Published online 5 July 2006
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison
Department of Chemistry, Metcalf Center for Science and Engineering, Boston University 590 Commonwealth Avenue, Boston, MA 02215, USA
*To whom correspondence should be addressed. Tel: +1 617 353 2500; Fax: +1 617 353 6466; Email: rgeorgia{at}bu.edu
Received February 21, 2006. Revised May 5, 2006. Accepted May 27, 2006.
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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