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Qamhieh K, Wong KY, Lynch GC, et al. THE MELTING MECHANISM OF DNA TETHERED TO A SURFACE. Int J Numer Anal Model. 2009;6(3):474-488
Qamhieh, K., Wong, K. Y., Lynch, G. C., & Pettitt, B. M. (2009). THE MELTING MECHANISM OF DNA TETHERED TO A SURFACE. International journal of numerical analysis and modeling, 6(3), 474-488.
Qamhieh, Khawla, et al. "THE MELTING MECHANISM OF DNA TETHERED TO A SURFACE." International journal of numerical analysis and modeling vol. 6,3 (2009): 474-488.
Qamhieh K, Wong KY, Lynch GC, Pettitt BM. THE MELTING MECHANISM OF DNA TETHERED TO A SURFACE. Int J Numer Anal Model. 2009 Mar 08;6(3):474-488. PMID: 19802357; PMCID: PMC2755589.
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Int J Numer Anal Model. 2009 Mar 08;6(3):474-488.

THE MELTING MECHANISM OF DNA TETHERED TO A SURFACE.

International journal of numerical analysis and modeling

Khawla Qamhieh, Ka-Yiu Wong, Gillian C Lynch, B Montgomery Pettitt

Affiliations

  1. Department of Chemistry and Institute for Molecular Design, University of Houston, Houston, TX 77204-5003, USA.

PMID: 19802357 PMCID: PMC2755589

Abstract

The details of melting of DNA immobilized on a chip or nanoparticle determines the sensitivity and operating characteristics of many analytical and synthetic biotechnological devices. Yet, little is known about the differences in how the DNA melting occurs between a homogeneous solution and that on a chip. We used molecular dynamics simulations to explore possible pathways for DNA melting on a chip. Simulation conditions were chosen to ensure that melting occurred in a submicrosecond timescale. The temperature was set to 400 K and the NaCl concentration was set to 0.1 M. We found less symmetry than in the solution case where for oligomeric double-stranded nucleic acids both ends melted with roughly equal probability. On a prepared silica surface we found melting is dominated by fraying from the end away from the surface. Strand separation was hindered by nonspecific surface adsorption at this temperature. At elevated temperatures the melted DNA was attracted to even uncharged organically coated surfaces demonstrating surface fouling. While hybridization is not the simple reverse of melting, this simulation has implications for the kinetics of hybridization.

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