Stability of a surface-bound oligonucleotide duplex inferred from molecular dynamics: a study of single nucleotide defects using DNA microarrays

Microarray technology uses the sequence dependent hybridization (binding) affinity of surface-bound oligonucleotide strands for the quantification of complex nucleic acid mixtures. In spite of its huge potential in life science and medicine, microarray oligonucleotide hybridization remains far from...

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Bibliographic Details
Published in:Physical review letters 2009-05, Vol.102 (21), p.218301-218301, Article 218301
Main Authors: Naiser, Thomas, Kayser, Jona, Mai, Timo, Michel, Wolfgang, Ott, Albrecht
Format: Article
Language:English
Subjects:
Algorithms
DNA - chemistry
Models, Chemical
Nucleic Acid Hybridization
Oligonucleotide Array Sequence Analysis
Oligonucleotides - chemistry
Thermodynamics
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Summary:Microarray technology uses the sequence dependent hybridization (binding) affinity of surface-bound oligonucleotide strands for the quantification of complex nucleic acid mixtures. In spite of its huge potential in life science and medicine, microarray oligonucleotide hybridization remains far from being understood. Taking advantage of microarray combinatorial possibilities we show that, although surface bound, the hybridization affinities of single-base mismatched oligonucleotides can be derived from first principles using parameters from bulk.
ISSN:0031-9007
1079-7114
DOI:10.1103/PhysRevLett.102.218301