Mechanical stability of low‐humidity single DNA molecules

Abstract

DNA electrostatic character is mostly determined by both water and counterions activities in the phosphate backbone, which together with base sequence, further confer its higher order structure. The authors overstretch individual double-stranded DNA molecules in water-ethanol solutions to investigate the modulation of its mechanical stability by hydration and polycations. The authors found that DNA denatures as ethanol concentration is increased and spermine concentration decreased. This is manifested by an increase in melting hysteresis between the stretch and release curves, with sharp transition at 10% ethanol and reentrant behavior at 60%, by a loss of cooperativity in the overstretching transition and by a dramatic decrease of both the persistence length and the flexural rigidity. Changes in base-stacking stability which are characteristic of the B-A transition between 70 and 80% ethanol concentration do not manifest in the mechanical properties of the double-helical molecule at low or high force or in the behavior of the overstretching and melting transitions within this ethanol concentration range. This is consistent with a mechanism in which A-type base-stacking is unstable in the presence of tension. Binding of motor proteins to DNA locally reduces the number of water molecules and therefore, our results may shed light on analogous reduced-water activity of DNA conditions caused by other molecules, which interact with DNA in vivo.

GC-Content Dependence of Elastic and Overstretching Properties of DNA:RNA Hybrid Duplexes

“…4, except for the tether breakage, which happened for DRH of 40% GC contents, a large hysteresis (which represents the energy dissipation during the stretching-relaxation cycle and shall be mainly related to the unpeeling processes) was observed for DRHs of 52 and 60% GC contents. Such an observation is distinct from the previously reported overstretching of dsDNA or dsRNA at the comparable temperature and buffer conditions (45,46) but similar to those occurred in mechanical stretching-relaxing dsDNA in water-ethanol mixtures (60) or at a temperature above 30 C (61) in which the basepairing interactions were seriously disturbed by the hydrophobic solvent or heat. Increasing GC contents and salt concentrations significantly diminished rips in the overstretching region as well as largely relieved the hysteresis.…”

A Temperature-Jump Optical Trap for Single-Molecule Manipulation

“…As a consequence, it avoids the systematic error associated with the definition of the zero in absolute distance or molecular extension measurements. The zero for extension measurements is difficult to determine precisely in single-trap tweezers because a significant uncertainty results from the fact that the molecule can be attached anywhere on the surface of the immobilized bead in the pipette, a problem that needs to be solved to compare single molecules in different conditions (36)(37)(38). Fig.…”

Entropy Involved in Fidelity of DNA Replication

“…9. Water exclusion in the DNA double helix has also been shown to decrease the axial base-stacking interactions, as reflected in the DNA stretch modulus [32]. It is therefore expected a type-dependent polymerase mechanism that optimizes fidelity towards reported values of 1 error out of ∼ 10 5 incorporated bases [28].…”