title: Sequence-Dependent Mechanism of DNA Oligonucleotide Dehybridization Resolved through Infrared Spectroscopy.
abstract: Despite its important role in biology and nanotechnology, many questions remain regarding the molecular mechanism and dynamics by which oligonucleotides recognize and hybridize to their complementary sequence. The thermodynamics and kinetics of DNA oligonucleotide hybridization and dehybridization are often assumed to involve an all-or-nothing two-state dissociation pathway, but deviations from this behavior can be considerable even for short sequences. We introduce a new strategy to characterize the base-pair-specific thermal dissociation mechanism of DNA oligonucleotides through steady-state and time-resolved infrared spectroscopy. Experiments are interpreted with a lattice model to provide a structure-specific interpretation. This method is applied to a model set of self-complementary 10-base-pair sequences in which the placement of GC base pairs is varied in an otherwise AT strand. Through a combination of Fourier transform infrared and two-dimensional infrared spectroscopy, experiments reveal varying degrees of deviation from simple two-state behavior. As the temperature is increased, duplexes dissociate through a path in which the terminal bases fray, without any significant contribution from loop configurations. Transient temperature jump experiments reveal time scales of 70-100 ns for fraying and 10-30 μs for complete dissociation near the melting temperature. Whether or not frayed states are metastable intermediates or short-lived configurations during the full dissociation of the duplex is dictated by the nucleobase sequence.
authors: Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States.
authors: Paul J
authors: PJ
authors: Sanstead
authors: Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States.|Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.
authors: Paul
authors: P
authors: Stevenson
authors: Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States.
authors: Andrei
authors: A
authors: Tokmakoff
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D009693:Nucleic Acid Hybridization; D009841:Oligonucleotides / Q000737:chemistry* / Q000235:genetics; D013055:Spectrophotometry, Infrared; D044366:Transition Temperature
chemical_list: D009841:Oligonucleotides; D004247:DNA