Binding Specificity and Stability of Duplexes Formed by Modified Oligonucleotides with a 4096-hexanucleotide Microarray

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2001 Jun 19

PMID 11410672

Citations 6

Authors

E Timofeev

A Mirzabekov

Affiliations

Soon will be listed here.

Abstract

The binding of oligodeoxynucleotides modified with adenine 2'-O-methyl riboside, 2,6-diaminopurine 2'-O-methyl riboside, cytosine 2'-O-methyl riboside, 2,6-diaminopurine deoxyriboside or 5-bromodeoxyuridine was studied with a microarray containing all possible (4096) polyacrylamide-bound hexadeoxynucleotides (a generic microchip). The generic microchip was manufactured by using reductive immobilization of aminooligonucleotides in the activated copolymer of acrylamide, bis-acrylamide and N-(2,2-dimethoxyethyl) acrylamide. The binding of the fluorescently labeled modified octanucleotides to the array was analyzed with the use of both melting profiles and the fluorescence distribution at selected temperatures. Up to three substitutions of adenosines in the octamer sequence by adenine 2'-O-methyl ribosides (A(m)), 2,6-diaminopurine 2'-O-methyl ribosides (D(m)) or 2,6-diaminopurine deoxyribosides (D) resulted in increased mismatch discrimination measured at the melting temperature of the corresponding perfect duplex. The stability of complexes formed by 2'-O-methyl-adenosine-modified oligodeoxynucleotides was slightly decreased with every additional substitution, yielding approximately 4 degrees C of total loss in melting temperature for three modifications, as followed from microchip thermal denaturation experiments. 2,6-Diaminopurine 2'-O-methyl riboside modifications led to considerable duplex stabilization. The cytosine 2'-O-methyl riboside and 5-bromodeoxyuridine modifications generally did not change either duplex stability or mismatch resolution. Denaturation experiments conducted with selected perfect duplexes on microchips and in solution showed similar results on thermal stabilities. Some hybridization artifacts were observed that might indicate the formation of parallel DNA.

Citing Articles

Microarrays for identifying binding sites and probing structure of RNAs.

Kierzek R, Turner D, Kierzek E Nucleic Acids Res. 2014; 43(1):1-12.

PMID: 25505162 PMC: 4288193. DOI: 10.1093/nar/gku1303.

Targeting duplex DNA with chimeric α,β-triplex-forming oligonucleotides.

Kolganova N, Shchyolkina A, Chudinov A, Zasedatelev A, Florentiev V, Timofeev E Nucleic Acids Res. 2012; 40(16):8175-85.

PMID: 22641847 PMC: 3439883. DOI: 10.1093/nar/gks410.

In situ reverse transcription: the magic of strength and anonymity.

Ligasova A, Koberna K Nucleic Acids Res. 2010; 38(16):e167.

PMID: 20627869 PMC: 2938209. DOI: 10.1093/nar/gkq619.

DNA multiplex hybridization on microarrays and thermodynamic stability in solution: a direct comparison.

Fish D, Horne M, Brewood G, Goodarzi J, Alemayehu S, Bhandiwad A Nucleic Acids Res. 2007; 35(21):7197-208.

PMID: 17947320 PMC: 2175334. DOI: 10.1093/nar/gkm865.

Evaluation of gel-pad oligonucleotide microarray technology by using artificial neural networks.

Pozhitkov A, Chernov B, Yershov G, Noble P Appl Environ Microbiol. 2005; 71(12):8663-76.

PMID: 16332861 PMC: 1317365. DOI: 10.1128/AEM.71.12.8663-8676.2005.

References

Schena M, Shalon D, Heller R, Chai A, Brown P, Davis R . Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci U S A. 1996; 93(20):10614-9. PMC: 38202. DOI: 10.1073/pnas.93.20.10614. View

Drobyshev A, Zasedatelev A, Yershov G, Mirzabekov A . Massive parallel analysis of DNA-Hoechst 33258 binding specificity with a generic oligodeoxyribonucleotide microchip. Nucleic Acids Res. 1999; 27(20):4100-5. PMC: 148679. DOI: 10.1093/nar/27.20.4100. View

McGall G, Labadie J, Brock P, Wallraff G, Nguyen T, Hinsberg W . Light-directed synthesis of high-density oligonucleotide arrays using semiconductor photoresists. Proc Natl Acad Sci U S A. 1996; 93(24):13555-60. PMC: 19343. DOI: 10.1073/pnas.93.24.13555. View

Drobyshev A, Mologina N, Shik V, Pobedimskaya D, Yershov G, Mirzabekov A . Sequence analysis by hybridization with oligonucleotide microchip: identification of beta-thalassemia mutations. Gene. 1997; 188(1):45-52. DOI: 10.1016/s0378-1119(96)00775-5. View

Weiler J, Gausepohl H, Hauser N, Jensen O, Hoheisel J . Hybridisation based DNA screening on peptide nucleic acid (PNA) oligomer arrays. Nucleic Acids Res. 1997; 25(14):2792-9. PMC: 146815. DOI: 10.1093/nar/25.14.2792. View

Guschin D, Yershov G, Zaslavsky A, Gemmell A, Shick V, Proudnikov D . Manual manufacturing of oligonucleotide, DNA, and protein microchips. Anal Biochem. 1997; 250(2):203-11. DOI: 10.1006/abio.1997.2209. View

FOTIN A, Drobyshev A, Proudnikov D, Perov A, Mirzabekov A . Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips. Nucleic Acids Res. 1998; 26(6):1515-21. PMC: 147416. DOI: 10.1093/nar/26.6.1515. View

Wang D, Fan J, Siao C, Berno A, Young P, Sapolsky R . Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science. 1998; 280(5366):1077-82. DOI: 10.1126/science.280.5366.1077. View

Proudnikov D, Timofeev E, Mirzabekov A . Immobilization of DNA in polyacrylamide gel for the manufacture of DNA and DNA-oligonucleotide microchips. Anal Biochem. 1998; 259(1):34-41. DOI: 10.1006/abio.1998.2620. View

10.

Lockhart D, Dong H, Byrne M, Follettie M, Gallo M, Chee M . Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol. 1996; 14(13):1675-80. DOI: 10.1038/nbt1296-1675. View

11.

Germann M, Kalisch B, van de Sande J . Structure of d(GT)n.d(GA)n sequences: formation of parallel stranded duplex DNA. Biochemistry. 1998; 37(37):12962-70. DOI: 10.1021/bi9726842. View

12.

Chechetkin V, Turygin A, Proudnikov D, Prokopenko D, Kirillov E, Mirzabekov A . Sequencing by hybridization with the generic 6-mer oligonucleotide microarray: an advanced scheme for data processing. J Biomol Struct Dyn. 2000; 18(1):83-101. DOI: 10.1080/07391102.2000.10506649. View

13.

Cullen B, Bick M . Thermal denaturation of DNA from bromodeoxyuridine substituted cells. Nucleic Acids Res. 1976; 3(1):49-62. PMC: 342876. DOI: 10.1093/nar/3.1.49. View

14.

HOWARD F, Miles H . Poly(2-aminodeoxyadenylic acid): circular dichroism and thermal stability of its complexes and their relevance to phage DNA in which a is replaced by 2NH2A. Biopolymers. 1983; 22(2):597-600. DOI: 10.1002/bip.360220204. View

15.

Inoue H, Hayase Y, Imura A, Iwai S, Miura K, Ohtsuka E . Synthesis and hybridization studies on two complementary nona(2'-O-methyl)ribonucleotides. Nucleic Acids Res. 1987; 15(15):6131-48. PMC: 306073. DOI: 10.1093/nar/15.15.6131. View

16.

Chollet A, Kawashima E . DNA containing the base analogue 2-aminoadenine: preparation, use as hybridization probes and cleavage by restriction endonucleases. Nucleic Acids Res. 1988; 16(1):305-17. PMC: 334628. DOI: 10.1093/nar/16.1.305. View

17.

Cheong C, Tinoco Jr I, Chollet A . Thermodynamic studies of base pairing involving 2,6-diaminopurine. Nucleic Acids Res. 1988; 16(11):5115-22. PMC: 336721. DOI: 10.1093/nar/16.11.5115. View

18.

Hoheisel J, Lehrach H . Quantitative measurements on the duplex stability of 2,6-diaminopurine and 5-chloro-uracil nucleotides using enzymatically synthesized oligomers. FEBS Lett. 1990; 274(1-2):103-6. DOI: 10.1016/0014-5793(90)81340-t. View

19.

Chazin W, Rance M, Chollet A, Leupin W . Comparative NMR analysis of the decadeoxynucleotide d-(GCATTAATGC)2 and an analogue containing 2-aminoadenine. Nucleic Acids Res. 1991; 19(20):5507-13. PMC: 328949. DOI: 10.1093/nar/19.20.5507. View

20.

Southern E, Maskos U, Elder J . Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics. 1992; 13(4):1008-17. DOI: 10.1016/0888-7543(92)90014-j. View