Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison.
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.
Gao
Yang
Y
Department of Chemistry, Metcalf Center for Science and Engineering, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA.
Wolf
Lauren K
LK
Georgiadis
Rosina M
RM
D015342:DNA Probes / Q000737:chemistry*; D007700:Kinetics; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D015345:Oligonucleotide Probes / Q000737:chemistry; D012996:Solutions; D013056:Spectrophotometry, Ultraviolet; D020349:Surface Plasmon Resonance
D015342:DNA Probes; D015345:Oligonucleotide Probes; D012996:Solutions