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.

J-factors of short DNA molecules

“…1, that the base pair separations in the current model are measured with respect to the helix diameter which, instead, had not been defined in ref. [26]. Accordingly, in the current path integral description, the path amplitudes should fluctuate with respect to R 0 .…”

DNA terminal base pairs have weaker hydrogen bonds especially for AT under low salt concentration

“…One of the attractive properties of this model is that its Hamiltonian can be easily adapted to reflect a number of different experimental situations such as DNA overstretching 24 or to include solvent interactions. 25 Several theoretical approaches also rely on the PB model parameters as for example the path integral method 26,27 or the mesoscopic model to study the mechanical response of DNA recently proposed by Nisoli and Bishop. 28 Here, we use the PB model to calculate the parameters for terminal DNA base pairs.…”

The effect of MgO doping on the structural, magnetic, and magnetotransport properties of La0.8Sr0.2MnO3 manganite

“…Newly, some scientists have investigated thermodynamics of DNA and calculated its entropy [1,2]. In another paper, they have argued that phonons which are causes of temperature and entropy have direct relations with electrons [3,4].…”

“…Recently, the thermodynamic properties of DNA circular molecules have been investigated by a new path integral computational method and the entropic reductions associated to the formation of the ordered helicoidal structure have been estimated [1,2]. Now, the question arises that is there any relation between thermodynamics of DNA and its radiated waves.…”

“…In fact, we use this model for spectroscopy of DNAs in ovo. To this aim, we mixed previous results in [1,3,4] with the electronic model for DNA which was discussed in [5]. In this paper, the structure of DNA was compared with an structure of electronic receiver or sender.…”