How dsDNA breathing enhances its flexibility and instability on short length scales

Abstract

We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the duplex and also forks at the ends, with the size distributions independent of the contour length. We find that these local denaturations at a physiological temperature, despite their rare and transient presence, can lower the persistence length drastically for a short DNA segment in agreement with experiment.

References in corpus (5)

• Order of the phase transition in models of DNA thermal denaturation
• Distribution Functions, Loop Formation Probabilities and Force-Extension Relations in a Model for Short Double-Stranded DNA Molecules
• Probability distribution of bubble lengths in DNA
• Scaling in DNA unzipping models: denaturated loops and end-segments as branches of a block copolymer network
• Effects of kink and flexible hinge defects on mechanical responses of short double stranded DNA molecules

Cited by in corpus (4)

• Single molecule study of the DNA denaturation phase transition in the force-torsion space
• Twist-bend coupling, twist waves and the shape of DNA loops
• Tensile elasticity of semiflexible polymers with hinge defects
• Effect of magnesium ions on dielectric relaxation in semidilute DNA aqueous solutions