10</figref> shows the hybridization results of fragmentation in 5 mM Tris with the addition of 5% NMF. Percent present and fragment size are shown compared to DNase I treated samples.</li><li><figref idref="f0011">Figure 11</figref> shows changes in percent present and fragmentation size in Tris plus NMF fragmentation in response to changes in DNA amount.</li><li><figref idref="f0012">Figure 12</figref> shows percent present calls after fragmentation of single stranded cDNA with Cu(OP)<sub>2</sub>.</li><li><figref idref="f0011">Figure 11</figref> shows that the percent present and the fragment size vary depending on the amount of DNA present in the fragmentation reaction for Tris/Endo IV fragmentation with NMF present and TdT/DLR labeling.</li></ul>
DETAILED DESCRIPTION OF THE INVENTION
0009The present invention has many preferred embodiments and relies on many patents, applications and other references for details known to those of the art.
0010As used in this application, the singular form "a," "an," and "the" include plural references unless the context clearly dictates otherwise. For example, the term "an agent" includes a plurality of agents, including mixtures thereof.
0011An individual is not limited to a human being but may also be other organisms including but not limited to mammals, plants, bacteria, or cells derived from any of the above.
0012Throughout this disclosure, various aspects of this invention can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies regardless of the breadth of the range.
0013The practice of the present invention may employ, unless otherwise indicated, conventional techniques and descriptions of organic chemistry, polymer technology, molecular biology (including recombinant techniques), cell biology, biochemistry, and immunology, which are within the skill of the art. Such conventional techniques include polymer array synthesis, hybridization, ligation, and detection of hybridization using a label. Specific illustrations of suitable techniques can be had by reference to the example herein below. However, other equivalent conventional procedures can, of course, also be used. Such conventional techniques and descriptions can be found in standard laboratory manuals such as <nplcit id="ncit0001" npl-type="b"><text>Genome Analysis: A Laboratory Manual Series (Vols. I-IV), Using Antibodies: A Laboratory Manual, Cells: A Laboratory Manual, PCR Primer: A Laboratory Manual, and Molecular Cloning: A Laboratory Manual (all from Cold Spring Harbor Laboratory Press</text></nplcit>), <nplcit id="ncit0002" npl-type="b"><text>Stryer, L. (1995) Biochemistry (4th Ed.) Freeman, New York</text></nplcit>, <nplcit id="ncit0003" npl-type="b"><text>Gait, "Oligonucleotide Synthesis: A Practical Approach" 1984, IRL Press, Lond</text></nplcit><i>on,</i><nplcit id="ncit0004" npl-type="b"><text>Nelson and Cox (2000), Lehninger, Principles of Biochemistry 3rd Ed., W. H. Freeman Pub., New York, NY</text></nplcit> and <nplcit id="ncit0005" npl-type="b"><text>Berg et al. (2002) Biochemistry, 5th Ed., W.H. Freeman Pub., New York, NY</text></nplcit>.
0014The present invention can employ solid substrates, including arrays in some preferred embodiments. Methods and techniques applicable to polymer (including protein) array synthesis have been described in United States Serial No. <patcit id="pcit0006" dnum="US09536841B"><text>09/536,841</text></patcit>, <patcit id="pcit0007" dnum="WO0058516A"><text>WO 00/58516</text></patcit>, United States Patent Nos. <patcit id="pcit0008" dnum="US5143854A"><text>5,143,854</text></patcit>, <patcit id="pcit0009" dnum="US5242974A"><text>5,242,974</text></patcit>, <patcit id="pcit0010" dnum="US5252743A"><text>5,252,743</text></patcit>,<patcit id="pcit0011" dnum="US5324633A"><text> 5,324,633</text></patcit>, <patcit id="pcit0012" dnum="US5384261A"><text>5,384,261</text></patcit>, <patcit id="pcit0013" dnum="US5405783A"><text>5,405,783</text></patcit>,<patcit id="pcit0014" dnum="US5424186A"><text> 5,424,186</text></patcit>, <patcit id="pcit0015" dnum="US5451683A"><text>5,451,683</text></patcit>, <patcit id="pcit0016" dnum="US5482867A"><text>5,482,867</text></patcit>, <patcit id="pcit0017" dnum="US5491074A"><text>5,491,074</text></patcit>, <patcit id="pcit0018" dnum="US5527681A"><text>5,527,681</text></patcit>, <patcit id="pcit0019" dnum="US5550215A"><text>5,550,215</text></patcit>, <patcit id="pcit0020" dnum="US5571639A"><text>5,571,639</text></patcit>, <patcit id="pcit0021" dnum="US5578832A"><text>5,578,832</text></patcit>, <patcit id="pcit0022" dnum="US5593839A"><text>5,593,839</text></patcit>, <patcit id="pcit0023" dnum="US5599695A"><text>5,599,695</text></patcit>,<patcit id="pcit0024" dnum="US5624711A"><text> 5,624,711</text></patcit>, <patcit id="pcit0025" dnum="US5631734A"><text>5,631,734</text></patcit>, <patcit id="pcit0026" dnum="US5795716A"><text>5,795,716</text></patcit>, <patcit id="pcit0027" dnum="US5831070A"><text>5,831,070</text></patcit>, <patcit id="pcit0028" dnum="US5837832A"><text>5,837,832</text></patcit>,<patcit id="pcit0029" dnum="US5856101A"><text> 5,856,101</text></patcit>, <patcit id="pcit0030" dnum="US5858659A"><text>5,858,659</text></patcit>, <patcit id="pcit0031" dnum="US5936324A"><text>5,936,324</text></patcit>,<patcit id="pcit0032" dnum="US5968740A"><text> 5,968,740</text></patcit>, <patcit id="pcit0033" dnum="US5974164A"><text>5,974,164</text></patcit>, <patcit id="pcit0034" dnum="US5981185A"><text>5,981,185</text></patcit>, <patcit id="pcit0035" dnum="US5981956A"><text>5,981,956</text></patcit>, <patcit id="pcit0036" dnum="US6025601A"><text>6,025,601</text></patcit>, <patcit id="pcit0037" dnum="US6033860A"><text>6,033,860</text></patcit>, <patcit id="pcit0038" dnum="US6040193A"><text>6,040,193</text></patcit>, <patcit id="pcit0039" dnum="US6090555A"><text>6,090,555</text></patcit>, <patcit id="pcit0040" dnum="US6136269A"><text>6,136,269</text></patcit>,<patcit id="pcit0041" dnum="US6269846B"><text> 6,269,846</text></patcit> and <patcit id="pcit0042" dnum="US6428752B"><text>6,428,752</text></patcit>, in PCT Applications Nos. <patcit id="pcit0043" dnum="US9900730W"><text>PCT/US99/00730</text></patcit> (International Publication Number <patcit id="pcit0044" dnum="WO9936760A"><text>WO 99/36760</text></patcit>) and <patcit id="pcit0045" dnum="US0104285W"><text>PCT/US01/04285</text></patcit>.
0015Patents that describe synthesis techniques in specific embodiments include United States Patent Nos. <patcit id="pcit0046" dnum="US5412087A"><text>5,412,087</text></patcit>, <patcit id="pcit0047" dnum="US6147205A"><text>6,147,205</text></patcit>, <patcit id="pcit0048" dnum="US6262216B"><text>6,262,216</text></patcit>, <patcit id="pcit0049" dnum="US6310189B"><text>6,310,189</text></patcit>,<patcit id="pcit0050" dnum="US5889165A"><text> 5,889,165</text></patcit>, and <patcit id="pcit0051" dnum="US5959098A"><text>5,959,098</text></patcit>. Nucleic acid arrays are described in many of the above patents, but the same techniques are applied to polypeptide arrays.
0016Nucleic acid arrays that are useful in the present invention include those that are commercially available from Affymetrix (Santa Clara, CA) under the brand name GeneChip®. Example arrays are shown on the website at affymetrix.com.
0017The present invention also contemplates many uses for polymers attached to solid substrates. These uses include gene expression monitoring, profiling, library screening, genotyping and diagnostics. Gene expression monitoring and profiling methods can be shown in United States Patents Nos. <patcit id="pcit0052" dnum="US5800992A"><text>5,800,992</text></patcit>, <patcit id="pcit0053" dnum="US6013449A"><text>6,013,449</text></patcit>, <patcit id="pcit0054" dnum="US6020135A"><text>6,020,135</text></patcit>, <patcit id="pcit0055" dnum="US6033860A"><text>6,033,860</text></patcit>, <patcit id="pcit0056" dnum="US6040138A"><text>6,040,138</text></patcit>,<patcit id="pcit0057" dnum="US6177248B"><text> 6,177,248</text></patcit> and <patcit id="pcit0058" dnum="US6309822B"><text>6,309,822</text></patcit>. Genotyping and uses therefore are shown in <patcit id="pcit0059" dnum="USSN60319253P" dnum-type="L"><text>USSN 60/319,253</text></patcit>, <patcit id="pcit0060" dnum="US10013598P" dnum-type="L"><text>10/013,598</text></patcit>, and United States Patent Nos. <patcit id="pcit0061" dnum="US5856092A"><text>5,856,092</text></patcit>, <patcit id="pcit0062" dnum="US6300063B"><text>6,300,063</text></patcit>,<patcit id="pcit0063" dnum="US5858659A"><text> 5,858,659</text></patcit>, <patcit id="pcit0064" dnum="US6284460B"><text>6,284,460</text></patcit>, <patcit id="pcit0065" dnum="US6361947B"><text>6,361,947</text></patcit>, <patcit id="pcit0066" dnum="US6368799B"><text>6,368,799</text></patcit> and <patcit id="pcit0067" dnum="US6333179B"><text>6,333,179</text></patcit>. Other uses are embodied in United States Patents Nos. <patcit id="pcit0068" dnum="US5871928A"><text>5,871,928</text></patcit>, <patcit id="pcit0069" dnum="US5902723A"><text>5,902,723</text></patcit>, <patcit id="pcit0070" dnum="US6045996A"><text>6,045,996</text></patcit>,<patcit id="pcit0071" dnum="US5541061A"><text> 5,541,061</text></patcit>, and <patcit id="pcit0072" dnum="US6197506B"><text>6,197,506</text></patcit>.
0018The present invention also contemplates sample preparation methods in certain preferred embodiments. Prior to or concurrent with genotyping, the genomic sample may be amplified by a variety of mechanisms, some of which may employ PCR. See, <i>e.g.,</i><nplcit id="ncit0006" npl-type="b"><text>PCR Technology: Principles and Applications for DNA Amplification (Ed. H.A. Erlich, Freeman Press, NY, NY, 1992</text></nplcit>); <nplcit id="ncit0007" npl-type="b"><text>PCR Protocols: A Guide to Methods and Applications (Eds. Innis, et al., Academic Press, San Diego, CA, 1990</text></nplcit>); <nplcit id="ncit0008" npl-type="s"><text>Mattila et al., Nucleic Acids Res. 19, 4967 (1991</text></nplcit>); <nplcit id="ncit0009" npl-type="b"><text>Eckert et al., PCR Methods and Applications 1, 17 (1991</text></nplcit>); <nplcit id="ncit0010" npl-type="b"><text>PCR (Eds. McPherson et al., IRL Press, Oxford</text></nplcit>); and United States Patent Nos. <patcit id="pcit0073" dnum="US4683202A"><text>4,683,202</text></patcit>, <patcit id="pcit0074" dnum="US4683195A"><text>4,683,195</text></patcit>, <patcit id="pcit0075" dnum="US4800159A"><text>4,800,159</text></patcit>, <patcit id="pcit0076" dnum="US4965188A"><text>4,965,188</text></patcit>, and <patcit id="pcit0077" dnum="US5333675A"><text>5,333,675</text></patcit>. The sample may be amplified on the array. See, for example, <patcit id="pcit0078" dnum="US6300070B"><text>U.S. Patent No 6,300,070</text></patcit> and United States Patent Application <patcit id="pcit0079" dnum="US09513300B"><text>09/513,300</text></patcit>.
0019Other suitable amplification methods include the ligase chain reaction (LCR) (e.g., <nplcit id="ncit0011" npl-type="s"><text>Wu and Wallace, Genomics 4, 560 (1989</text></nplcit>), <nplcit id="ncit0012" npl-type="s"><text>Landegren et al., Science 241, 1077 (1988</text></nplcit>) and <nplcit id="ncit0013" npl-type="s"><text>Barringer et al. Gene 89:117 (1990</text></nplcit>)), transcription amplification (<nplcit id="ncit0014" npl-type="s"><text>Kwoh et al., Proc. Natl. Acad. Sci. USA 86, 1173 (1989</text></nplcit>) and <patcit id="pcit0080" dnum="WO8810315A"><text>WO88/10315</text></patcit>), self-sustained sequence replication (<nplcit id="ncit0015" npl-type="s"><text>Guatelli et al., Proc. Nat. Acad. Sci. USA, 87, 1874 (1990</text></nplcit>) and <patcit id="pcit0081" dnum="WO9006995A"><text>WO90/06995</text></patcit>), selective amplification of target polynucleotide sequences (United States Patent No. <patcit id="pcit0082" dnum="US6410276B"><text>6,410,276</text></patcit>), consensus sequence primed polymerase chain reaction (CP-PCR) (United States Patent No. <patcit id="pcit0083" dnum="US4437975A"><text>4,437,975</text></patcit>), arbitrarily primed polymerase chain reaction (AP-PCR) (United States Patent Nos. <patcit id="pcit0084" dnum="US5413909A"><text>5,413,909</text></patcit>, <patcit id="pcit0085" dnum="US5861245A"><text>5,861,245</text></patcit>) and nucleic acid based sequence amplification (NABSA). (See, United States Patents Nos. <patcit id="pcit0086" dnum="US5409818A"><text>5,409,818</text></patcit>, <patcit id="pcit0087" dnum="US5554517A"><text>5,554,517</text></patcit>, and <patcit id="pcit0088" dnum="US6063603A"><text>6,063,603</text></patcit>). Other amplification methods that may be used are described in, United States Patent Nos. <patcit id="pcit0089" dnum="US5242794A"><text>5,242,794</text></patcit>,<patcit id="pcit0090" dnum="US5494810A"><text> 5,494,810</text></patcit>, <patcit id="pcit0091" dnum="US4988617A"><text>4,988,617</text></patcit> and in United States Serial No. <patcit id="pcit0092" dnum="US09854317B"><text>09/854,317</text></patcit>.
0020Additional methods of sample preparation and techniques for reducing the complexity of a nucleic sample are described in <nplcit id="ncit0016" npl-type="s"><text>Dong et al., Genome Research 11, 1418 (2001</text></nplcit>), in United States Patent No <patcit id="pcit0093" dnum="US6361947B"><text>6,361,947</text></patcit>, <patcit id="pcit0094" dnum="US6391592B"><text>6,391,592</text></patcit> and United States Patent Application Nos. <patcit id="pcit0095" dnum="US09916135B"><text>09/916,135</text></patcit>, <patcit id="pcit0096" dnum="US09920491B"><text>09/920,491</text></patcit>, <patcit id="pcit0097" dnum="US09910292B"><text>09/910,292</text></patcit>, and <patcit id="pcit0098" dnum="US10013598B"><text>10/013,598</text></patcit>.
0021Methods for conducting polynucleotide hybridization assays have been well developed in the art. Hybridization assay procedures and conditions will vary depending on the application and are selected in accordance with the general binding methods known including those referred to in: <nplcit id="ncit0017" npl-type="b"><text>Maniatis et al. Molecular Cloning: A Laboratory Manual (2nd Ed. Cold Spring Harbor, N.Y, 1989</text></nplcit>); <nplcit id="ncit0018" npl-type="b"><text>Berger and Kimmel Methods in Enzymology, Vol. 152, Guide to Molecular Cloning Techniques (Academic Press, Inc., San Diego, CA, 1987</text></nplcit>); <nplcit id="ncit0019" npl-type="s"><text>Young and Davis, P.N.A.S, 80: 1194 (1983</text></nplcit>). Methods and apparatus for carrying out repeated and controlled hybridization reactions have been described in <patcit id="pcit0099" dnum="US5871928A"><text>US patent 5,871,928</text></patcit>, <patcit id="pcit0100" dnum="US5874219A"><text>5,874,219</text></patcit>, <patcit id="pcit0101" dnum="US6045996A"><text>6,045,996</text></patcit> and <patcit id="pcit0102" dnum="US6386749B"><text>6,386,749</text></patcit>, <patcit id="pcit0103" dnum="US6391623B"><text>6,391,623</text></patcit>.
0022The present invention also contemplates signal detection of hybridization between ligands in certain preferred embodiments. See United States Patent Nos. <patcit id="pcit0104" dnum="US5143854A"><text>5,143,854</text></patcit>,<patcit id="pcit0105" dnum="US5578832A"><text> 5,578,832</text></patcit>; <patcit id="pcit0106" dnum="US5631734A"><text>5,631,734</text></patcit>; <patcit id="pcit0107" dnum="US5834758A"><text>5,834,758</text></patcit>; <patcit id="pcit0108" dnum="US5936324A"><text>5,936,324</text></patcit>; <patcit id="pcit0109" dnum="US5981956A"><text>5,981,956</text></patcit>; <patcit id="pcit0110" dnum="US6025601A"><text>6,025,601</text></patcit>; <patcit id="pcit0111" dnum="US6141096A"><text>6,141,096</text></patcit>; <patcit id="pcit0112" dnum="US6185030B"><text>6,185,030</text></patcit>; <patcit id="pcit0113" dnum="US6201639B"><text>6,201,639</text></patcit>; <patcit id="pcit0114" dnum="US6218803B"><text>6,218,803</text></patcit>; and <patcit id="pcit0115" dnum="US6225625B"><text>6,225,625</text></patcit>, in United States Patent Application <patcit id="pcit0116" dnum="US60364731B"><text>60/364,731</text></patcit> and in PCT Application <patcit id="pcit0117" dnum="US9906097W"><text>PCT/US99/06097</text></patcit> (published as <patcit id="pcit0118" dnum="WO9947964A"><text>WO99/47964</text></patcit>).
0023Methods and apparatus for signal detection and processing of intensity data are disclosed in, for example, United Patent Nos. <patcit id="pcit0119" dnum="US5143854A"><text>5,143,854</text></patcit>, <patcit id="pcit0120" dnum="US5547839A"><text>5,547,839</text></patcit>, <patcit id="pcit0121" dnum="US5578832A"><text>5,578,832</text></patcit>, <patcit id="pcit0122" dnum="US5631734A"><text>5,631,734</text></patcit>, <patcit id="pcit0123" dnum="US5800992A"><text>5,800,992</text></patcit>, <patcit id="pcit0124" dnum="US5834758A"><text>5,834,758</text></patcit>;<patcit id="pcit0125" dnum="US5856092A"><text> 5,856,092</text></patcit>,<patcit id="pcit0126" dnum="US5902723A"><text> 5,902,723</text></patcit>, <patcit id="pcit0127" dnum="US5936324A"><text>5,936,324</text></patcit>, <patcit id="pcit0128" dnum="US5981956A"><text>5,981,956</text></patcit>, <patcit id="pcit0129" dnum="US6025601A"><text>6,025,601</text></patcit>,<patcit id="pcit0130" dnum="US6090555A"><text> 6,090,555</text></patcit>, <patcit id="pcit0131" dnum="US6141096A"><text>6,141,096</text></patcit>, <patcit id="pcit0132" dnum="US6185030B"><text>6,185,030</text></patcit>, <patcit id="pcit0133" dnum="US6201639B"><text>6,201,639</text></patcit>; <patcit id="pcit0134" dnum="US6218803B"><text>6,218,803</text></patcit>; and <patcit id="pcit0135" dnum="US6225625B"><text>6,225,625</text></patcit>, in United States Patent Application <patcit id="pcit0136" dnum="US60364731B"><text>60/364,731</text></patcit> and in PCT Application <patcit id="pcit0137" dnum="US9906097W"><text>PCT/US99/06097</text></patcit> (published as <patcit id="pcit0138" dnum="WO9947964A"><text>WO99/47964</text></patcit>).
0024The practice of the present invention may also employ conventional biology methods, software and systems. Computer software products of the invention typically include computer readable medium having computer-executable instructions for performing the logic steps of the method of the invention. Suitable computer readable medium include floppy disk, CD-ROM/DVD/DVD-ROM, hard-disk drive, flash memory, ROM/RAM, magnetic tapes and etc. The computer executable instructions may be written in a suitable computer language or combination of several languages. Basic computational biology methods are described in, e.g. <nplcit id="ncit0020" npl-type="b"><text>Setubal and Meidanis et al., Introduction to Computational Biology Methods (PWS Publishing Company, Boston, 1997</text></nplcit>); <nplcit id="ncit0021" npl-type="b"><text>Salzberg, Searles, Kasif, (Ed.), Computational Methods in Molecular Biology, (Elsevier, Amsterdam, 1998</text></nplcit>); <nplcit id="ncit0022" npl-type="b"><text>Rashidi and Buehler, Bioinformatics Basics: Application in Biological Science and Medicine (CRC Press, London, 2000</text></nplcit>) and <nplcit id="ncit0023" npl-type="b"><text>Oueletter and Bzevanis Bioinformatics: A Practical Guide for Analysis of Gene and Proteins (Wiley & Sons, Inc., 2nd ed., 2001</text></nplcit>). See United States Patent <patcit id="pcit0139" dnum="US6420108B"><text>6,420,108</text></patcit>.
0025The present invention may also make use of various computer program products and software for a variety of purposes, such as probe design, management of data, analysis, and instrument operation. See, United States Patent Nos. <patcit id="pcit0140" dnum="US5593839A"><text>5,593,839</text></patcit>, <patcit id="pcit0141" dnum="US5795716A"><text>5,795,716</text></patcit>, <patcit id="pcit0142" dnum="US5733729A"><text>5,733,729</text></patcit>, <patcit id="pcit0143" dnum="US5974164A"><text>5,974,164</text></patcit>,<patcit id="pcit0144" dnum="US6066454A"><text> 6,066,454</text></patcit>,<patcit id="pcit0145" dnum="US6090555A"><text> 6,090,555</text></patcit>,<patcit id="pcit0146" dnum="US6185561B"><text> 6,185,561</text></patcit>, <patcit id="pcit0147" dnum="US6188783B"><text>6,188,783</text></patcit>, <patcit id="pcit0148" dnum="US6223127B"><text>6,223,127</text></patcit>, <patcit id="pcit0149" dnum="US6229911B"><text>6,229,911</text></patcit> and <patcit id="pcit0150" dnum="US6308170B"><text>6,308,170</text></patcit>.
0026The present invention may also make use of the several embodiments of the array or arrays and the processing described in United States Patent Nos. <patcit id="pcit0151" dnum="US5545531A"><text>5,545,531</text></patcit> and <patcit id="pcit0152" dnum="US5874219A"><text>5,874,219</text></patcit>.
0027Additionally, the present invention may have preferred embodiments that include methods for providing genetic information over networks such as the Internet as shown in United States Patent applications <patcit id="pcit0153" dnum="US10063559B"><text>10/063,559</text></patcit>, <patcit id="pcit0154" dnum="US60349546B"><text>60/349,546</text></patcit>, <patcit id="pcit0155" dnum="US60376003B"><text>60/376,003</text></patcit>, <patcit id="pcit0156" dnum="US60394574B"><text>60/394,574</text></patcit>, <patcit id="pcit0157" dnum="US60403381B"><text>60/403,381</text></patcit>.
b) Definitions
0028The term "array" as used herein refers to an intentionally created collection of molecules which can be prepared either synthetically or biosynthetically. The molecules in the array can be identical or different from each other. The array can assume a variety of formats, <i>for example,</i> libraries of soluble molecules; libraries of compounds tethered to resin beads, silica chips, or other solid supports.
0029The term "array plate" as used herein refers to a body having a plurality of arrays in which each microarray is separated by a physical barrier resistant to the passage of liquids and forming an area or space, referred to as a well, capable of containing liquids in contact with the probe array.
0030The term "combinatorial synthesis strategy" as used herein refers to a combinatorial synthesis strategy is an ordered strategy for parallel synthesis of diverse polymer sequences by sequential addition of reagents which may be represented by a reactant matrix and a switch matrix, the product of which is a product matrix. A reactant matrix is a 1 column by m row matrix of the building blocks to be added. The switch matrix is all or a subset of the binary numbers, preferably ordered, between 1 and m arranged in columns. A "binary strategy" is one in which at least two successive steps illuminate a portion, often half, of a region of interest on the substrate. In a binary synthesis strategy, all possible compounds which can be formed from an ordered set of reactants are formed. In most preferred embodiments, binary synthesis refers to a synthesis strategy which also factors a previous addition step. For example, a strategy in which a switch matrix for a masking strategy halves regions that were previously illuminated, illuminating about half of the previously illuminated region and protecting the remaining half (while also protecting about half of previously protected regions and illuminating about half of previously protected regions). It will be recognized that binary rounds may be interspersed with non-binary rounds and that only a portion of a substrate may be subjected to a binary scheme. A combinatorial "masking" strategy is a synthesis which uses light or other spatially selective deprotecting or activating agents to remove protecting groups from materials for addition of other materials such as amino acids.
0031The term "complementary" as used herein refers to the hybridization or base pairing between nucleotides or nucleic acids, such as, for instance, between the two strands of a double stranded DNA molecule or between an oligonucleotide primer and a primer binding site on a single stranded nucleic acid to be sequenced or amplified. Complementary nucleotides are, generally, A and T (or A and U), or C and G. Two single stranded RNA or DNA molecules are said to be complementary when the nucleotides of one strand, optimally aligned and compared and with appropriate nucleotide insertions or deletions, pair with at least about 80% of the nucleotides of the other strand, usually at least about 90% to 95%, and more preferably from about 98 to 100%. Alternatively, complementarity exists when an RNA or DNA strand will hybridize under selective hybridization conditions to its complement. Typically, selective hybridization will occur when there is at least about 65% complementary over a stretch of at least 14 to 25 nucleotides, preferably at least about 75%, more preferably at least about 90% complementary. See, <nplcit id="ncit0024" npl-type="s"><text>M. Kanehisa Nucleic Acids Res. 12:203 (1984</text></nplcit>).
0032The term "genome" as used herein is all the genetic material in the chromosomes of an organism. DNA derived from the genetic material in the chromosomes of a particular organism is genomic DNA. A genomic library is a collection of clones made from a set of randomly generated overlapping DNA fragments representing the entire genome of an organism.
0033The term "hybridization" as used herein refers to the process in which two single-stranded polynucleotides bind non-covalently to form a stable double-stranded polynucleotide; triple-stranded hybridization is also theoretically possible. The resulting (usually) double-stranded polynucleotide is a "hybrid.". The proportion of the population of polynucleotides that forms stable hybrids is referred to herein as the "degree of hybridization". Hybridizations are usually performed under stringent conditions, for example, at a salt concentration of no more than 1 M and a temperature of at least 25°C. For example, conditions of 5X SSPE (750 mM NaCl, 50 mM NaPhosphate, 5 mM EDTA, pH 7.4) and a temperature of 25-30°C are suitable for allele-specific probe hybridizations. For stringent conditions, see, for example, <nplcit id="ncit0025" npl-type="b"><text>Sambrook, Fritsche and Maniatis. "Molecular Cloning A laboratory Manual" 2nd Ed. Cold Spring Harbor Press (1989</text></nplcit>).
0034The term "label" as used herein refers to a luminescent label, a light scattering label or a radioactive label. Fluorescent labels include, <i>inter alia,</i> the commercially available fluorescein phosphoramidites such as Fluoreprime (Pharmacia), Fluoredite (Millipore) and FAM (ABI). See United States Patent <patcit id="pcit0158" dnum="US6287778B"><text>6,287,778</text></patcit>.
0035The term "microtiter plates" as used herein refers to arrays of discrete wells that come in standard formats (96, 384 and 1536 wells) which are used for examination of the physical, chemical or biological characteristics of a quantity of samples in parallel.
0036The term "mixed population" or sometimes refer by "complex population" as used herein refers to any sample containing both desired and undesired nucleic acids. As a non-limited example, a complex population of nucleic acids may to total genomic DNA, total genomic RNA or a combination thereof. Moreover, a complex population of nucleic acids may have been enriched for a given population but include other undesirable populations. For example, a complex population of nucleic acids may be a sample which has been enriched for desired messenger RNA (mRNA) sequences but still includes some undesired ribosomal RNA sequences (rRNA).
0037The term "mRNA" or sometimes refer by "mRNA transcripts" as used herein, include, but not limited to pre-mRNA transcript(s), transcript processing intermediates, mature mRNA(s) ready for translation and transcripts of the gene or genes, or nucleic acids derived from the mRNA transcript(s). Transcript processing may include splicing, editing and degradation. As used herein, a nucleic acid derived from an mRNA transcript refers to a nucleic acid for whose synthesis the mRNA transcript or a subsequence thereof has ultimately served as a template. Thus, a cDNA reverse transcribed from an mRNA, an RNA transcribed from that cDNA, a DNA amplified from the cDNA, an RNA transcribed from the amplified DNA, <i>etc</i>., are all derived from the mRNA transcript and detection of such derived products is indicative of the presence and/or abundance of the original transcript in a sample. Thus, mRNA derived samples include, but are not limited to, mRNA transcripts of the gene or genes, cDNA reverse transcribed from the mRNA, cRNA transcribed from the cDNA, DNA amplified from the genes, RNA transcribed from amplified DNA, and the like.
0038The term "nucleic acids" as used herein may include any polymer or oligomer of pyrimidine and purine bases, preferably cytosine, thymine, and uracil, and adenine and guanine, respectively. <i>See</i><nplcit id="ncit0026" npl-type="b"><text>Albert L. Lehninger, PRINCIPLES OF BIOCHEMISTRY, at 793-800 (Worth Pub. 1982</text></nplcit>). Indeed, the present invention contemplates any deoxyribonucleotide, ribonucleotide or peptide nucleic acid component, and any chemical variants thereof, such as methylated, hydroxymethylated or glucosylated forms of these bases, and the like. The polymers or oligomers may be heterogeneous or homogeneous in composition, and may be isolated from naturally-occurring sources or may be artificially or synthetically produced. In addition, the nucleic acids may be DNA or RNA, or a mixture thereof, and may exist permanently or transitionally in single-stranded or double-stranded form, including homoduplex, heteroduplex, and hybrid states.
0039The term "oligonucleotide" or sometimes refer by "polynucleotide" as used herein refers to a nucleic acid ranging from at least 2, preferable at least 8, and more preferably at least 20 nucleotides in length or a compound that specifically hybridizes to a polynucleotide. Polynucleotides of the present invention include sequences of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) which may be isolated from natural sources, recombinantly produced or artificially synthesized and mimetics thereof. A further example of a polynucleotide of the present invention may be peptide nucleic acid (PNA). The invention also encompasses situations in which there is a nontraditional base pairing such as Hoogsteen base pairing which has been identified in certain tRNA molecules and postulated to exist in a triple helix. "Polynucleotide" and "oligonucleotide" are used interchangeably in this application.
0040The term "primer" as used herein refers to a single-stranded oligonucleotide capable of acting as a point of initiation for template-directed DNA synthesis under suitable conditions for example, buffer and temperature, in the presence of four different nucleoside triphosphates and an agent for polymerization, such as, for example, DNA or RNA polymerase or reverse transcriptase. The length of the primer, in any given case, depends on, for example, the intended use of the primer, and generally ranges from 15 to 30 nucleotides. Short primer molecules generally require cooler temperatures to form sufficiently stable hybrid complexes with the template. A primer need not reflect the exact sequence of the template but must be sufficiently complementary to hybridize with such template. The primer site is the area of the template to which a primer hybridizes. The primer pair is a set of primers including a 5' upstream primer that hybridizes with the 5' end of the sequence to be amplified and a 3' downstream primer that hybridizes with the complement of the 3' end of the sequence to be amplified.
0041The term "probe" as used herein refers to a surface-immobilized molecule that can be recognized by a particular target. See <patcit id="pcit0159" dnum="US6582908B"><text>U.S. Patent No. 6,582,908</text></patcit> for an example of arrays having all possible combinations of probes with 10, 12, and more bases. Examples of probes that can be investigated by this invention include, but are not restricted to, agonists and antagonists for cell membrane receptors, toxins and venoms, viral epitopes, hormones (for example, opioid peptides, steroids, etc.), hormone receptors, peptides, enzymes, enzyme substrates, cofactors, drugs, lectins, sugars, oligonucleotides, nucleic acids, oligosaccharides, proteins, and monoclonal antibodies.
0042The term "solid support", "support", and "substrate" as used herein are used interchangeably and refer to a material or group of materials having a rigid or semi-rigid surface or surfaces. In many embodiments, at least one surface of the solid support will be substantially flat, although in some embodiments it may be desirable to physically separate synthesis regions for different compounds with, for example, wells, raised regions, pins, etched trenches, or the like. According to other embodiments, the solid support(s) will take the form of beads, resins, gels, microspheres, or other geometric configurations. See <patcit id="pcit0160" dnum="US5744305A"><text>U.S. Patent No. 5,744,305</text></patcit> for exemplary substrates.
0043The term "target" as used herein refers to a molecule that has an affinity for a given probe. Targets may be naturally-occurring or man-made molecules. Also, they can be employed in their unaltered state or as aggregates with other species. Targets may be attached, covalently or noncovalently, to a binding member, either directly or via a specific binding substance. Examples of targets which can be employed by this invention include, but are not restricted to, antibodies, cell membrane receptors, monoclonal antibodies and antisera reactive with specific antigenic determinants (such as on viruses, cells or other materials), drugs, oligonucleotides, nucleic acids, peptides, cofactors, lectins, sugars, polysaccharides, cells, cellular membranes, and organelles. Targets are sometimes referred to in the art as anti-probes. As the term targets is used herein, no difference in meaning is intended. A "Probe Target Pair" is formed when two macromolecules have combined through molecular recognition to form a complex.
0044An abasic site or AP site in DNA or RNA results from loss of the base, frequently resulting from hydrolytic cleavage of the N-glycosylic bond. AP sites may also be oxidized, for example at the C-1', C-2', C-4' or C-5', resulting in modification of the deoxyribose moiety. The process is increased by any factor or chemical modification that develops a positive charge on the nucleic base and labilizes the glycosylic bond. Abasic sites are recognized by a set of endonucleases which recognize the AP site and cleave the DNA either at the 5' side of the AP site, <i>E.coli</i> exonuclease III and endonuclease IV, or at the 3' side of the AP site, for example, <i>E.coli</i> endonuclease III and bacteriophage T4 endonuclease V. may be cleaved by AP endonucleases. Abasic sites are also alkali-labile and can lead to strand breakage through β- and δ- elimination. For a discussion of abasic sites in DNA see <nplcit id="ncit0027" npl-type="s"><text>Lhomme et al., Biopolymers 52-65-83 (1999</text></nplcit>). Generally all AP endonucleases recognize "regular" AP sites but may vary in their ability to recognize different oxidized AP sites, <nplcit id="ncit0028" npl-type="s"><text>Povirk and Steighner Mutat. Res. 214:13-22 (1989</text></nplcit>) and <nplcit id="ncit0029" npl-type="s"><text>Haring et al., Nuc. Acids Res. 22:2010-2015 (1994</text></nplcit>). AP endonucleases include, for example, FPG protein, endonuclease III, T4 endonuclease V, endonuclease IV and exonuclease III.
0045<i>E.coli</i> Endonuclease IV specifically catalyzes the formation of single strand breaks at apurinic and apyriminic sites in DNA. It also removes 3'-blocking groups (e.g. 3'-phosphoglycolate and 3'-phosphate) from damaged ends of DNA. Endonuclease IV is a class II AP (apurinic/apyrimidic) endonuclease with an associated 3'-diesterase activity and no associated N-glycosylase activity. Endonuclease IV can remove phosphoglycoaldhyde, deoxyribose-5-phospate, 4-hydroxy-2-pentanal, and phosphate groups from the 3' ends of DNA. Endonuclease IV does not contain 3' exonuclease activity. The enzyme has no magnesium requirement and is fully active in EDTA. The enzyme is further described in the following references: <nplcit id="ncit0030" npl-type="s"><text>Ljungquist, S., et al., J. Biol. Chem., 252, 2808-2814 (1977</text></nplcit>), <nplcit id="ncit0031" npl-type="s"><text>Levin, J.D., J. Biol. Chem., 263, 8066-8071 (1988</text></nplcit>), <nplcit id="ncit0032" npl-type="s"><text>Demple, B. and Harrison, L., Annu. Rev. Biochem., 63: 915-948 (1994</text></nplcit>), and <nplcit id="ncit0033" npl-type="s"><text>Levin, J.D. and Demple, B., Nucleic Acids Res., 24:885-889 (1996</text></nplcit>). APE 1 is described, for example, in <nplcit id="ncit0034" npl-type="s"><text>Demple et al. P.N.A.S. 88:11450-11454 (1991</text></nplcit>).
0046Reference will now be made in detail to exemplary embodiments of the invention. While the invention will be described in conjunction with the exemplary embodiments, it will be understood that they are not intended to limit the invention to these embodiments. On the contrary, the invention is intended to cover alternatives, modifications and equivalents, which may be included within the scope of the invention.
Chemical Fragmentation of Nucleic Acids for Array analysis
0047Microarray technology provides rapid, high-throughput, massively parallel methods for analysis of genetic information, including, for example, gene expression and genotype. In many applications of the technology a sample containing nucleic acids to be analyzed is obtained and nucleic acids in the sample are amplified. Methods for amplification are well known in the art and include, for example, (1) amplification of the population of mRNA by reverse transcription using a primer that includes a polyT region and a promoter region for an RNA polymerase, such as T7, T3 or SP6, followed by in vitro transcription of many copies of the mRNAs from the starting material: (2) amplification of a representation of a genome by fragmenting the sample, ligating adaptors to the fragments and amplifying a subset of the fragments by PCR using a primer complementary to the adaptor sequence (whole genome sampling assay-WGSA) for additional description of WGSA see <nplcit id="ncit0035" npl-type="s"><text>Matsuzaki et al., Gen. Res. 14:414-425 (2004</text></nplcit>); (3) other whole genome amplification methods such as multiple displacement amplification (MDA) and (4) the Whole Transcript Assays (WTA) which is described in greater detail below.
0048Methods for fragmentation and labeling nucleic acids for hybridization to nucleic acid arrays are disclosed. In preferred aspects the fragmentation method used is an alternative to methods that use DNaseI, such as those described in <nplcit id="ncit0036" npl-type="s"><text>Wodicka et al., Nat. Biotech. 15: 1359-1367 (1997</text></nplcit>) and <nplcit id="ncit0037" npl-type="s"><text>Matsuzaki et al., Gen. Res. 14:414-425 (2004</text></nplcit>). In many aspects DNA or RNA is amplified to generate an amplified DNA sample and the amplified sample is subjected to random fragmentation and labeling of fragments with a detectable label, such as biotin. The labeled fragments are hybridized to an array and the hybridization pattern may be detected and analyzed. In preferred aspects amplified samples are fragmented in preparation for labeling and hybridization to nucleic acid probe arrays. In one aspect the methods include a fragmentation step and a labeling step that may occur sequentially or simultaneously. The fragmentation step includes at least one chemical step, and the chemical step includes a treatment that generates abasic sites in the nucleic acid that may be cleaved to generate a strand break. In some aspects an AP endonuclease is used to cleave at abasic sites. In some aspects the fragmentation generates ends that are compatible with known methods of labeling nucleic acids, but in other aspects the fragments are subsequently treated to generate ends compatible with labeling. Some fragmentation methods may generate a mixture of ends and the mixture may be subsequently treated to generate ends compatible with labeling. In a particularly preferred embodiment the fragmentation and subsequent processing steps result in fragments that have a 3' OH and the fragments are substrates for end-labeling with terminal deoxynucleotidyl transferase (TdT).
0049In one aspect, fragmentation of nucleic acids comprises breaking nucleic acid molecules into smaller fragments. Fragmentation of nucleic acid may be desirable to optimize the size of nucleic acid molecules for subsequent analysis and minimize three dimensional structure. For example, fragmented nucleic acids allow more efficient hybridization of target DNA to nucleic acid probes than non-fragmented DNA and fragmented DNA that is to be end labeled allows for the incorporation of additional labels. According to a preferred embodiment, before hybridization to a microarray, target nucleic acid is fragmented to sizes ranging from about 40 to about 200 bases long, and more preferably from about 50 to about 150 bases long, to improve target specificity and sensitivity. In some aspects, the average size of fragments obtained is at least 10, 20, 30, 40, 50, 60, 70, 80, 100 or 200 bases. If the fragments are double stranded this length refers to base pairs and if single stranded this length refers to bases. Conditions of the fragmentation reaction may be optimized to select for fragments of a desired size range. One of skill in the art will recognize that a nucleic acid sample when fragmented will result in a distribution of fragment sizes, preferably the distribution is centered about a selected length, for example, the center of the distribution of fragment sizes may be about 20, 40, 50, 60, 70, 80 or 100 bases or base pairs. In a preferred aspect the methods reproducibly generate fragments that have approximately the same size distribution.
0050Chemical fragmentation methods that may be used include, for example, hydrolysis catalyzed by metal ion complexes, such as Cu<sup>+2</sup> and Ce<sup>+2</sup> complexes; oxidative cleavage by metal ion complexes, such as Fe<sup>+2</sup> and Cu<sup>+2</sup> complexes, photochemical cleavage, and acid-catalzyed depurination. The methods may also be used in conjunction with chemical DNA labeling methods, such as, biotin-amine, biotin-hydrazides, diazo-biotin, biotin-platinum, biotin-psoralen, and biotin-aryl azide methods.
0051In some aspects hydrolysis methods generate 5' phosphates and 3' hydroxyl ends which are compatible with labeling methods such as end labeling with terminal transferases and oxidative methods generate 5' and 3' carbonyl residues. Carbonyls may be chemically labeled, for example, with biotin-amines and -hydrazides. The phosphate backbone may be labeled, for example, with diazo-biotin and specific bases can be labeled, for example, with biotin-platinum, -psoralen and -aryl azide.
0052In preferred embodiments the methods may be used, for example, for fragmenting nucleic acid sample prior to labeling and hybridization to an array of probes. Preferred arrays of probes included high density arrays of oligonucleotides such as those made by Affymetrix, Inc. (Santa Clara, CA), for example, the 10K and 100K Mapping Arrays, tiling arrays, and expression arrays such as the Human Genome U133 Plus 2.0 array. The array may have probes for about 10, 20, 30, 40, 50, 75 or 100% of a selective genome. In one aspect the probes may be complementary to transcribed regions or to a combination of transcribed and non-transcribed regions. The array may include probes to detect each known or predicted exon in a plurality of genes, for example, more than 1,000, 2,000, 5,000, 10,000 or 30,000 genes.
0053In a preferred embodiment the nucleic acids to be fragmented by the disclosed methods are an amplification product. In one embodiment a biological sample containing RNA transcripts is amplified. The RNA may be used as template for a reverse transcription reaction to synthesize cDNA. Methods for synthesizing cDNA are well known in the art. Sample preparation for Whole Transcript Assays are described for example in <patcit id="pcit0161" dnum="US917643A" dnum-type="L"><text>U.S. Patent application Serial number 10/917,643</text></patcit>. Enzymatic methods of fragmentation are also disclosed in <patcit id="pcit0162" dnum="US951983A" dnum-type="L"><text>U.S. Patent Application No. 10/951,983</text></patcit>.
0054In another aspect the fragments are an amplification product resulting from Whole Genome Sampling Assay (WGSA) which is described, for example, in <patcit id="pcit0163" dnum="US20040146890A"><text>US patent publication Nos. 20040146890</text></patcit> and <patcit id="pcit0164" dnum="US20040067493A"><text>20040067493</text></patcit>. In general, genomic DNA is fragmented with one or more restriction enzymes, adaptors are ligated to the fragments and the adaptor ligated fragments are subjected to PCR amplification using a primer to the adaptor sequence. The PCR preferentially amplifies fragments that are less than about 2kb and greater than about 200 base pairs so a representative subset of the genome is amplified. The disclosed chemical fragmentation methods may be used to fragment the resulting WGSA amplification product prior to end labeling and hybridization to an array, for example, a genotyping array.
0055Both single-stranded and double-stranded DNA targets may be fragmented. The methods of the invention are particularly suitable for use with tiling array such as those described in <patcit id="pcit0165" dnum="US815333A" dnum-type="L"><text>U.S. Patent application Serial Number 10/815,333</text></patcit>. While the methods of the invention have broad applications and are not limited to any particular detection methods, they are particularly suitable for detecting a large number of different target nucleic acids, such as more than 1000, 5000, 10,000, 50,000 different transcript features.
0056In a preferred aspect the fragments are end labeled using a terminal transferase enzyme (TdT). Terminal transferase catalyzes the template independent addition of deoxy- and dideoxynucleoside triphosphates to the 3'OH ends of double- and single-stranded DNA fragments and oligonucleotides. TdT can also add homopolymers of ribonucleotides to the 3' end of DNA. The preferred substrate for TdT is a protruding 3' end but the enzyme will also add nucleotides to blunt and 3'-recessed ends of DNA fragments. The enzyme uses cobalt as a cofactor. Terminal transferase may be used to incorporate, for example, digoxigenin-, biotin-, and fluorochrome-labeled deoxy- and dideoxynucleoside triphosphates as well as radioactive labeled deoxy- and dideoxynucleoside triphosphates. In a preferred embodiment a biotinylated compound is added by TdT to the 3' end of the DNA. In a preferred aspect fragments are labeled with biotinylated compounds such as those disclosed in <patcit id="pcit0166" dnum="US20030180757A"><text>US Patent Publication No. 20030180757</text></patcit>. The biotin may be detected by contacting it with streptavidin with a fluorescent conjugate, such as Streptavidin-Phycoerythrin (Molecular Probes). A number of labeled and unlabelled streptavidin conjugates are available. Conjugates include fluorescent dyes such as fluorescein and rhodamine and phycobiliproteins such as phycoerythrin. Biotinylated antibodies to streptavidin may be used to amplify signal. For additional labeling methods, see for example, <patcit id="pcit0167" dnum="US4520110A"><text>U.S. Patent Nos. 4,520,110</text></patcit> and <patcit id="pcit0168" dnum="US5055556A"><text>5,055,556</text></patcit>. See also, <patcit id="pcit0169" dnum="US452519A" dnum-type="L"><text>U.S. Patent Application Nos. 10/452,519</text></patcit>, which discloses labeling compounds and <patcit id="pcit0170" dnum="US10617992B"><text>10/617,992</text></patcit>, which discloses labeling methods.
0057In some aspects the 3' end of fragments that are modified, for example, with a phosphoglycolate or 2' deoxyribolactone may be labeled using a 3' end repair system, tailing with dGTP/GTP and labeling with DLR using TdT. This is described in <patcit id="pcit0171" dnum="WO03050242A"><text>WO 03/050242</text></patcit>. In some aspects, fragments may be labeled disproportionation and exchange of a labeled nucleotide to the 3' end by TdT in the presence of metal ions Co<sup>2+,</sup> Mn<sup>2+</sup> or Mg<sup>2+,</sup> Co<sup>2+</sup> being preferredl, as described in <nplcit id="ncit0038" npl-type="s"><text>Anderson et al., Nuc. Acids Res. 27:3190-3196 (1999</text></nplcit>). Optimal concentration of the metal ion is 1-2 mM.
0058There are a number of chemical methods for fragmentation of nucleic acids that are known in the art. These methods include: hydrolytic methods (see <nplcit id="ncit0039" npl-type="s"><text>Sreedhara et al., J. Amer. Chem Soc. 2000, 122, 8814-8824</text></nplcit>), oxidative-based metallo-nucleases (see <nplcit id="ncit0040" npl-type="s"><text>Pogozelski and Tullius, Chem. Rev. 1998, 98:1089-1107</text></nplcit> and <nplcit id="ncit0041" npl-type="s"><text>James G. Muller; et al., Chem. Rev. 1998, 98:1109-1151</text></nplcit>), photocleavage (see <nplcit id="ncit0042" npl-type="s"><text>Nielson, J. Amer. Chem. Soc., 1992, 114:4967-4975</text></nplcit>), acid catalyzed depurination, (see <nplcit id="ncit0043" npl-type="s"><text>Proudnikov and Mirzabekov, Nucleic Acids Res. 1996, 24, 4535-4532</text></nplcit>), alkylation (see <nplcit id="ncit0044" npl-type="s"><text>Kenneth A. Browne, Amer. Chem. Soc. 2002, 124, 7950-7962</text></nplcit>) or fragmentation facilitated by reagents used in Maxam-Gilbert type sequencing methods. Fragmentation of DNA in low salt buffers at pH 6-9 has also been reported, see, for example, <patcit id="pcit0172" dnum="WO03050242A2"><text>WO 03/050242 A2</text></patcit>, <patcit id="pcit0173" dnum="US20030143599A"><text>US 20030143599</text></patcit> and <patcit id="pcit0174" dnum="US20040209299A"><text>US 20040209299</text></patcit>.
0059In preferred embodiments amplified DNA is incubated under conditions that result in acid catalyzed depurination as shown in <figref idref="f0003">Figure 3</figref>. The reaction can generate a mixture of products. In the first step an abasic site is generated. The depurination does not break the phosphate backbone but depurinated positions are reactive and can result in strand breakage as shown, generating a variety of 5' and 3' ends for the resulting fragments. The abasic product can undergo beta elimination resulting in fragmentation and generating a 3' phosphoglycoaldehyde and a 5' phosphate product as shown. A second beta elimination can also take place generating a 3' phosphate end. The second beta elimination occurs slowly but can be facilitated by addition of base, for example NaOH. The 3'-phosphoglycoaldehyde can be labeled chemically, for example, by biotin-ARP.
0060The DNA may be single stranded or double stranded and may be cDNA derived from mRNA or amplified products from a sample containing genomic DNA. In a preferred embodiment the DNA is in a solution that includes a buffer that is neutral (pH 6 to 9) at a temperature of about 22-30°C but acidic (pH less than 6.0) at higher temperatures, for example between 80 and 100°C. In a preferred aspect the DNA is in a solution that includes about 10 mM Tris-HCl, pH ~7.2-7.5 at 25°C. The pH of Tris buffer changes at a rate of-0.028 pH units per degree so if the pH is ~7.2-7.5 at about 25°C it will be ~5.2-5.5 at about 95°C, resulting in an acidic environment at high temperature and facilitating depurination of the DNA and generates abasic sites in the DNA at the site of depurination. For additional description of Tris buffers see <nplcit id="ncit0045" npl-type="s"><text>Bates and Bower, Analyt. Chem. 28:1322 (1956</text></nplcit>) and <nplcit id="ncit0046" npl-type="s"><text>Bates and Hetzer, Analyt. Chem. 33:1285 (1960</text></nplcit>).
0061Abasic sites can be treated by a variety of methods to generate strand breaks thus generating free 3' and 5' ends that can be labeled. In preferred embodiments the depurination reaction is incubated for about 10 to 30 or about 30 to 60 minutes. The fragments produced may be treated with Endonuclease IV or other 3'-end conditioning enzymes (like APE 1) to facilitate removal of 3'-modifications, such as 3' phosphates, facilitating efficient labeling with TdT.
0062In some aspects the mechanism of fragmentation is acid catalyzed depurination followed by thermal fragmentation or fragmentation by an AP endonuclease or a combination of treatments. Following acid depurination with thermal fragmentation generally results in incomplete fragmentation and generates fragments with 3' modifications, like those previously described by <nplcit id="ncit0047" npl-type="s"><text>Proudnikov; et al., Nucleic Acids Research 1996, 24, 4535-4532</text></nplcit>, that may be compatible with chemical labeling methods, for example, labeling with biotin-amine, but are generally not compatible with TdT labeling, In preferred aspects the sample is treated with an AP endonuclease to cleave at unfragmented abasic sites and to remove 3' modifications, leaving 3'-hydroxyl groups that are compatible with TdT labeling. In a preferred embodiment <i>E.coli</i> Endo IV or the human Endo IV homolog, APE 1, is used after acid depurination, with or without heat treatment, to generate strand breaks at residual abasic sites and to remove 3' end blocking groups, leaving free 3'-hydroxyls that can be efficiently end-labeled by TdT.
0063DNA is mixed with a buffer that is neutral or basic in a first temperature range and acidic in a second temperature range. The DNA is mixed with the buffer at a temperature within the first temperature range and then incubated at a temperature in the second temperature range. The buffer is acidic in the second temperature range and the DNA is fragmented or apurinic sites are generated that may be subsequently fragmented by chemical or enzymatic means. Depurination and fragmentation may be stopped by returning the reaction to a temperature in the first temperature range, where the pH of the buffer is neutral. After fragmentation the sample may be treated with a nuclease such as Endo IV or APE1 prior to labeling. Fragmentation reactions that result in generation of 3' phosphates may be followed by treatment with a phosphatase to remove the phosphate and generate 3' hydroxyl for labeling, Endo IV also has a 3' phosphatase activity.
0064Many buffers are available that are neutral or basic at a first temperature range and acidic at a second temperature range. For detailed information about buffers see, for example, <nplcit id="ncit0048" npl-type="b"><text>Data for Biochemical Research, 3rd Edition, Eds. Dawson et al. Oxford Scientific Publications (1995), see especially pages 417-448</text></nplcit>. In a preferred embodiment the buffer is Tris-HCl (other counter ions may also be used). Other buffers that change from a neutral pH at about 20 to 30°C to an acidic pH at about 85-100°C may also be used. Other buffers that may be used include, for example, TE, imidazole and colamine (2-aminoethanol/ethanolamine/2-hydroxyelylamine). Fragmentation can be stopped by changing the incubation temperature back to a temperature that results in a neutral or basic pH. This is particularly useful for high throughput sample preparation methods because the reaction can be stopped by changing the temperature so it can be done rapidly and without the need to add reagents. Incubation at the higher temperature may be for 10-30 min, 25-30 min, 30-40 min, 40-50 min, 50-60 min or 60-120 min or longer. In a preferred embodiment the incubation is for about 10, 20, 30, 40, 45 or 60 minutes. The fragmentation reaction may then be incubated in TdT buffer with 70 units Endo IV for 37°C for about 2 hours then at 70°C for 15 minutes. End labeling may be with TdT and Affymetrix biotinylated DNA Labeling Reagent (DLR). See also, <patcit id="pcit0175" dnum="US545417P" dnum-type="L"><text>U.S. Patent Application Nos. 60/545,417</text></patcit>, <patcit id="pcit0176" dnum="US60542933P" dnum-type="L"><text>60/542,933</text></patcit>, <patcit id="pcit0177" dnum="US60512569P" dnum-type="L"><text>60/512,569</text></patcit>, <patcit id="pcit0178" dnum="US10452519P" dnum-type="L"><text>10/452,519</text></patcit> and <patcit id="pcit0179" dnum="US10617992P" dnum-type="L"><text>10/617,992</text></patcit>.
0065In one embodiment 3 µg single stranded cDNA in 10 mM TE, pH 7.4 is incubated at 95°C for 30, 40, 45 or 60 minutes. TdT buffer and 70 units Endo IV is added and incubated at 37°C for 2 hours then at 70°C for 15 minutes. The reaction is then end labeled with Affymetrix biotinylated DNA Labeling Reagent, DLR (Affymetrix, Santa Clara, CA, USA) using TdT and hybridized to an array under standard conditions. Fragment sizes were about 80 base pairs after a 45 min incubation and about 50 base pairs after a 60 minute incubation. These fragment sizes are similar to what is observed with DNase I treatment and hybridization results were also similar. In another example fragmentation was with 1X TE pH 7.4 for 30 or 40 min at 95°C and 100 U of APE 1 or 70 U of Endo IV were used. In another embodiment 10 mM Tris-HCl buffer, pH 7.2 is used for fragmentation. Fragmentation rates for double stranded cDNA may be slower than single stranded cDNA.
0066See also, <patcit id="pcit0180" dnum="US545417P" dnum-type="L"><text>U.S. Patent Application Nos. 60/545,417</text></patcit>, which discloses methods of fragmentation, <patcit id="pcit0181" dnum="US60542933B"><text>60/542,933</text></patcit>, which discloses methods of whole transcript amplification, <patcit id="pcit0182" dnum="US10452519B"><text>10/452,519</text></patcit>, which discloses labeling compounds and <patcit id="pcit0183" dnum="US10617992B"><text>10/617,992</text></patcit>, which discloses labeling methods. In preferred embodiments the resulting fragments range in size from about 50 to about 200 base pairs, and more preferably from about 50 to about 100.
0067In a preferred embodiment the multiple copies of cDNA generated by the disclosed methods are analyzed by hybridization to an array of probes. The nucleic acids generated by the methods may be analyzed by hybridization to nucleic acid arrays. Those of skill in the art will appreciate that an enormous number of array designs are suitable for the practice of this invention. High density arrays may be used for a variety of applications, including, for example, gene expression analysis, genotyping and variant detection. Array based methods for monitoring gene expression are disclosed and discussed in detail in <patcit id="pcit0184" dnum="US5800992A"><text>U.S. Pat. Nos. 5,800,992</text></patcit>, <patcit id="pcit0185" dnum="US5871928A"><text>5,871,928</text></patcit>, <patcit id="pcit0186" dnum="US5925525A"><text>5,925,525</text></patcit>, <patcit id="pcit0187" dnum="US6040138A"><text>6,040,138</text></patcit> and <patcit id="pcit0188" dnum="WO9210588A"><text>PCT Application WO92/10588 (published on Jun. 25, 1992</text></patcit>). Suitable arrays are available, for example, from Affymetrix, Inc. (Santa Clara, CA). Bead based array systems may also be used.
0068In another aspect N-methylformamide (NMF) is included in the fragmentation reaction. The Maxam-Gilbert type fragmentation chemistry in one approach uses a concentrated aqueous solution (~80%) of formamide which reacts with purines and pyrimidines at high temperature (>100°C) resulting in deglycosylation, see <nplcit id="ncit0049" npl-type="s"><text>Raffaele Saladino; et al., J. Amer. Chem. Soc. 1996, 118, 5615-5619</text></nplcit>. Subsequent heating and base treatment, for example with piperidine, may be used to facilitate the β-elimination and fragmentation reactions to produce 5' and 3'-phosphate modified DNA fragments. In another modification of this procedure, it was discovered that NMF in the presence of 3 mM MnCl<sub>2</sub> at 110°C could effect both deglycosylation and fragmentation simultaneously, see <nplcit id="ncit0050" npl-type="s"><text>Rodolfo Negri; et al. BioTechniques, 21, 910-917 (1996</text></nplcit>). This reaction, although sufficient for sequencing protocols, is relatively inefficient and may not result in complete fragmentation.
0069In one aspect of the present invention methods for fragmenting in the presence of NMF are disclosed. The methods preferably generate fragments with 3' hydroxyl groups that are substrates for labeling by TdT. In some aspects NMF is added to the fragmentation reaction to increase the rate of fragmentation. In a preferred embodiment a reagent formulation of between 5 and 10% NMF in tris or phosphate buffer at about pH 7 to 8.5 at 95°C is used. In a preferred embodiment the fragmentation proceeds for 30 to 60 minutes. In some embodiments the single stranded DNA may be fragmented for less time than double stranded, for example, about 30 min for ssDNA and about 60 min for dsDNA. Double and single-stranded DNA may be fragmented by the disclosed methods and may be desalted prior to fragmentation.
0070The resulting fragments may be treated with an endonuclease, such as Endo IV, or other 3'-end conditioning enzyme, for example, APE 1, to facilitate deglycosylation and to remove 3'-modifications. Endo IV treatment may be by addition of TdT buffer, CoCl2 and Endo IV followed by incubation at 37°C for about 1, 2 or 3 hours and then at 65°C for 5-30 min, preferably about 15 min. For APE1 treatment NEB buffer and APE1 may be added to the fragmentation reaction and incubation may be for 1-3 hours at about 37°C, followed by incubation at 95°C for about 5 min.
0071The fragments may then be end labeled with a detectable label, for example, by TdT end labeling. End labeling of the Endo IV reaction mixture may be by addition of DNA labeling reagent (DLR) and TdT followed by incubation at 37°C for about 1 hour followed by addition of EDTA. For the APE1 treated sample labeling may be by the addition of TdT buffer, CoCl<sub>2</sub>, DLR and TdT, followed by incubation at 37°C for about 1 hour. The reaction may be stopped by addition of EDTA. The labeled fragments may then be hybridized to an array of nucleic acids, for example oligonucleotide or cDNA arrays. The resulting hybridization pattern may be analyzed to measure the presence or absence of targets and to approximate the amount of individual targets in the starting sample.
0072DNA may also be fragmented using metal complexes as catalysts for oxidative fragmentation of DNA. In general metallo-based oxidative methods for DNA cleavage use a metal complex in the presence of an oxidant like oxygen or hydrogen peroxide and may use a reductant which at elevated temperature results in oxidation of the sugar backbone. Subsequent heating or base treatment, for example, treatment with piperidine, may be used to facilitate the beta-elimination and fragmentation reactions to generate 5' and 3' phosphate modified DNA fragments.
0073In preferred embodiments the fragments may be treated with an AP endonuclease, such as Endonuclease IV or another 3' end conditioning enzyme, such as APE 1 to facilitate deglycosylation and removal of 3' modifications to facilitate efficient end labeling, for example, with TdT.
0074Known chemical nucleases that nick nucleases under physiological conditions include the 1,10-phenanthroline-copper complex, derivatives of ferrous-EDTA, various metalloporphoryins and octahedral complexes of 4,7-diphenyl-1,10-phenanthroline. Bis (1,10-phenanthroline)copper (II) (abbreviated Cu(OP)<sub>2</sub>) degrades DNA in the presence of coreactants, such as hydrogen peroxide and ascorbate. For more information on cleavage by Cu(OP)<sub>2</sub> see Pogozelski and Tullius (1998) at pp 1094-1095 and <nplcit id="ncit0051" npl-type="s"><text>Signam, Biochemistry 29:9097-9105 (1990</text></nplcit>). In one mechanism proposed for DNA cleavage by Cu(OP)<sub>2</sub> strand breakage is observed at room temperature and does not require heat and alkali treatment.
0075Metal complexes such as Cu(OP)<sub>2</sub> and Fe<sup>+2</sup> (EDTA) in the presence of hydrogen peroxide can be used to fragment cDNA efficiently and reproducibly. Treatment of DNA or RNA results in abstraction of a hydrogen from the sugar moiety, producing a carbon-based radical that can rearrange to generate a reactive abasic site as a result of deglycosylation. The abasic site can be subsequently cleaved to generate a strand break. Cleavage at the abasic site may be by a variety of mechanisms that may be chemical or enzymatic. In a preferred aspect, for example, by an AP endonuclease. The fragments can be labeled with DLR by TdT with an efficiency greater than or equal to 95%. The fragments can be hybridized to probe arrays. The DNA may be incubated with a concentration of Cu(OP)<sub>2</sub> between about 0.75 mM to about 1.5 mM. The DNA may be incubated at 95°C to further fragment abasic sites. Endo IV or APE1 may be used to give 3'-OH ends.
0076A protocol and reagent formulation containing a copper-phenanthroline complex (Cu(OP)<sub>2</sub>) and a reductant are enclosed.
0077A reagent formulation of about 5 µM Cu(OP)<sub>2</sub> with about 1 mM sodium ascorbate (C<sub>6</sub>H<sub>7</sub>O<sub>6</sub>Na) or 10 mM mercaptopropionic acid (HSCH<sub>2</sub>CH<sub>2</sub>COOH) in a tris or phosphate buffer pH 7-8.5 at 65°C may be used to fragment single and double stranded DNA. The fragmentation reaction may proceed for about 10 to 30, or about 30 to 60 minutes at about 65°C.
0078Iron-EDTA complex (Fe<sup>+2</sup>(EDTA)) in the presence of hydrogen peroxide may be used for fragmentation. In the Fenton-Udenfriend reaction [Fe(EDTA)]<sup>2-</sup> is oxidized by hydrogen peroxide generating highly reactive hydroxyl radicals. The Fenton-generated hydroxyl radical is diffusible and can cleave nucleic acids without specificity for a particular nucleotide. The hydroxyl radical is able to abstract hydrogen from each deoxyribose carbon but the 5' and 4' positions are preferred.
0079Copper derivatives of aminoglycosides have been shown to be highly efficient catalysts for cleavage of DNA under physiological conditions. See <nplcit id="ncit0052" npl-type="s"><text>Sreedhara et al., J.Am.Chem.Soc., 122: 8814-8824, (2000</text></nplcit>), and <nplcit id="ncit0053" npl-type="s"><text>Sreedhara et al., Chem. Commun., 1147 (1999</text></nplcit>). Strand cleavage at the abasic sites may be by heating the reaction mixture, for example at 85°C for about 20 min or by an AP endonuclease, for example, Endo IV and APE 1. The copper aminoglycoside, copper neamine, may also result in nucleic acid cleavage in the presence of peroxide or ascorbate. See, <nplcit id="ncit0054" npl-type="s"><text>Patwardhan and Cowan, Chem. Commun., 1490-1491 (2001</text></nplcit>).
0080A copper kanamycin Complex (Cu(kanA) or Cu(kanA)<sub>2</sub>) may be used for hydrolytic cleavage of DNA. Chemical fragmentation of nucleic acid may be by way of a hydrolytic mechanism resulting in phosphodiester hydrolysis. Examples of reagents that may be used to catalyze hydrolysis include transition metals and lanthanides, such as Cu(kanA), Ce(EDTA) and Ce<sub>2</sub>(HXTA). Generally these reagents fragment by a hydrolytic mechanisms that is generally slower than DNase-1 and generates 5' phosphate and 3' hydroxyl end that are compatible with TdT labeling and chemical labeling. In one aspect a dicerium complex, Ce<sub>2</sub>(HXTA) may be used for cleavage of nucleic acid. (HXTA = 5-methyl-2-hydroxy-1,4-xylene-alpha, alpha-diamine-N,N,N',N'-tetraacetic acid.) Ce(2)(HXTA) has been shown to hydrolyze DNA at pH 8 and 37°C. See, <nplcit id="ncit0055" npl-type="s"><text>Branum et al. J. Am. Chem. Soc. 123:1898-904 (2001</text></nplcit>). A large percentage of the fragments, more than 90%, have 3'-OH ends, ready for end labeling, for example, by TdT.
0081Examples of reagents that cleave via an oxidative sugar fragmentation include, for example, fenton-type reagents such as Fe(EDTA)/H<sub>2</sub>O<sub>2</sub>, Cu(phen)/H<sub>2</sub>O<sub>2</sub> and metalloporphyrin complexes and photochemical reagents such as Rh<sup>+3</sup> complexes and uranyl acetate. The mechanism of cleavage is oxidative, the rate of cleavage is comparable to DNase-1 and results in fragments that have 3'-modifications. Acids, such as formic acid, can be used to fragment via a depurination method. The rate of cleavage is comparable to DNase I, and fragments with 3' modifications are generated.
0082In another aspect DNA may be cleaved by a first step involving acid catalyzed depurination followed by cleavage with a beta-lyase. Examples of β-lyases that may be used include, <i>E. coli</i> endonuclease III, T4 endonuclease V and <i>E. coli</i> FPG protein. Many β -lyases generate a strand break at the 3' side of the AP site by a β-elimination mechanism, see <nplcit id="ncit0056" npl-type="s"><text>Mazumder et al., Biochemistry 30:1119 (1991</text></nplcit>). An exemplary schematic is shown in <figref idref="f0006">Fig. 6</figref>. In a first step the DNA (1) is depurinated. Depurination may be, for example, by incubation in a buffer that has a pH of about 5 at 95°C, for example Tris. The depurinated DNA is then cleaved using a beta-lyase, for example, Endo III. In a preferred aspect a thermostable beta-lyase that is functional at pH below 6 may be used so that depurination and cleavage can occur in the same reaction, simultaneously. A thermostable endonuclease II homolog is available, see <nplcit id="ncit0057" npl-type="s"><text>Yang et al., Nuc. Acids Res. 29:604-613 (2001</text></nplcit>). The cleavage generates 5' phosphate ends and 3' phosphoglycoaldehyde ends, as shown (4). The fragments can be end labeled with a biotin amine reagent, for example, biotin-ARP (biotin aldehyde-reactive probe) (Molecular Probes), resulting in imine (5). Labeling may also be performed using reductive amination with RNH<sub>2</sub>, for example incubation with Biotin-NH<sub>2</sub> and NaBH<sub>4</sub> or NaCNBH<sub>3</sub>, may be used to generate a stable amine (6), see <nplcit id="ncit0058" npl-type="s"><text>Kelly et al., Analytical Biochem. 311:103-118 (2002</text></nplcit>) and <figref idref="f0006">Fig 6</figref>. The biotin-ARP (or ARP-biotin) is a biotinylated hydroxylamine that reacts with aldehyde groups formed when reactive oxygen species depurinate DNA. The reaction forms a covalent bond linking the DNA to biotin. The biotin can then be deteced using a fluorophore- or enzyme-linked streptavidin.
0083A labeled nucleotide such as the one shown in <figref idref="f0007">Fig. 7</figref> may be incorporated into the first strand cDNA during reverse transcription. The strand with the incorporated label can be fragmented using DNase I, Cu(OP)<sub>2</sub> or the Tris methods described above. Incorporation of a label during synthesis eliminates the need to label the fragments after fragmentation by, for example, TdT labeling or chemical labeling of the fragments.
EXAMPLES
Example 1: Fragmentation of single-stranded DNA in Tris Buffer at high temperature.
0084Fragmentation Reaction Mix: Mix 3 µl 10 X Tris Buffer, pH 7.24 at room temp, 20-25 µl ss cDNA (final concentration is 3 µg), and nuclease free water to a total volume of 30 µl. Incubate the reaction at 95°C for 60 minutes. The fragmented cDNA is applied directly to Endo IV treatment and the terminal labeling reaction. Alternatively, the material can be stored at -20°C for later use.
0085Endo IV treatment: Mix14 µl 5 X TdT Reaction Buffer (final concentration is 1X), 14 µl 25 mM CoCl<sub>2</sub> (final concentration is 5mM), 3.5 µl Endo IV (20 U/µl) (final concentration is 70U/3µg cDNA), 30 µl cDNA template (1.5-5 µg) and Nuclease-free H<sub>2</sub>O for a final volume of 70 µl. Higher concentrations of Endo IV have been observed to result in more efficient labeling. Incubate the reaction at 37°C for 120 minutes. Inactive Endo IV at 65°C for 15 minutes.
0086Terminal Label Reaction: Mix 70 µl cDNA template (1.5-5 µg), 4.375 µl rTDT (400 U/ul) for final concentration of 5.8 U/pmol, and µl 5 mM DLR for final concentration of 0.07 mM. The final reaction volume is about 75.4 µl. Incubate the reaction at 37°C for 60 minutes. Stop the reaction by adding 2 µL of 0.5 M EDTA (PH 8.0). The target is ready to be hybridized onto probe arrays. Alternatively, it may be stored at -20°C for later use.
Example 2: Fragmentation of ds cDNA with Tris Buffer at high temperature.
0087Fragmentation mixtures containing 10 µg ds cDNA, 10 mM Tris-HCl, pH 7.2 at room temperature were incubated at 95°C for 75, 90, 105 and 120 minutes. The reactions were then treated by either: (A) incubation with 100 unites APE 1, in NEB buffer 4 for 1 hour at 37°C and then 95°C for 50 min or (B) incubation with 70 units Endo IV in TdT buffer for 2 hours at 37°C and 15 min at 65°C. Both were then end labeled with DLR and TdT and hybridized to arrays using standard conditions. For those reactions that were treated with APE 1 the average size of fragments was approximately 200, 150, 90 or 60 bp after 75, 90, 105 or 120 min of incubation, respectively. For those reactions that were treated with Endo IV the average size of fragments was approximately 160, 110, 80 or 50 bp after 75, 90, 105 or 120 min of incubation, respectively. Percent present calls were 60.2, 58.9, 60.7, and 63.4 for Endo IV treated samples at 75, 90, 105 and 120 min respectively and 42.7, 45.0, 38.1, and 32.1 for APE 1 treated samples at 75, 90, 105 and 120 min respectively.
0088Results are shown in <figref idref="f0008">Fig. 8</figref> as percent present (%P) and average fragment size compared to a DNase I control. Scaled intensity data is shown in <figref idref="f0009">Fig. 9</figref>.
Example 3: NMF fragmentation with 10 or 20% NMF.
0089Fragmentation was tested at 10% NMF for 60 min or 20% NMF for 30 min, both at 100°C using cDNA in ~10 mM Tris-HCl buffer at pH 8 at 25°C. The NMF did not interfere with the activities of Endo IV or TdT enzymes.
0090Tubes 1-6 were incubated at 100°C for 90 min and tubes 7-12, w1 and w2 were incubated at 100°C for 40 min. Reactions were as indicated in Table 1. <tables id="tabl0001" num="0001"><table frame="all"><title>Table 1.</title><tgroup cols="9"><colspec colnum="1" colname="col1" colwidth="17mm" /><colspec colnum="2" colname="col2" colwidth="19mm" /><colspec colnum="3" colname="col3" colwidth="14mm" /><colspec colnum="4" colname="col4" colwidth="28mm" /><colspec colnum="5" colname="col5" colwidth="14mm" /><colspec colnum="6" colname="col6" colwidth="25mm" /><colspec colnum="7" colname="col7" colwidth="14mm" /><colspec colnum="8" colname="col8" colwidth="23mm" /><colspec colnum="9" colname="col9" colwidth="14mm" /><thead valign="top"><row valign="middle"><entry align="center">Reaction</entry><entry align="center">Water (µl)</entry><entry align="center">cDNA</entry><entry align="center">Buffer</entry><entry align="center">CoCl</entry><entry align="center">Enzyme</entry><entry align="center">SAP</entry><entry align="center">Total volume</entry><entry align="center">NMF</entry></row></thead><tbody><row valign="middle"><entry align="center">1</entry><entry align="center">23</entry><entry align="right">15µl</entry><entry align="center">14µl 5x</entry><entry align="center">14µl</entry><entry align="center">6µl EndoIV</entry><entry align="center">--</entry><entry align="right">72µl</entry><entry align="center">10%</entry></row><row valign="middle"><entry align="center">2</entry><entry align="center">23</entry><entry align="right">15µl</entry><entry align="center">14µl 5x</entry><entry align="center">14µl</entry><entry align="center">6µl EndoIV</entry><entry align="center">--</entry><entry align="right">72µl</entry><entry align="center">10%</entry></row><row valign="middle"><entry align="center">3</entry><entry align="center">17</entry><entry align="right">15µl</entry><entry align="center">14µl 5x</entry><entry align="center">14µl</entry><entry align="center">--</entry><entry align="center">12 µl</entry><entry align="right">72µl</entry><entry align="center">10%</entry></row><row valign="middle"><entry align="center">4</entry><entry align="center">17</entry><entry align="right">15µl</entry><entry align="center">14µl 5x</entry><entry align="center">14µl</entry><entry align="center">--</entry><entry align="center">12 µl</entry><entry align="right">72µl</entry><entry align="center">10%</entry></row><row valign="middle"><entry align="center">5</entry><entry align="center">20</entry><entry align="right">15µl</entry><entry align="center">5µl 10x NEB</entry><entry align="center">--</entry><entry align="center">10µl APE</entry><entry align="center">--</entry><entry align="right">50µl</entry><entry align="center">10%</entry></row><row valign="middle"><entry align="center">6</entry><entry align="center">20</entry><entry align="right">15µl</entry><entry align="center">5µl 10x NEB</entry><entry align="center">--</entry><entry align="center">10µl APE</entry><entry align="center">--</entry><entry align="right">50µl</entry><entry align="center">10%</entry></row><row valign="middle"><entry align="center">7</entry><entry align="center">23</entry><entry align="right">15µl</entry><entry align="center">14µl 5x</entry><entry align="center">14µl</entry><entry align="center">6µl</entry><entry align="center">--</entry><entry align="right">72µl</entry><entry align="center">20%</entry></row><row valign="middle"><entry align="center">8</entry><entry align="center">23</entry><entry align="right">15µl</entry><entry align="center">14µl 5x</entry><entry align="center">14µl</entry><entry align="center">6µl EndoIV</entry><entry align="center">--</entry><entry align="right">72µl</entry><entry align="center">20%</entry></row><row valign="middle"><entry align="center">9</entry><entry align="center">17</entry><entry align="right">15µl</entry><entry align="center">14µl 5x</entry><entry align="center">14µl</entry><entry align="center">--</entry><entry align="center">12 µl</entry><entry align="right">72µl</entry><entry align="center">20%</entry></row><row valign="middle"><entry align="center">10</entry><entry align="center">17</entry><entry align="right">15µl</entry><entry align="center">14µl 5x</entry><entry align="center">14µl</entry><entry align="center">--</entry><entry align="center">12 µl</entry><entry align="right">72µl</entry><entry align="center">20%</entry></row><row valign="middle"><entry align="center">11</entry><entry align="center">20</entry><entry align="right">15µl</entry><entry align="center">5µl 10x NEB</entry><entry align="center">--</entry><entry align="center">10µl</entry><entry align="center">--</entry><entry align="right">50µl</entry><entry align="center">20%</entry></row><row valign="middle"><entry align="center">12</entry><entry align="center">20</entry><entry align="right">15µl</entry><entry align="center">5µl 10x NEB</entry><entry align="center">--</entry><entry align="center">10µl APE</entry><entry align="center">--</entry><entry align="right">50µl</entry><entry align="center">20%</entry></row><row valign="middle"><entry align="center">W1</entry><entry align="center">29.3</entry><entry align="right">10µl</entry><entry align="center">4.5µl 10x one phor-all</entry><entry align="center">--</entry><entry align="center">1.2µl DNase I</entry><entry align="center">--</entry><entry align="right">45µl</entry><entry align="center">--</entry></row><row valign="middle"><entry align="center">W2</entry><entry align="center">29.3</entry><entry align="right">10µl</entry><entry align="center">4.5µl 10x one phor-all</entry><entry align="center">--</entry><entry align="center">1.2µl DNase I</entry><entry align="center">--</entry><entry align="right">45µl</entry><entry align="center">--</entry></row></tbody></tgroup></table></tables> After fragmentation the products were end labeled using DLR and TdT. For labeling 1 µl of DLR and 4.4 µl of TdT were added to tubes 1-4 and 7-10 and 14 µl 5x buffer, 14 µl of CoCl<sub>2</sub>, 1 µl of DLR and 4.4 µl of TdT were added to tubes 5, 6, 11, 12, w1 and w2. After hybridization to a test array the percent present were as follows: 59.8% for w1 and w2 controls, 48.7% for 10% NMF Endo IV, 36.3% for 10% NMF SAP, 39.6% for 10% NMF APE, 39.7% for 20% NMF Endo IV, 18.3% for 20% NMF SAP and 30.1% for 20% NMF APE. Background measurements were similar for all conditions.
Example 4: Fragmentation in a reaction including 5% NMF.
00911.5µl of 50% aqueous NMF is added to 10 µl of ~ 3µg DNA in 1mM Tris or phosphate buffer, followed by 3.5 µl of H<sub>2</sub>O to a final reaction volume of 15µl. The fragmentation mixture is incubated at 95°C about 30 min for ss-DNA and about 60 min. for ds-DNA.
0092Deglycosylation and removal of 3'-modifications: Endo IV treatment: 14 µl of 5xTdT buffer, 14µl of 25mM CoCl<sub>2</sub> and 6µl of Endo IV (2U/µl) is added to the 15 µl of fragmentation mixture. (Higher concentrations of Endo IV may be used, for example, instead of 12 units about 70 units or more may be used.) Add water to make the final reaction volume 70µl. Incubate at 37°C for 2 hours and at 65°C for 15 min. 3'-end labeling with TdT and DLR reagent: Endo IV reaction mixture: 1 µl of DNA labeling reagent and 4.4 µl of TdT (400U/µl) is added to 70µl of reaction mixture and incubated at 37°C for 1 hour, followed by the addition of 2µl of 0.5M EDTA, pH 8.
0093APE 1 may be used instead of EndoIV as follows: 5 µl 10x NEB buffer and 10µl of APE 1 (10U/µl) is added to 15 µl of fragmentation mixture. Add water to a final reaction volume of 50µl. Incubate at 37°C for 2 hours and at 95°C for 5 min.
00943'-end labeling with TdT and DLR reagent: APE 1: add 14 µl of 5xTdT buffer, 14µl of 25mM CoCl<sub>2</sub>, 1 µl of DNA labeling reagent and 4.4 µl of TdT (400U/µl) to 50 µl of reaction mixture. Incubate at 37°C for 1 hour followed by the addition of 2µl of 0.5M EDTA, pH 8. Hybridize labeled fragments to an array according to standard protocols.
0095Results for Tris fragmentation in the presence of 5% NMF are shown in <figref idref="f0010">Fig. 10</figref>. The percent present observed is comparable to DNase I. The observed rate of fragmentation in the presence of 5% NMF was about two-fold faster than in the absence of NMF. This was observed for both single and double-stranded cDNA. The observed scaled signal intensities were 26.7 at 30 min, 27.8 at 35 min, 26.9 at 40 min and 28.5 at 45 min, compared to 47.9 and 41.9 for DNase I at 1/100 bp and 1/60 bp respectively.
Example 5: Tris/Endo IV fragmentation with 5 or 10% NMF.
0096Desalted plasmid DNA was fragmented in 5 or 10mM Tris-HCL buffer, pH7.2 with 0, 5 or 10% NMF and desalted double stranded cDNA was fragmented in 5 mM Tris-HCl buffer with or without 5% NMF. Fragmentation was tested at 30, 60 or 90 minutes at 95°C.
0097The 10mM Tris fragmentation of Cre plasmid ds-cDNA resulted in average fragment size of 190 bp at 30 min and 42 bp at 60 min with 0% NMF, with 5% NMF fragments were average size of 60 bp after 30 min and with 10% NMF fragments were 40 bp after 30 min. In 5 mM Tris the Cre plasmid fragments were 170bp after 30 min and 40 bp after 60 min without NMF. Fragments were 30 bp after 30 min in 5% NMF and 23 bp after 30 min in 10% NMF. The ds cDNA (desalted and stored in 5 mM Tris-HCL ph 7.2 buffer) fragmentation in 5 mM Tris-HCL buffer without NMF gave average fragment sizes of 165, 75 and 40 bp after 30, 45 and 60 min of incubation at 65°C, respectively. With 5% NMF the fragment sizes were 320, 40 and 20 bp after 15, 30 or 45 min of incubation at 95°C, respectively. The ds cDNA fragmentation after desalting and exchanging buffer to 5 mM Tris-HCl, pH 7.2 took 30 to 45 min at 95°C, this improved rate of fragmentation may be the result of the removal of inhibitors to fragmentation that are present in the ds cDNA synthesis.
Example 6 Cu(OP)
2
and Endo IV fragmentation of cDNA.
00983µl of 100mM phosphate buffer, pH~7.0, 3 µl 10mM sodium ascorbate buffer and 3µl 50µM Cu(OP)<sub>2</sub> solution were added to 3µg DNA in 1 mM tris or phosphate buffer. Water was added to a final reaction volume of 30µl. The fragmentation reaction was incubated at 65°C for 10 min. The resulting fragments were cleaned up using a Biospin column according to the manufacturer's instructions. Deglycosylation and removal of 3' modifications was done by incubating about 33 µl of the cleaned up fragmentation reaction with 14 µl of 5x TdT buffer, 14µl of 25mM CoCl<sub>2</sub> and 6µl of Endo IV (2U/µl) and incubating at 37°C for 2 hours and at 65°C for 15 min. 3' end labeling with TdT and DLR was done by adding 1 µl of DLR and 4.4 µl of TdT (400U/µl) to the ~70 µl reaction mixture and incubating at 37°C for 1 hour, followed by the addition of 2 µl of 0.5M EDTA, pH 8. The labeled fragments were hybridized to an array using standard protocols.
Example 7: Cu(OP)
2
and Endo IV fragmentation of cDNA with Phosphatase.
0099Mix 3µg cDNA, 1.5 mM Cu(OP)<sub>2</sub>, 10mM H<sub>2</sub>O<sub>2</sub> and incubate for 15 min at 37°C. Quench by adding EDTA to 10mM. Purify by bio-spin purification according to manufacturer's instructions. This purification step is optional and may be left out in some embodiments. Incubate at 95°C for 10 min. Add 5 Units Endo IV, 5 Units Shrimp Alkaline Phosphatase (optional) and incubate at 37°C for 16 hours then 65°C for 15 min. Standard TdT labeling conditions and hybridization to microarray.
Example 8: Cu(OP)
2
and Endo IV fragmentation of single-stranded cDNA.
01003 ug ss-cDNA was mixed in a solution of 10 mM phosphate pH ~7, 5 µM Cu(OP)<sub>2</sub>, and 1 mM ascorbate and incubated at 65°C for10 or 15 min. EDTA was added to 0.5 mM and the products were either subjected to bio-spin purification or not. This was followed by an incubation at 95°C for 10 min. 12 units of Endo-IV was added and incubated at 37°C for 2 hours, followed by incubation at 65°C for 15 min to inactivate the Endo-IV. The products were subjected to a standard TdT/DLR labeling reaction and the labeled fragments were hybridized to a test array and a hybridization pattern was analyzed using standard conditions. The percent present calls for samples treated with the bio-spin column (bio-spin) or untreated (crude), compared to a DNase I treated sample, are shown in <figref idref="f0012">Fig. 12</figref>. The results are comparable to DNase I treatment, with the bio-spin percent present call being higher than crude and the 10 min fragmentation being higher than the 15 min fragmentation.
0101The observed fragmentation was rapid and reproducible and resulted in fragments that could be labeled by TdT after treatment with Endo IV. Higher levels of Endo IV may improve the labeling by reducing residual abasic sites and 3' ends that are blocked from TdT labeling by modifications.
Example 9. Fe(EDTA) fragmentation of cDNA with Biotin-LC-hydrazide (Pierce, Rockford, IL) labeling.
0102137 µM ss-cDNA was incubated with 2.5 mM Fe-EDTA, and 53 mM H<sub>2</sub>O<sub>2</sub> at 95°C for 30 min. The reaction was purified using a bio-spin column (Bio-Rad Laboratories). To label the fragments 2 µl of 5 mM Biotin-LC-hydrazide in DMSO was added and the reaction was incubated at 25°C for 70 min. The reaction was purified with a bio-spin column and analyzed by hybridization to a test array. Fragmentation was efficient and rapid and biotin incorporation was efficient.
Example 10: Fragmentation of cDNA in Imidazole Buffer at High Temperature.
01033 ug of single-stranded cDNA was incubated in 10mM imidazole-HCl buffer at 95°C for 15 minutes. The total volume was 30 µl. After cooling to room temp, 30 µl of fragmented ss cDNA was treated with 100U of Endo III. Reaction conditions were 1x Endonuclease III buffer supplemented with 100µg/ml BSA. The reaction was incubated at 37°C for 2 hours. The total volume was 60 µl. ARP-Biotin in DMSO:H2O (1:2) was added to the reaction mixture to a final concentration of 5mM. The total volume was 80 µl. The reaction mixture was incubated at 65°C for 30 minutes. The reaction mixture was then loaded on a Microcon YM-3 column. The column was centrifuged at 10,000g for 20 minutes. The flow through was discarded at 100µl of 10mM tris-HCl buffer was added. The buffer exchange was repeated 4 times. The results were analysed by PAGE using streptavidin to quantitate the amount of biotin incorporation. Endo III efficiently fragmented the abasic sites generated by imidazole (pH ~6.4 at 25°C) after incubation for 15 min. at 37°C and 45°C. Biotin-ARP reacted with the fragmented cDNA efficiently (> 95%) as judged by streptavidin gel shift assay.
CONCLUSION
0104Many variations of the invention will be apparent to those of skill in the art upon reviewing the above description. The scope of the invention should be determined with reference to the appended claims.
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Every citation, both ways
| Document | Relation | Office |
|---|---|---|
| WO0024939A | Cites | World Intellectual Property Organization (WIPO) |
| WO02090584A | Cites | World Intellectual Property Organization (WIPO) |
| WO2004007751A | Cites | World Intellectual Property Organization (WIPO) |
| WO2004011665A | Cites | World Intellectual Property Organization (WIPO) |
| WO2005045060A | Cites | World Intellectual Property Organization (WIPO) |
| PROUDNIKOV D ET AL: "Chemical methods of DNA and RNA fluorescent labeling" NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 24, no. 22, 1996, pages 4535-4542, XP002255070 ISSN: 0305-1048 | Non-patent | – |
| LHOMME JEAN ET AL: "Abasic DNA structure, reactivity, and recognition" BIOPOLYMERS, vol. 52, no. 2, 1999, pages 65-83, XP002331444 ISSN: 0006-3525 | Non-patent | – |
| WODICKA ET AL: "GENOME-WIDE EXPRESSION MONITORING IN SACCHAROMYCES CEREVISIAE" NATURE BIOTECHNOLOGY, NATURE PUBLISHING, US, vol. 15, December 1997 (1997-12), pages 1359-1367, XP002100297 ISSN: 1087-0156 | Non-patent | – |
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Numbers
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Titles3
- German
- Verfahren zur Fragmentierung und Markierung von DNS
- English
- Methods for fragmenting and labeling DNA
- French
- Procédé de fragmentation et de marquage d'ADN
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