Predicting DNA duplex stability on oligonucleotide arrays.

Arnold Vainrub, Norha Deluge, Xiaolin Zhang, Xiaochuan Zhou, Xiaolian Gao

    Research output: Contribution to journalArticle

    5 Citations (Scopus)

    Abstract

    DNA duplex stability on oligonucleotide microarray was calculated using recently developed electrostatic theory of on-array hybridization thermodynamics. In this method, the first step is to finding the enthalpy and entropy of duplex formation in solution. This standard calculation was done with nearest-neighbor scheme and on-line software. Next the defined parameters and the array's single characteristic, the surface density of probes, are used to predict on-array duplex melting behavior. Reasonable accords of calculated and experimental melting curves for in situ synthesized microfluidic array were observed. The proposed method could be useful in microarray design and hybridization optimization. However, lack of melting curve measurements for different microarray platforms makes more experiments desirable to determine the method's accuracy.

    Original languageEnglish (US)
    Pages (from-to)393-403
    Number of pages11
    JournalMethods in molecular biology (Clifton, N.J.)
    Volume382
    StatePublished - 2007

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    Oligonucleotide Array Sequence Analysis
    Freezing
    DNA
    Microfluidics
    Entropy
    Static Electricity
    Thermodynamics
    Software

    ASJC Scopus subject areas

    • Molecular Biology
    • Genetics

    Cite this

    Vainrub, A., Deluge, N., Zhang, X., Zhou, X., & Gao, X. (2007). Predicting DNA duplex stability on oligonucleotide arrays. Methods in molecular biology (Clifton, N.J.), 382, 393-403.

    Predicting DNA duplex stability on oligonucleotide arrays. / Vainrub, Arnold; Deluge, Norha; Zhang, Xiaolin; Zhou, Xiaochuan; Gao, Xiaolian.

    In: Methods in molecular biology (Clifton, N.J.), Vol. 382, 2007, p. 393-403.

    Research output: Contribution to journalArticle

    Vainrub, A, Deluge, N, Zhang, X, Zhou, X & Gao, X 2007, 'Predicting DNA duplex stability on oligonucleotide arrays.', Methods in molecular biology (Clifton, N.J.), vol. 382, pp. 393-403.
    Vainrub, Arnold ; Deluge, Norha ; Zhang, Xiaolin ; Zhou, Xiaochuan ; Gao, Xiaolian. / Predicting DNA duplex stability on oligonucleotide arrays. In: Methods in molecular biology (Clifton, N.J.). 2007 ; Vol. 382. pp. 393-403.
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