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DNA Multiplex Hybridization on Microarrays and Thermodynamic Stability in Solution: A Direct Comparison

Description: 
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.
Record Format: 
application/pdf
Record Date: 
2007-01-01T08:00:00Z
Publisher: 
PDXScholar
Subject: 
Thermodynamics
Oligonucleotide Array Sequence Analysis
DNA microarray
Biochemistry
Chemistry
Nucleic Acids, Nucleotides, and Nucleosides
Type: 
text
Raw Url: 
https://pdxscholar.library.pdx.edu/do/oai/?metadataPrefix=&verb=GetRecord&identifier=oai:pdxscholar.library.pdx.edu:chem_fac-1048
Source: 
Chemistry Faculty Publications and Presentations
Repository Record Id: 
oai:pdxscholar.library.pdx.edu:chem_fac-1048
SetSpec: 
publication:clas
publication:communities
publication:chem_fac
publication:chem
Record Title: 
DNA Multiplex Hybridization on Microarrays and Thermodynamic Stability in Solution: A Direct Comparison
Identifier: 
https://pdxscholar.library.pdx.edu/chem_fac/50
https://pdxscholar.library.pdx.edu/cgi/viewcontent.cgi?article=1048&context=chem_fac
Author: 
Fish, Daniel J.
Horne, M. Todd
Brewood, Greg P.
Goodarzi, Jim P.
Alemayehu, Saba
Bhandiwad, Ashwini
Searles, Robert P.
Benight, Albert S.
Database: 
Resource OE Format: 
randomness