ibschwartz's dna [3 articles]

Abstract

DNA containing repetitive sequences displays richer dynamics than heterogeneous sequences. In the genome the number of repeat units of repetitive sequences, known as microsatellites, may vary during replication by DNA slippage and their expansion gives rise to serious disorders. We studied the mechanical properties of repetitive DNA using dynamic force spectroscopy and found striking differences compared with ordinary heterogeneous sequences. Repetitive sequences dissociate at lower forces and elongate above a certain threshold force. This yield force was found to be rate ...

Abstract

The scaling properties of DNA knots of different complexities were studied by atomic force microscope. Following two different protocols DNA knots are adsorbed onto a mica surface in regimes of (i) strong binding, that induces a kinetic trapping of the three-dimensional (3D) configuration, and of (ii) weak binding, that permits (partial) relaxation on the surface. In (i) the radius of gyration of the adsorbed DNA knot scales with the 3D Flory exponent 0.60 within error. In (ii), we find 0.66, a value between the ...

Abstract

We study the dynamics of denaturation bubbles in double-stranded DNA. Demonstrating that the associated Fokker-Planck equation is equivalent to a Coulomb problem, we derive expressions for the bubble survival distribution W(t). Below Tm, W(t) is associated with the continuum of scattering states of the repulsive Coulomb potential. At Tm, the Coulomb potential vanishes and W(t) assumes a power-law tail with nontrivial dynamic exponents: the critical exponent of the entropy loss factor may cause a finite mean lifetime. Above Tm (attractive potential), ...