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- Title
Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison.
- Authors
Gao, Yang; Wolf, Lauren K; Georgiadis, Rosina M
- Abstract
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.
- Publication
Nucleic acids research, 2006, Vol 34, Issue 11, p3370
- ISSN
1362-4962
- Publication type
Journal Article
- DOI
10.1093/nar/gkl422