Volume 6, Issue 3
The Melting Mechanism of DNA Tethered to a Surface

K. Qamhieh, K.-Y. Wong, G. C. Lynch & B. M. Pettitt

Int. J. Numer. Anal. Mod., 6 (2009), pp. 474-488.

Published online: 2009-06

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  • 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.

  • Keywords

DNA, melting, microarray

  • AMS Subject Headings

92C05, 92C40

  • Copyright

COPYRIGHT: © Global Science Press

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@Article{IJNAM-6-474, author = {Qamhieh , K. and Wong , K.-Y. and Lynch , G. C. and Pettitt , B. M.}, title = {The Melting Mechanism of DNA Tethered to a Surface}, journal = {International Journal of Numerical Analysis and Modeling}, year = {2009}, volume = {6}, number = {3}, pages = {474--488}, 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.

}, issn = {2617-8710}, doi = {https://doi.org/}, url = {http://global-sci.org/intro/article_detail/ijnam/779.html} }
TY - JOUR T1 - The Melting Mechanism of DNA Tethered to a Surface AU - Qamhieh , K. AU - Wong , K.-Y. AU - Lynch , G. C. AU - Pettitt , B. M. JO - International Journal of Numerical Analysis and Modeling VL - 3 SP - 474 EP - 488 PY - 2009 DA - 2009/06 SN - 6 DO - http://doi.org/ UR - https://global-sci.org/intro/article_detail/ijnam/779.html KW - DNA, melting, microarray AB -

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.

K. Qamhieh, K.-Y. Wong, G. C. Lynch & B. M. Pettitt. (1970). The Melting Mechanism of DNA Tethered to a Surface. International Journal of Numerical Analysis and Modeling. 6 (3). 474-488. doi:
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