Accurate prediction of binding thermodynamics for DNA on surfaces

Arnold Vainrub, Bernard Pettitt

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

For DNA mounted on surfaces for microarrays, microbeads, and nanoparticles, the nature of the random attachment of oligonucleotide probes to an amorphous surface gives rise to a locally inhomogeneous probe density. These fluctuations of the probe surface density are inherent to all common surface or bead platforms, regardless of whether they exploit either an attachment of presynthesized probes or probes synthesized in situ on the surface. Here, we demonstrate for the first time the crucial role of the probe surface density fluctuations in the performance of DNA arrays. We account for the density fluctuations with a disordered two-dimensional surface model and derive the corresponding array hybridization isotherm that includes a counterion screened electrostatic repulsion between the assayed DNA and probe array. The calculated melting curves are in excellent agreement with published experimental results for arrays with both presynthesized and in situ synthesized oligonucleotide probes. The approach developed allows one to accurately predict the melting curves of DNA arrays using only the known sequence-dependent hybridization enthalpy and entropy in solution and the experimental macroscopic surface density of probes. This opens the way to high-precision theoretical design and optimization of probes and primers in widely used DNA array-based high-throughput technologies for gene expression, genotyping, next-generation sequencing, and surface polymerase extension.

Original languageEnglish (US)
Pages (from-to)13300-13303
Number of pages4
JournalJournal of Physical Chemistry B
Volume115
Issue number45
DOIs
StatePublished - Nov 17 2011
Externally publishedYes

Fingerprint

DNA
deoxyribonucleic acid
Thermodynamics
thermodynamics
probes
predictions
Oligonucleotide Probes
oligonucleotides
Oligonucleotides
Melting
attachment
melting
primers
DNA Probes
sequencing
Microarrays
gene expression
Gene expression
curves
Isotherms

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Materials Chemistry
  • Surfaces, Coatings and Films

Cite this

Accurate prediction of binding thermodynamics for DNA on surfaces. / Vainrub, Arnold; Pettitt, Bernard.

In: Journal of Physical Chemistry B, Vol. 115, No. 45, 17.11.2011, p. 13300-13303.

Research output: Contribution to journalArticle

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