Single-molecule dissection of stacking forces in DNA

Abstract

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.

On the Stability of Interactions between Pairs of Anions – Complexes of MCl3− (M=Be, Mg, Ca, Sr, Ba) with Pyridine and CN−

“…Some of these are rather straightforward in terms of the underlying forces, such as the strong Coulombic attractions between ions of opposite charge in salt bridges or ionic liquids. Others are more subtle and complicated, as for example the stacking interactions between aromatic systems which are a staple of nucleic acids, protein structure, or of benzene dimers . The H‐bond can be considered as intermediate between these extremes.…”

Self-assembly of precisely defined DNA nanotube superstructures using DNA origami seeds

“…Other possible reasons for reduced yield include incomplete linker hybridization during the annealing process, which would make nunchuck seeds susceptible to dissociation and recombination. A recent study 25 suggests that longer incubation times of the individual nanotube seeds prior to co-incubation for assembly of the nunchuck seed structure could address this problem by minimizing kinetic traps that prevent hybridization from going to completion. Minor interference between the two types of tiles, REs and SEs, could also interfere with nucleation kinetics and result in lower yields.…”

How We Make DNA Origami

“…Because of the enhanced rigidity, multilayer objects have thus been employed as structural scaffolds in applications that require rigid positioning in solution (e.g., refs. , , and ), whereas single‐layered objects are often chosen for applications on a solid support (e.g., ref. ).…”