A method for DNA sequencing by hybridization with oligonucleotide matrix - PubMed (original) (raw)
A method for DNA sequencing by hybridization with oligonucleotide matrix
K R Khrapko et al. DNA Seq. 1991.
Abstract
A new technique of DNA sequencing by hybridization with oligonucleotide matrix (SHOM) which could also be applied for DNA mapping and fingerprinting, mutant diagnostics, etc., has been tested in model experiments. A dot matrix was prepared which contained 9 overlapping octanucleotides (8-mers) complementary to a common 17-mer. Each of the 8-mers was immobilized as individual dot in thin layer of polyacrylamide gel fixed on a glass plate. The matrix was hybridized with the 32P-labeled 17-mer and three other 17-mers differing from the first one by a single base change. The hybridization enabled us to distinguish perfect duplexes from those containing mismatches in 32 out of 35 cases. These results are discussed with respect to the applicability of the approach for sequencing. It was shown that hybridization of DNA with an immobilized 8-mer in the presence of a labeled 5-mer led to the formation of a stable duplex with the 5-mer only if the 5- and the 8-mers were in continuous stacking making a perfect nicked duplex 13 (5+8) base pairs long. These experiments and computer simulations suggest that continuous stacking hybridization may increase the efficiency of sequencing so that random or natural coding DNA fragments about 1000 bases long could be sequenced in more than 97% of cases. Miniaturized matrices or sequencing chips were designed, where oligonucleotides were immobilized within 100 x 100 micron dots disposed at 100 micron intervals. Hybridization of fluorescently labeled DNA fragments with microchips may simplify sequencing and ensure sensitivity of at least 10 attomoles per dot. The perspectives and limitations of SHOM are discussed.
Similar articles
- [Hybridization of DNA with oligonucleotides immobilized in a gel: a convenient method for recording single base replacements].
Khrapko KR, Khorlin AA, Ivanov IB, Chernov BK, Lysov IuP, Vasilenko SK, Florent'ev VL, Mirzabekov AD. Khrapko KR, et al. Mol Biol (Mosk). 1991 May-Jun;25(3):718-30. Mol Biol (Mosk). 1991. PMID: 1944254 Russian. - An oligonucleotide hybridization approach to DNA sequencing.
Khrapko KR, Lysov YuP, Khorlyn AA, Shick VV, Florentiev VL, Mirzabekov AD. Khrapko KR, et al. FEBS Lett. 1989 Oct 9;256(1-2):118-22. doi: 10.1016/0014-5793(89)81730-2. FEBS Lett. 1989. PMID: 2680594 - DNA sequencing by hybridization to oligonucleotide matrix. Calculation of continuous stacking hybridization efficiency.
Lysov YuP, Chernyi AA, Balaeff AA, Beattie KL, Mirzabekov AD. Lysov YuP, et al. J Biomol Struct Dyn. 1994 Feb;11(4):797-812. doi: 10.1080/07391102.1994.10508033. J Biomol Struct Dyn. 1994. PMID: 8204215 - DNA sequencing by hybridization--a megasequencing method and a diagnostic tool?
Mirzabekov AD. Mirzabekov AD. Trends Biotechnol. 1994 Jan;12(1):27-32. doi: 10.1016/0167-7799(94)90008-6. Trends Biotechnol. 1994. PMID: 7764555 Review. - [Biological microchips with hydrogel-immobilized nucleic acids, proteins, and other compounds: properties and applications in genomics].
Barskiĭ BE, Kolchinskiĭ AM, Lysov IuP, Murzabekov AD. Barskiĭ BE, et al. Mol Biol (Mosk). 2002 Jul-Aug;36(4):563-84. Mol Biol (Mosk). 2002. PMID: 12173458 Review. Russian.
Cited by
- Oligonucleotide hybridizations on glass supports: a novel linker for oligonucleotide synthesis and hybridization properties of oligonucleotides synthesised in situ.
Maskos U, Southern EM. Maskos U, et al. Nucleic Acids Res. 1992 Apr 11;20(7):1679-84. doi: 10.1093/nar/20.7.1679. Nucleic Acids Res. 1992. PMID: 1579459 Free PMC article. - A bacterial microchip: the principle of operation as exemplified by detection of antibiotics.
Fesenko DO, Nasedkina TV, Mirzabekov AD. Fesenko DO, et al. Dokl Biochem Biophys. 2001 Nov-Dec;381:427-9. doi: 10.1023/a:1013379900603. Dokl Biochem Biophys. 2001. PMID: 11813561 No abstract available. - Hybridization of glass-tethered oligonucleotide probes to target strands preannealed with labeled auxiliary oligonucleotides.
Maldonado-Rodriguez R, Espinosa-Lara M, Calixto-Suárez A, Beattie WG, Beattie KL. Maldonado-Rodriguez R, et al. Mol Biotechnol. 1999 Feb;11(1):1-12. doi: 10.1007/BF02789172. Mol Biotechnol. 1999. PMID: 10367278 - Search for genetic markers and functional variants involved in the development of opiate and cocaine addiction and treatment.
Yuferov V, Levran O, Proudnikov D, Nielsen DA, Kreek MJ. Yuferov V, et al. Ann N Y Acad Sci. 2010 Feb;1187:184-207. doi: 10.1111/j.1749-6632.2009.05275.x. Ann N Y Acad Sci. 2010. PMID: 20201854 Free PMC article. Review. - Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays.
Shchepinov MS, Case-Green SC, Southern EM. Shchepinov MS, et al. Nucleic Acids Res. 1997 Mar 15;25(6):1155-61. doi: 10.1093/nar/25.6.1155. Nucleic Acids Res. 1997. PMID: 9092624 Free PMC article.
MeSH terms
Substances
LinkOut - more resources
Other Literature Sources
Miscellaneous