biostudies-literatureGao YNCI NIH HHS3370-7https://www.ebi.ac.uk/biostudies/studies/S-EPMC1488884biostudies-literatureUnknown34(11)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 soNucleic acids researchSecondary structure effects on DNA hybridization kinetics: a solution versus surface comparison.PMC1488884CA 89562R01 CA089562Wolf LKGeorgiadis RMGao YfalseSecondary 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 so2006-01-01T00:00:00Z20062025-04-19T15:46:59.044Z2019-03-27T01:45:33ZS-EPMC14888841682285810.1093/nar/gkl422