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Title:
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Secondary structure effects on DNA hybridization kinetics: a solution
versus surface comparison
|
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Author:
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Gao, Yang; Wolf, Lauren K.; Georgiadis, Rosina M. |
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Abstract:
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The hybridization kinetics for a series of designed 25mer probe�target
pairs having varying degrees of secondary structure have been measured by UV absorbance and
surface plasmon resonance (SPR) spectroscopy in solution and on the surface, respectively.
Kinetic rate constants derived from the resultant data decrease with increasing probe and
target secondary structure similarly in both solution and surface environments.
Specifically, addition of three intramolecular base pairs in the probe and target structure
slow hybridization by a factor of two. For individual strands containing four or more
intramolecular base pairs, hybridization cannot be described by a traditional two-state
model in solution-phase nor on the surface. Surface hybridization rates are also 20- to
40-fold slower than solution-phase rates for identical sequences and conditions. These
quantitative findings may have implications for the design of better biosensors,
particularly those using probes with deliberate secondary structure. |
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URI:
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10.1093/nar/gkl422
http://hdl.handle.net/2144/1006
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Date:
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2006 |
