title: Elasticity of the transition state for oligonucleotide hybridization.
abstract: Despite its fundamental importance in cellular processes and abundant use in biotechnology, we lack a detailed understanding of the kinetics of nucleic acid hybridization. In particular, the identity of the transition state, which determines the kinetics of the two-state reaction, remains poorly characterized. Here, we used optical tweezers with single-molecule fluorescence to observe directly the binding and unbinding of short oligonucleotides (7-12 nt) to a complementary strand held under constant force. Binding and unbinding rate constants measured across a wide range of forces (1.5-20 pN) deviate from the exponential force dependence expected from Bell's equation. Using a generalized force dependence model, we determined the elastic behavior of the transition state, which we find to be similar to that of the pure single-stranded state. Our results indicate that the transition state for hybridization is visited before the strands form any significant amount of native base pairs. Such a transition state supports a model in which the rate-limiting step of the hybridization reaction is the alignment of the two strands prior to base pairing.
authors.affiliation: Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, 1110 West Green St., Urbana, IL 61801, USA.
authors.forename: Kevin D
authors.initials: KD
authors.lastname: Whitley
authors.affiliation: Department of Physics, University of Illinois, Urbana-Champaign, 1110 West Green St., Urbana, IL 61801, USA.|Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, 1110 West Green St., Urbana, IL 61801, USA.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Comstock
authors.affiliation: Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, 1110 West Green St., Urbana, IL 61801, USA ychemla@illinois.edu.|Department of Physics, University of Illinois, Urbana-Champaign, 1110 West Green St., Urbana, IL 61801, USA.|Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, 1110 West Green St., Urbana, IL 61801, USA.
authors.forename: Yann R
authors.initials: YR
authors.lastname: Chemla
mesh_terms: D000465:Algorithms; D004247:DNA / Q000737:chemistry; D007700:Kinetics; D008956:Models, Chemical; D009693:Nucleic Acid Hybridization; D009841:Oligonucleotides / Q000737:chemistry; D012313:RNA / Q000737:chemistry
chemical_list: D009841:Oligonucleotides; D012313:RNA; D004247:DNA