Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1993 Oct 11;21(20):4663–4669. doi: 10.1093/nar/21.20.4663

A study of oligonucleotide reassociation using large arrays of oligonucleotides synthesised on a glass support.

U Maskos 1, E M Southern 1
PMCID: PMC331488  PMID: 8233815

Abstract

An extensive analysis of oligonucleotide interactions was carried out by hybridising a synthetic pool of 256 10mers, A(C,T)8A, representing all oligopyrimidine octamer sequences to an array of four copies of all 256 different octapurine sequences. The resulting 256 duplexes were quantified by phosphorimaging and analysed to determine the dependence of duplex formation on base composition, sequence, and salt concentration. The results show that the base composition dependence of duplex formation can be reduced by high concentrations of tetramethylammonium chloride. This chaotropic solvent also increases duplex yield by up to fifty-fold.

Full text

PDF
4663

Images in this article

4664Image
on p.4664

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Aboul-ela F., Koh D., Tinoco I., Jr, Martin F. H. Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,T). Nucleic Acids Res. 1985 Jul 11;13(13):4811–4824. doi: 10.1093/nar/13.13.4811. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. 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]
  3. Frank R., Köster H. DNA chain length markers and the influence of base composition on electrophoretic mobility of oligodeoxyribonucleotides in polyacrylamide-gels. Nucleic Acids Res. 1979;6(6):2069–2087. doi: 10.1093/nar/6.6.2069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Gruenwedel D. W., Hsu C. H., Lu D. S. The effects of aqueous neutral-salt solutions on the melting temperatures of deoxyribonucleic acids. Biopolymers. 1971;10(1):47–68. doi: 10.1002/bip.360100106. [DOI] [PubMed] [Google Scholar]
  5. Jacobs K. A., Rudersdorf R., Neill S. D., Dougherty J. P., Brown E. L., Fritsch E. F. The thermal stability of oligonucleotide duplexes is sequence independent in tetraalkylammonium salt solutions: application to identifying recombinant DNA clones. Nucleic Acids Res. 1988 May 25;16(10):4637–4650. doi: 10.1093/nar/16.10.4637. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Johnston R. F., Pickett S. C., Barker D. L. Autoradiography using storage phosphor technology. Electrophoresis. 1990 May;11(5):355–360. doi: 10.1002/elps.1150110503. [DOI] [PubMed] [Google Scholar]
  7. Maskos U., Southern E. M. Oligonucleotide hybridizations on glass supports: a novel linker for oligonucleotide synthesis and hybridization properties of oligonucleotides synthesised in situ. Nucleic Acids Res. 1992 Apr 11;20(7):1679–1684. doi: 10.1093/nar/20.7.1679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Maskos U., Southern E. M. Parallel analysis of oligodeoxyribonucleotide (oligonucleotide) interactions. I. Analysis of factors influencing oligonucleotide duplex formation. Nucleic Acids Res. 1992 Apr 11;20(7):1675–1678. doi: 10.1093/nar/20.7.1675. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. McBride L. J., McCollum C., Davidson S., Efcavitch J. W., Andrus A., Lombardi S. J. A new, reliable cartridge for the rapid purification of synthetic DNA. Biotechniques. 1988 Apr;6(4):362–367. [PubMed] [Google Scholar]
  11. Melchior W. B., Jr, Von Hippel P. H. Alteration of the relative stability of dA-dT and dG-dC base pairs in DNA. Proc Natl Acad Sci U S A. 1973 Feb;70(2):298–302. doi: 10.1073/pnas.70.2.298. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Mellema J. R., van der Woerd R., van der Marel G. A., van Boom J. H., Altona C. Proton NMR study and conformational analysis of d(CGT), d(TCG) and d(CGTCG) in aqueous solution. The effect of a dangling thymidine and of a thymidine mismatch on DNA mini-duplexes. Nucleic Acids Res. 1984 Jun 25;12(12):5061–5078. doi: 10.1093/nar/12.12.5061. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Orosz J. M., Wetmur J. G. DNA melting temperatures and renaturation rates in concentrated alkylammonium salt solutions. Biopolymers. 1977 Jun;16(6):1183–1199. doi: 10.1002/bip.1977.360160603. [DOI] [PubMed] [Google Scholar]
  14. Plum G. E., Park Y. W., Singleton S. F., Dervan P. B., Breslauer K. J. Thermodynamic characterization of the stability and the melting behavior of a DNA triplex: a spectroscopic and calorimetric study. Proc Natl Acad Sci U S A. 1990 Dec;87(23):9436–9440. doi: 10.1073/pnas.87.23.9436. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Shapiro J. T., Stannard B. S., Felsenfeld G. The binding of small cations to deoxyribonucleic acid. Nucleotide specificity. Biochemistry. 1969 Aug;8(8):3233–3241. doi: 10.1021/bi00836a015. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. Wood W. I., Gitschier J., Lasky L. A., Lawn R. M. Base composition-independent hybridization in tetramethylammonium chloride: a method for oligonucleotide screening of highly complex gene libraries. Proc Natl Acad Sci U S A. 1985 Mar;82(6):1585–1588. doi: 10.1073/pnas.82.6.1585. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. de Wachter R., Fiers W. Preparative two-dimensional polyacrylamide gel electrophoresis of 32 P-labeled RNA. Anal Biochem. 1972 Sep;49(1):184–197. doi: 10.1016/0003-2697(72)90257-6. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES