The melting mechanism of DNA tethered to a surface

Khawla Qamhieh, Ka Yiu Wong, Gillian C. Lynch, Bernard Pettitt

Research output: Contribution to journalArticle

24 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)474-488
Number of pages15
JournalInternational Journal of Numerical Analysis and Modeling
Volume6
Issue number3
StatePublished - 2009
Externally publishedYes

Fingerprint

Melting
DNA
Chip
Operating Characteristics
Nucleic acids
Fouling
Silica
Adsorption
Temperature
Molecular Dynamics Simulation
Nanoparticles
Molecular dynamics
Reverse
Pathway
Simulation
Time Scales
Kinetics
Symmetry
Computer simulation

Keywords

  • And microarray
  • DNA
  • Melting

ASJC Scopus subject areas

  • Numerical Analysis

Cite this

The melting mechanism of DNA tethered to a surface. / Qamhieh, Khawla; Wong, Ka Yiu; Lynch, Gillian C.; Pettitt, Bernard.

In: International Journal of Numerical Analysis and Modeling, Vol. 6, No. 3, 2009, p. 474-488.

Research output: Contribution to journalArticle

Qamhieh, Khawla ; Wong, Ka Yiu ; Lynch, Gillian C. ; Pettitt, Bernard. / The melting mechanism of DNA tethered to a surface. In: International Journal of Numerical Analysis and Modeling. 2009 ; Vol. 6, No. 3. pp. 474-488.
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