Extension of torsionally stressed DNA by external force

Force and twist dependence of RepC nicking activity on torsionally-constrained DNA molecules

Many bacterial plasmids replicate by an asymmetric rolling-circle mechanism that requires sequence-specific recognition for initiation, nicking of one of the template DNA strands and unwinding of the duplex prior to subsequent leading strand DNA synthesis. Nicking is performed by a replication-initiation protein (Rep) that directly binds to the plasmid double-stranded origin and remains covalen...

Monte Carlo implementation of supercoiled double-stranded DNA.

Metropolis Monte Carlo simulation is used to investigate the elasticity of torsionally stressed double-stranded DNA, in which twist and supercoiling are incorporated as a natural result of base-stacking interaction and backbone bending constrained by hydrogen bonds formed between DNA complementary nucleotide bases. Three evident regimes are found in extension versus torsion and force versus ext...

Impact of DNA twist accumulation on progressive helical wrapping of torsionally constrained DNA.

DNA wrapping is an important mechanism for chromosomal DNA packaging in cells and viruses. Previous studies of DNA wrapping have been performed mostly on torsionally unconstrained DNA, while in vivo DNA is often under torsional constraint. In this study, we extend a previously proposed theoretical model for wrapping of torsionally unconstrained DNA to a new model including the contribution of D...

Confocal microscopy on fluorescently labelled single DNA molecules and force - extension measurements on DNA carpets

Optimization of grasping by using a required external force set

In this paper, we consider an optimization of grasping by using a required external force set. By using the set, we can not only deal with whatever a desired grasp is, such as force closure or equilibrium grasp, but also evaluate the magnitudes of the resistible external forces and moments. Then, we define an optimization problem from the viewpoint of decreasing the magnitudes of the contact fo...