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 - <p style="text-align: justify;">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.</p>