Single-molecule dissection of stacking forces in DNA.
We directly measured at the single-molecule level the forces and lifetimes of DNA base-pair stacking interactions for all stack sequence combinations. Our experimental approach combined dual-beam optical tweezers with DNA origami components to allow positioning of blunt-end DNA helices so that the weak stacking force could be isolated. Base-pair stack arrays that lacked a covalent backbone connection spontaneously dissociated at average rates ranging from 0.02 to 500 per second, depending on the sequence combination and stack array size. Forces in the range from 2 to 8 piconewtons that act along the helical direction only mildly accelerated the stochastic unstacking process. The free-energy increments per stack that we estimate from the measured forward and backward kinetic rates ranged from -0.8 to -3.4 kilocalories per mole, depending on the sequence combination. Our data contributes to understanding the mechanics of DNA processing in biology, and it is helpful for designing the kinetics of DNA-based nanoscale devices according to user specifications.
Labor für Biomolekulare Nanotechnologie, Physik Department and Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, Garching near Munich, Germany.
Fabian
F
Kilchherr
Labor für Biomolekulare Nanotechnologie, Physik Department and Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, Garching near Munich, Germany.
Christian
C
Wachauf
Lehrstuhl für Molekulare Biophysik, Physik Department, Technische Universität München, James-Franck-Strasse 1, Garching near Munich, Germany.
Benjamin
B
Pelz
Lehrstuhl für Molekulare Biophysik, Physik Department, Technische Universität München, James-Franck-Strasse 1, Garching near Munich, Germany. Munich Center for Integrated Protein Science, 81377 Munich, Germany.
Matthias
M
Rief
Lehrstuhl für Theoretische Biophysik, Physik Department, Technische Universität München, James-Franck-Strasse 1, Garching near Munich, Germany. Munich Center for Integrated Protein Science, 81377 Munich, Germany.
Martin
M
Zacharias
Labor für Biomolekulare Nanotechnologie, Physik Department and Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, Garching near Munich, Germany. Munich Center for Integrated Protein Science, 81377 Munich, Germany. Institute for Advanced Study, TUM, Germany. dietz@tum.de.
Hendrik
H
Dietz
D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D036103:Nanotechnology; D009690:Nucleic Acid Conformation; D052898:Optical Tweezers
D004247:DNA