Abstract
The efficiency of sequencing by hybridization to an oligonucleotide microchip grows with an increase in the number and in the length of the oligonucleotides; however, such increases raise enormously the complexity of the microchip and decrease the accuracy of hybridization. We have been developing the technique of contiguous stacking hybridization (CSH) to circumvent these shortcomings. Stacking interactions between adjacent bases of two oligonucleotides stabilize their contiguous duplex with DNA. The use of such stacking increases the effective length of microchip oligonucleotides, enhances sequencing accuracy and allows the sequencing of longer DNA. The effects of mismatches, base composition, length and other factors on the stacking are evaluated. Contiguous stacking hybridization of DNA with immobilized 8mers and one or two 5mers labeled with two different fluorescent dyes increases the effective length of sequencing oligonucleotides from 8 to 13 and 18 bases, respectively. The incorporation of all four bases or 5-nitroindole as a universal base into different positions of the 5mers permitted a decrease in the number of additional rounds of hybridization. Contiguous stacking hybridization appears to be a promising approach to significantly increasing the efficiency of sequencing by hybridization.
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- Bains W., Smith G. C. A novel method for nucleic acid sequence determination. J Theor Biol. 1988 Dec 7;135(3):303–307. doi: 10.1016/s0022-5193(88)80246-7. [DOI] [PubMed] [Google Scholar]
- Breslauer K. J., Frank R., Blöcker H., Marky L. A. Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3746–3750. doi: 10.1073/pnas.83.11.3746. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Broude N. E., Sano T., Smith C. L., Cantor C. R. Enhanced DNA sequencing by hybridization. Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):3072–3076. doi: 10.1073/pnas.91.8.3072. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Doktycz M. J., Morris M. D., Dormady S. J., Beattie K. L., Jacobson K. B. Optical melting of 128 octamer DNA duplexes. Effects of base pair location and nearest neighbors on thermal stability. J Biol Chem. 1995 Apr 14;270(15):8439–8445. doi: 10.1074/jbc.270.15.8439. [DOI] [PubMed] [Google Scholar]
- Drmanac R., Labat I., Brukner I., Crkvenjakov R. Sequencing of megabase plus DNA by hybridization: theory of the method. Genomics. 1989 Feb;4(2):114–128. doi: 10.1016/0888-7543(89)90290-5. [DOI] [PubMed] [Google Scholar]
- Fodor S. P., Read J. L., Pirrung M. C., Stryer L., Lu A. T., Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science. 1991 Feb 15;251(4995):767–773. doi: 10.1126/science.1990438. [DOI] [PubMed] [Google Scholar]
- Guo Z., Guilfoyle R. A., Thiel A. J., Wang R., Smith L. M. Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. Nucleic Acids Res. 1994 Dec 11;22(24):5456–5465. doi: 10.1093/nar/22.24.5456. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Khrapko K. R., Lysov YuP, Khorlin A. A., Ivanov I. B., Yershov G. M., Vasilenko S. K., Florentiev V. L., Mirzabekov A. D. A method for DNA sequencing by hybridization with oligonucleotide matrix. DNA Seq. 1991;1(6):375–388. doi: 10.3109/10425179109020793. [DOI] [PubMed] [Google Scholar]
- Khrapko K. R., Lysov YuP, Khorlyn A. A., Shick V. V., Florentiev V. L., Mirzabekov A. D. An oligonucleotide hybridization approach to DNA sequencing. FEBS Lett. 1989 Oct 9;256(1-2):118–122. doi: 10.1016/0014-5793(89)81730-2. [DOI] [PubMed] [Google Scholar]
- Kieleczawa J., Dunn J. J., Studier F. W. DNA sequencing by primer walking with strings of contiguous hexamers. Science. 1992 Dec 11;258(5089):1787–1791. doi: 10.1126/science.1465615. [DOI] [PubMed] [Google Scholar]
- Kotler L. E., Zevin-Sonkin D., Sobolev I. A., Beskin A. D., Ulanovsky L. E. DNA sequencing: modular primers assembled from a library of hexamers or pentamers. Proc Natl Acad Sci U S A. 1993 May 1;90(9):4241–4245. doi: 10.1073/pnas.90.9.4241. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lamture J. B., Beattie K. L., Burke B. E., Eggers M. D., Ehrlich D. J., Fowler R., Hollis M. A., Kosicki B. B., Reich R. K., Smith S. R. Direct detection of nucleic acid hybridization on the surface of a charge coupled device. Nucleic Acids Res. 1994 Jun 11;22(11):2121–2125. doi: 10.1093/nar/22.11.2121. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lin P. K., Brown D. M. Synthesis of oligodeoxyribonucleotides containing degenerate bases and their use as primers in the polymerase chain reaction. Nucleic Acids Res. 1992 Oct 11;20(19):5149–5152. doi: 10.1093/nar/20.19.5149. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lipshutz R. J., Morris D., Chee M., Hubbell E., Kozal M. J., Shah N., Shen N., Yang R., Fodor S. P. Using oligonucleotide probe arrays to access genetic diversity. Biotechniques. 1995 Sep;19(3):442–447. [PubMed] [Google Scholar]
- Loakes D., Brown D. M. 5-Nitroindole as an universal base analogue. Nucleic Acids Res. 1994 Oct 11;22(20):4039–4043. doi: 10.1093/nar/22.20.4039. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Loakes D., Brown D. M., Linde S., Hill F. 3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR. Nucleic Acids Res. 1995 Jul 11;23(13):2361–2366. doi: 10.1093/nar/23.13.2361. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lysov YuP, Chernyi A. A., Balaeff A. A., Beattie K. L., Mirzabekov A. D. DNA sequencing by hybridization to oligonucleotide matrix. Calculation of continuous stacking hybridization efficiency. J Biomol Struct Dyn. 1994 Feb;11(4):797–812. doi: 10.1080/07391102.1994.10508033. [DOI] [PubMed] [Google Scholar]
- Lysov Iu P., Florent'ev V. L., Khorlin A. A., Khrapko K. R., Shik V. V. Opredelenie nukleotidnoi posledovatel'nosti DNK gibridizatsiei s oligonukleotidami. Novyi metod. Dokl Akad Nauk SSSR. 1988;303(6):1508–1511. [PubMed] [Google Scholar]
- Pease A. C., Solas D., Sullivan E. J., Cronin M. T., Holmes C. P., Fodor S. P. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci U S A. 1994 May 24;91(11):5022–5026. doi: 10.1073/pnas.91.11.5022. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pieters J. M., Mans R. M., van den Elst H., van der Marel G. A., van Boom J. H., Altona C. Conformational and thermodynamic consequences of the introduction of a nick in duplexed DNA fragments: an NMR study augmented by biochemical experiments. Nucleic Acids Res. 1989 Jun 26;17(12):4551–4565. doi: 10.1093/nar/17.12.4551. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Southern E. M., Maskos U., Elder J. K. Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics. 1992 Aug;13(4):1008–1017. doi: 10.1016/0888-7543(92)90014-j. [DOI] [PubMed] [Google Scholar]
- Wetmur J. G. DNA probes: applications of the principles of nucleic acid hybridization. Crit Rev Biochem Mol Biol. 1991;26(3-4):227–259. doi: 10.3109/10409239109114069. [DOI] [PubMed] [Google Scholar]
- Yershov G., Barsky V., Belgovskiy A., Kirillov E., Kreindlin E., Ivanov I., Parinov S., Guschin D., Drobishev A., Dubiley S. DNA analysis and diagnostics on oligonucleotide microchips. Proc Natl Acad Sci U S A. 1996 May 14;93(10):4913–4918. doi: 10.1073/pnas.93.10.4913. [DOI] [PMC free article] [PubMed] [Google Scholar]