• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of biophysjLink to Publisher's site
Biophys J. Nov 1996; 71(5): 2795–2801.
PMCID: PMC1233765

Theoretical analysis of the kinetics of DNA hybridization with gel-immobilized oligonucleotides.

Abstract

A new method of DNA sequencing by hybridization using a microchip containing a set of immobilized oligonucleotides is being developed. A theoretical analysis is presented of the kinetics of DNA hybridization with deoxynucleotide molecules chemically tethered in a polyacrylamide gel layer. The analysis has shown that long-term evolution of the spatial distribution and of the amount of DNA bound in a hybridization cell is governed by "retarded diffusion," i.e., diffusion of the DNA interrupted by repeated association and dissociation with immobile oligonucleotide molecules. Retarded diffusion determines the characteristic time of establishing a final equilibrium state in a cell, i.e., the state with the maximum quantity and a uniform distribution of bound DNA. In the case of cells with the most stable, perfect duplexes, the characteristic time of retarded diffusion (which is proportional to the equilibrium binding constant and to the concentration of binding sites) can be longer than the duration of the real hybridization procedure. This conclusion is indirectly confirmed by the observation of nonuniform fluorescence of labeled DNA in perfect-match hybridization cells (brighter at the edges). For optimal discrimination of perfect duplexes from duplexes with mismatches the hybridization process should be brought to equilibrium under low-temperature nonsaturation conditions for all cells. The kinetic differences between perfect and nonperfect duplexes in the gel allow further improvement in the discrimination through additional washing at low temperature after hybridization.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.4M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Bains W, Smith GC. A novel method for nucleic acid sequence determination. J Theor Biol. 1988 Dec 7;135(3):303–307. [PubMed]
  • Braunlin WH, Bloomfield VA. 1H NMR study of the base-pairing reactions of d(GGAATTCC): salt effects on the equilibria and kinetics of strand association. Biochemistry. 1991 Jan 22;30(3):754–758. [PubMed]
  • Cantor CR, Mirzabekov A, Southern E. Report on the sequencing by hybridization workshop. Genomics. 1992 Aug;13(4):1378–1383. [PubMed]
  • Chan V, Graves DJ, McKenzie SE. The biophysics of DNA hybridization with immobilized oligonucleotide probes. Biophys J. 1995 Dec;69(6):2243–2255. [PMC free article] [PubMed]
  • Doktycz MJ, Morris MD, Dormady SJ, Beattie KL, Jacobson KB. 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. [PubMed]
  • 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. [PubMed]
  • Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science. 1991 Feb 15;251(4995):767–773. [PubMed]
  • Gotoh M, Hasegawa Y, Shinohara Y, Shimizu M, Tosu M. A new approach to determine the effect of mismatches on kinetic parameters in DNA hybridization using an optical biosensor. DNA Res. 1995 Dec 31;2(6):285–293. [PubMed]
  • Guo Z, Guilfoyle RA, Thiel AJ, Wang R, Smith LM. Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. Nucleic Acids Res. 1994 Dec 11;22(24):5456–5465. [PMC free article] [PubMed]
  • Khrapko KR, Lysov YuP, Khorlyn AA, Shick VV, Florentiev VL, Mirzabekov AD. An oligonucleotide hybridization approach to DNA sequencing. FEBS Lett. 1989 Oct 9;256(1-2):118–122. [PubMed]
  • Khrapko KR, Lysov YuP, Khorlin AA, Ivanov IB, Yershov GM, Vasilenko SK, Florentiev VL, Mirzabekov AD. A method for DNA sequencing by hybridization with oligonucleotide matrix. DNA Seq. 1991;1(6):375–388. [PubMed]
  • Lamture JB, Beattie KL, Burke BE, Eggers MD, Ehrlich DJ, Fowler R, Hollis MA, Kosicki BB, Reich RK, Smith SR, et al. Direct detection of nucleic acid hybridization on the surface of a charge coupled device. Nucleic Acids Res. 1994 Jun 11;22(11):2121–2125. [PMC free article] [PubMed]
  • Livache T, Roget A, Dejean E, Barthet C, Bidan G, Téoule R. Preparation of a DNA matrix via an electrochemically directed copolymerization of pyrrole and oligonucleotides bearing a pyrrole group. Nucleic Acids Res. 1994 Aug 11;22(15):2915–2921. [PMC free article] [PubMed]
  • Livshits MA, Florentiev VL, Mirzabekov AD. Dissociation of duplexes formed by hybridization of DNA with gel-immobilized oligonucleotides. J Biomol Struct Dyn. 1994 Feb;11(4):783–795. [PubMed]
  • Mirzabekov AD. DNA sequencing by hybridization--a megasequencing method and a diagnostic tool? Trends Biotechnol. 1994 Jan;12(1):27–32. [PubMed]
  • Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes CP, Fodor SP. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci U S A. 1994 May 24;91(11):5022–5026. [PMC free article] [PubMed]
  • Senior M, Jones RA, Breslauer KJ. Influence of dangling thymidine residues on the stability and structure of two DNA duplexes. Biochemistry. 1988 May 17;27(10):3879–3885. [PubMed]
  • Southern EM, Maskos U, Elder JK. Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics. 1992 Aug;13(4):1008–1017. [PubMed]
  • Williams JC, Case-Green SC, Mir KU, Southern EM. Studies of oligonucleotide interactions by hybridisation to arrays: the influence of dangling ends on duplex yield. Nucleic Acids Res. 1994 Apr 25;22(8):1365–1367. [PMC free article] [PubMed]
  • Yershov G, Barsky V, Belgovskiy A, Kirillov E, Kreindlin E, Ivanov I, Parinov S, Guschin D, Drobishev A, Dubiley S, et al. DNA analysis and diagnostics on oligonucleotide microchips. Proc Natl Acad Sci U S A. 1996 May 14;93(10):4913–4918. [PMC free article] [PubMed]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • Compound
    Compound
    PubChem Compound links
  • PubMed
    PubMed
    PubMed citations for these articles
  • Substance
    Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...