DNA confined in nanochannels: Hairpin tightening by entropic depletion

A theory is presented of the elongation of double-stranded DNA confined in a nanochannel based on a study of the formation of hairpins. A hairpin becomes constrained as it approaches the wall of a channel which leads to an entropic force causing the hairpin to tighten. The DNA in the hairpin remains double-stranded. The free energy of the...

The persistence length of double stranded DNA determined using dark field tethered particle motion

The wormlike chain model describes the micromechanics of semiflexible polymers by introducing the persistence length. We propose a method of measuring the persistence length of DNA in a controllable near-native environment. Using a dark field microscope, the projected positions of a gold nanoparticle undergoing constrained Brownian motion are...

Scaling theory of DNA confined in nanochannels and nanoslits

A scaling analysis is presented of the statistics of long DNA confined in nanochannels and nanoslits. It is argued that there are several regimes in between the de Gennes and Odijk limits introduced long ago. The DNA chain folds back on itself giving rise to a global persistence length that may be very large owing to entropic deflection....

A method to track rotational motion for use in single-molecule biophysics

The double helical nature of DNA links many cellular processes such as DNA replication, transcription, and repair to rotational motion and the accumulation of torsional strain. Magnetic tweezers (MTs) are a single-molecule technique that enables the application of precisely calibrated stretching forces to nucleic acid tethers and to control...

Numerical simulation on the mechanical characteristics of double-stranded DNA under axial stretching and lateral unzipping

The mechanical characteristics of the long-chain double-stranded DNA (dsDNA) molecule under the axial stretching and lateral unzipping are studied by the clustered atomistic-continuum method (CACM). The CACM consisted of the clustered atom method (CAM) and the atomistic-continuum method (ACM). The CAM treats the specific atomic group as the...