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Nucleic Acids Research, 1993, Vol. 21, No. 20 4663-4669
© 1993

CHEMISTRY

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

Uwe Maskos* and Edwin M. Southern

Department of Biochemistry, University of Oxford, South Parks Road Oxford 0X1 3QU, UK

*To whom correspondence should be addressed at: Laboratory of Molecular Biology, National Institute of Neurological Disorder and Stroke, National Institutes of Health Bethesda, MD 20892, USA

Received August 13, 1993. Accepted September 6, 1993.

An extensive analysis of oligonucleotide interactions was carried out by hybridising a synthetic pool of 256 10mers, A(C,T)gA, 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 fiftyfold.


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