Entropic Penalties in Circular DNA Assembly

Abstract

The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to the classical action are evaluated separately by simulating a broad ensemble of twisted conformations. We obtain, for two short sequences, a free energy landscape with multiple wells corresponding to the most convenient values of helical repeat. Our results point to a intrinsic flexibility of the circular structures in which the base pair fluctuations move the system from one well to the next thus causing the local unwinding of the helix. The latter is more pronounced in the shorter sequence whose cyclization causes a higher bending stress. The entropic reductions associated to the formation of the ordered helicoidal structure are estimated.

The Journal of Chemical Physics (2014) in press

References in corpus (7)

• Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation
• Thermal denaturation of fluctuating finite DNA chains: the role of bending rigidity in bubble nucleation
• Statistical mechanics of base stacking and pairing in DNA melting
• The probability analysis of opening of DNA
• Path Integral Method for DNA Denaturation
• Denaturation Patterns in Heterogeneous DNA
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Cited by in corpus (4)

• Base pair fluctuations in helical models for nucleic acids
• First-passage probability: a test for DNA Hamiltonian parameters
• Stretching DNA in hard-wall potential channels
• Unwinding of circular helicoidal molecules versus size