Sequence dependence of DNA bending rigidity.

Sequence-dependent elastic properties of DNA.

Harmonic elastic constants of 3-11 bp duplex DNA fragments were evaluated using four 5 ns unrestrained molecular dynamics simulation trajectories of 17 bp duplexes with explicit inclusion of solvent and counterions. All simulations were carried out with the Cornell et al. force-field and particle mesh Ewald method for long-range electrostatic interactions. The elastic constants including anisot...

Comment on "Length scale dependence of DNA mechanical properties".

Recent experimental data [1–7] indicate that the elastic wormlike rod (WLR) model of DNA that works well on long length scales may break down on shorter scales relevant to biology. According to Noy and Golestanian (N&G) [8] molecular dynamics (MD) simulations predict DNA rigidity close to experimental data and confirm one scenario of such breakdown, namely, that for lengths of a few helical tur...

Applying Fuzzy Logic Model for Bending Rigidity Evaluation of Woven Fabrics

High-throughput approach for detection of DNA bending and flexibility based on cyclization.

We have developed a high-throughput approach to the labor-intensive problems of DNA cyclization, which we use to characterize DNA curvature and mechanical properties. The method includes a combinatorial approach to make the DNA constructs needed and automated real-time measurement of the kinetics using fluorescence. We validated the approach and investigated the flexibility of two kinds of nick...

DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics

Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariabl...