Sensitive quantitative nucleic acid detection using oligonucleotide microarrays

Arnold Vainrub, Bernard Pettitt

Research output: Contribution to journalArticle

63 Citations (Scopus)

Abstract

We report a new theoretical approach to optimize the performance and quantify the results of gene expression oligonucleotide microarrays which are widely used in biomedical research. An on-array hybridization isotherm that takes into account the screened Coulomb repulsion between the assayed nucleic acid target and the layer of surface tethered oligonucleotide probes is presented. The hybridization efficiency is found as a function of the genomic target (sequence, length, and concentration), array parameters (probe sequence and length, surface probe density), and hybridization conditions (temperature and buffer ionic strength). We present simple relations for the hybridization signal maximum and the linear dynamic detection range and show explicit criteria for optimization. The approach is based on an extension of our recently published theory (Vainrub, A.; Pettitt, B. M. Phys. Rev. E 2002, 66, art. no.-041905) which we generalize here for the cases of target depletion effects and arbitrary target length.

Original languageEnglish (US)
Pages (from-to)7798-7799
Number of pages2
JournalJournal of the American Chemical Society
Volume125
Issue number26
DOIs
StatePublished - Jul 2 2003
Externally publishedYes

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Oligonucleotide Probes
Oligonucleotides
Nucleic acids
Microarrays
Art
Oligonucleotide Array Sequence Analysis
Osmolar Concentration
Nucleic Acids
Biomedical Research
Buffers
Gene Expression
Temperature
Ionic strength
Gene expression
Isotherms
endoribonuclease Phy M

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Sensitive quantitative nucleic acid detection using oligonucleotide microarrays. / Vainrub, Arnold; Pettitt, Bernard.

In: Journal of the American Chemical Society, Vol. 125, No. 26, 02.07.2003, p. 7798-7799.

Research output: Contribution to journalArticle

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