2 research outputs found
Dynamic force spectroscopy of DNA hairpins. I. Force kinetics and free energy landscapes
We investigate the thermodynamics and kinetics of DNA hairpins that
fold/unfold under the action of applied mechanical force. We introduce the
concept of the molecular free energy landscape and derive simplified
expressions for the force dependent Kramers-Bell rates. To test the theory we
have designed a specific DNA hairpin sequence that shows two-state cooperative
folding under mechanical tension and carried out pulling experiments using
optical tweezers. We show how we can determine the parameters that characterize
the molecular free energy landscape of such sequence from rupture force kinetic
studies. Finally we combine such kinetic studies with experimental
investigations of the Crooks fluctuation relation to derive the free energy of
formation of the hairpin at zero force.Comment: 28 pages, 12 figure
Single-molecule derivation of salt dependent base-pair free energies in DNA
Accurate knowledge of the thermodynamic properties of nucleic acids is
crucial to predicting their structure and stability. To date most measurements
of base-pair free energies in DNA are obtained in thermal denaturation
experiments, which depend on several assumptions. Here we report measurements
of the DNA base-pair free energies based on a simplified system, the mechanical
unzipping of single DNA molecules. By combining experimental data with a
physical model and an optimization algorithm for analysis, we measure the 10
unique nearest-neighbor base-pair free energies with 0.1 kcal mol-1 precision
over two orders of magnitude of monovalent salt concentration. We find an
improved set of standard energy values compared with Unified Oligonucleotide
energies and a unique set of 10 base-pair-specific salt-correction values. The
latter are found to be strongest for AA/TT and weakest for CC/GG. Our new
energy values and salt corrections improve predictions of DNA unzipping forces
and are fully compatible with melting temperatures for oligos. The method
should make it possible to obtain free energies, enthalpies and entropies in
conditions not accessible by bulk methodologies.Comment: Main text: 27 pages, 4 figures, 2 tables. Supporting Information: 51
pages, 19 figures, 4 table