Journal Article

Steric Factors Influencing Hybridisation Of Nucleic Acids To Oligonucleotide Arrays

M. S. Shchepinov, S. C. Case-Green and E. M. Southern

in Nucleic Acids Research

Volume 25, issue 6, pages 1155-1161
Published in print March 1997 | ISSN: 0305-1048
Published online March 1997 | e-ISSN: 1362-4962 | DOI: http://dx.doi.org/10.1093/nar/25.6.1155
Steric Factors Influencing Hybridisation Of Nucleic Acids To Oligonucleotide Arrays

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We have investigated the use of spacer molecules to reduce steric interference of the support on the hybridisation behaviour of immobilised oligonucleo-tides. These spacers are built up from a variety of monomeric units, using phosphoramidite chemistry, by condensation onto an amine-functionalised polypropylene support. The optimal spacer length was determined to be at least 40 atoms in length, giving up to 150-fold increase in the yield of hybridisation. The effects of different charged groups in the spacer were also examined, and it was shown that both positively and negatively charged groups in the spacer diminish the yield of hybridisation. Steric hindrance in hybridisation can also be a problem if the oligonucleotides attached to the support are too close to each other. Surface coverage was varied using a combination of cleavable and stable linkers, giving the highest hybridisation yields for surfaces containing ∼50% of the maximum concentration of oligonucleotides.

Journal Article.  4048 words.  Illustrated.

Subjects: Chemistry ; Biochemistry ; Bioinformatics and Computational Biology ; Genetics and Genomics ; Molecular and Cell Biology

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