Flexibility of short DNA helices under mechanical stretching

Abstract

The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair. The elastic response of a set of homogeneous helices to externally applied forces is obtained by computing the average bending angles between adjacent base pairs along the molecule axis. The ensemble averages are performed over a room temperature equilibrium distribution of base pair separations and bending fluctuations. The analysis of the end-to-end distances and persistence lengths shows that even short sequences with less than $100$ base pairs maintain a significant bendability ascribed to thermal fluctuational effects and kinks with large bending angles. The discrepancies between the outcomes of the discrete model and those of the worm-like-chain model are examined pointing out the inadequacy of the latter on short length scales.

Physical Chemistry Chemical Physics (2016). Final version available at DOI below. arXiv admin note: text overlap with arXiv:1606.01357

References in corpus (13)

• Probing the elastic limit of DNA bending
• Flexibility of short DNA helices with finite-length effect: from base pairs to tens of base pairs
• Chain morphology, swelling exponent, persistence length, like-charge attraction, and charge distribution around a chain in polyelectrolyte solutions: effects of salt concentration and ion size studied by molecular dynamics simulations
• Effect of salt concentration on the stability of heterogeneous DNA
• The probability analysis of opening of DNA
• Path Integral Method for DNA Denaturation
• Denaturation Patterns in Heterogeneous DNA
• Stacking Interactions in Denaturation of DNA Fragments
• Dependence on temperature and GC content of bubble length distributions in DNA
• J-factors of short DNA molecules
• Twisting and Bending Stress in DNA Minicircles
• Entropic Penalties in Circular DNA Assembly
• Mesoscopic models for DNA stretching under force: new results and comparison to experiments

Cited by in corpus (12)

• Ionic liquids make DNA rigid
• End-to-end distance and contour length distribution functions of DNA helices
• DNA size in confined environments
• Base pair fluctuations in helical models for nucleic acids
• Twisting short dsDNA with applied tension
• First-passage probability: a test for DNA Hamiltonian parameters
• Twist-stretch profiles of DNA chains
• Mesoscopic helical models for DNA
• Twist-stretch relations in nucleic acids
• Stiffer double-stranded DNA in two-dimensional confinement due to bending anisotropy
• Mesoscopic model for nano-channel confined DNA
• Statistical method for A-RNA and B-DNA