Published In
Nucleic Acids Research
Document Type
Article
Publication Date
2007
Subjects
Thermodynamics, Oligonucleotide Array Sequence Analysis, DNA microarray
Abstract
Hybridization intensities of 30 distinct short duplex DNAs measured on spotted microarrays, were directly compared with thermodynamic stabilities measured in solution. DNA sequences were designed to promote formation of perfect match, or hybrid duplexes containing tandem mismatches. Thermodynamic parameters DeltaH degrees , DeltaS degrees and DeltaG degrees of melting transitions in solution were evaluated directly using differential scanning calorimetry. Quantitative comparison with results from 63 multiplex microarray hybridization experiments provided a linear relationship for perfect match and most mismatch duplexes. Examination of outliers suggests that both duplex length and relative position of tandem mismatches could be important factors contributing to observed deviations from linearity. A detailed comparison of measured thermodynamic parameters with those calculated using the nearest-neighbor model was performed. Analysis revealed the nearest-neighbor model generally predicts mismatch duplexes to be less stable than experimentally observed. Results also show the relative stability of a tandem mismatch is highly dependent on the identity of the flanking Watson-Crick (w/c) base pairs. Thus, specifying the stability contribution of a tandem mismatch requires consideration of the sequence identity of at least four base pair units (tandem mismatch and flanking w/c base pairs). These observations underscore the need for rigorous evaluation of thermodynamic parameters describing tandem mismatch stability.
DOI
10.1093/nar/gkm865
Persistent Identifier
http://archives.pdx.edu/ds/psu/11089
Citation Details
Fish, D., Horne, M., Brewood, G., Goodarzi, J., Alemayehu, S., Bhandiwad, A., & ... Benight, A. (2007). DNA multiplex hybridization on microarrays and thermodynamic stability in solution: a direct comparison. Nucleic Acids Research, 35(21), 7197-7208.
Included in
Biochemistry Commons, Chemistry Commons, Nucleic Acids, Nucleotides, and Nucleosides Commons
Description
This is the publisher's final PDF. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.