Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1994 Apr 25;22(8):1368–1373. doi: 10.1093/nar/22.8.1368

Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids.

E M Southern 1, S C Case-Green 1, J K Elder 1, M Johnson 1, K U Mir 1, L Wang 1, J C Williams 1
PMCID: PMC307992  PMID: 7514785

Abstract

Arrays of oligonucleotides corresponding to a full set of complements of a known sequence can be made in a single series of base couplings in which each base in the complement is added in turn. Coupling is carried out on the surface of a solid support such as a glass plate, using a device which applies reagents in a defined area. The device is displaced by a fixed movement after each coupling reaction so that consecutive couplings overlap only a portion of previous ones. The shape and size of the device and the amount by which it is displaced at each step determines the length of the oligonucleotides. Certain shapes create arrays of oligonucleotides from mononucleotides up to a given length in a single series of couplings. The array is used in a hybridisation reaction to a labelled target sequence, and shows the hybridisation behaviour of every oligonucleotide in the target sequence with its complement in the array. Applications include sequence comparison to test for mutation, analysis of secondary structure, and optimisation of PCR primer and antisense oligonucleotide design.

Full text

PDF
1372

Images in this article

1371Image
on p.1371

Selected References

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

  1. 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]
  2. Conner B. J., Reyes A. A., Morin C., Itakura K., Teplitz R. L., Wallace R. B. Detection of sickle cell beta S-globin allele by hybridization with synthetic oligonucleotides. Proc Natl Acad Sci U S A. 1983 Jan;80(1):278–282. doi: 10.1073/pnas.80.1.278. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Jaeger J. A., Turner D. H., Zuker M. Improved predictions of secondary structures for RNA. Proc Natl Acad Sci U S A. 1989 Oct;86(20):7706–7710. doi: 10.1073/pnas.86.20.7706. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Maskos U., Southern E. M. A novel method for the parallel analysis of multiple mutations in multiple samples. Nucleic Acids Res. 1993 May 11;21(9):2269–2270. doi: 10.1093/nar/21.9.2269. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. 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]
  6. 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]
  7. Saiki R. K., Walsh P. S., Levenson C. H., Erlich H. A. Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes. Proc Natl Acad Sci U S A. 1989 Aug;86(16):6230–6234. doi: 10.1073/pnas.86.16.6230. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. 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]
  9. 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]
  10. 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]
  11. Zielenski J., Rozmahel R., Bozon D., Kerem B., Grzelczak Z., Riordan J. R., Rommens J., Tsui L. C. Genomic DNA sequence of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Genomics. 1991 May;10(1):214–228. doi: 10.1016/0888-7543(91)90503-7. [DOI] [PubMed] [Google Scholar]

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

RESOURCES