Entropic Penalties in Circular DNA Assembly
arXiv:1411.0520 · doi:10.1063/1.4901116
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.
arXiv commentThe Journal of Chemical Physics (2014) in press
References in corpus (15)
- Theory of Bubble Nucleation and Cooperativity in DNA Melting
- Localization of Denaturation Bubbles in Random DNA Sequences
- Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation
- DNA flexibility on short length scales probed by atomic force microscopy
- Thermodynamics of Twisted DNA with Solvent Interaction
- Thermal denaturation of fluctuating finite DNA chains: the role of bending rigidity in bubble nucleation
- Healing Length and Bubble Formation in DNA
- 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
- Helix untwisting and bubble formation in circular DNA
- Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization
- Twisting and Bending Stress in DNA Minicircles
- DNA breathing dynamics: Analytic results for distribution functions of relevant Brownian functionals
Cited by in corpus (11)
- End-to-end distance and contour length distribution functions of DNA helices
- J-factors of short DNA molecules
- Flexibility of short DNA helices under mechanical stretching
- 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
- Mesoscopic helical models for DNA
- Twist-stretch relations in nucleic acids
- Unwinding of circular helicoidal molecules versus size
- Mesoscopic model for nano-channel confined DNA
- Statistical method for A-RNA and B-DNA