DNA multiplex hybridization on microarrays and thermodynamic stability in solution: A direct comparison

Daniel J. Fish, M. Todd Horne, Greg P. Brewood, Jim P. Goodarzi, Saba Alemayehu, Ashwini Bhandiwad, Robert Searles, Albert S. Benight

    Research output: Contribution to journalArticle

    28 Citations (Scopus)

    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 ΔH°, ΔS° and ΔG° 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.

    Original languageEnglish (US)
    Pages (from-to)7197-7208
    Number of pages12
    JournalNucleic Acids Research
    Volume35
    Issue number21
    DOIs
    StatePublished - Dec 2007

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    Thermodynamics
    Base Pairing
    DNA
    Differential Scanning Calorimetry
    Freezing

    ASJC Scopus subject areas

    • Genetics

    Cite this

    Fish, D. J., Horne, M. T., Brewood, G. P., Goodarzi, J. P., Alemayehu, S., Bhandiwad, A., ... Benight, A. S. (2007). DNA multiplex hybridization on microarrays and thermodynamic stability in solution: A direct comparison. Nucleic Acids Research, 35(21), 7197-7208. https://doi.org/10.1093/nar/gkm865

    DNA multiplex hybridization on microarrays and thermodynamic stability in solution : A direct comparison. / Fish, Daniel J.; Horne, M. Todd; Brewood, Greg P.; Goodarzi, Jim P.; Alemayehu, Saba; Bhandiwad, Ashwini; Searles, Robert; Benight, Albert S.

    In: Nucleic Acids Research, Vol. 35, No. 21, 12.2007, p. 7197-7208.

    Research output: Contribution to journalArticle

    Fish, DJ, Horne, MT, Brewood, GP, Goodarzi, JP, Alemayehu, S, Bhandiwad, A, Searles, R & Benight, AS 2007, 'DNA multiplex hybridization on microarrays and thermodynamic stability in solution: A direct comparison', Nucleic Acids Research, vol. 35, no. 21, pp. 7197-7208. https://doi.org/10.1093/nar/gkm865
    Fish DJ, Horne MT, Brewood GP, Goodarzi JP, Alemayehu S, Bhandiwad A et al. DNA multiplex hybridization on microarrays and thermodynamic stability in solution: A direct comparison. Nucleic Acids Research. 2007 Dec;35(21):7197-7208. https://doi.org/10.1093/nar/gkm865
    Fish, Daniel J. ; Horne, M. Todd ; Brewood, Greg P. ; Goodarzi, Jim P. ; Alemayehu, Saba ; Bhandiwad, Ashwini ; Searles, Robert ; Benight, Albert S. / DNA multiplex hybridization on microarrays and thermodynamic stability in solution : A direct comparison. In: Nucleic Acids Research. 2007 ; Vol. 35, No. 21. pp. 7197-7208.
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