Effect of salt concentration on the stability of heterogeneous DNA
arXiv:1509.08191 · doi:10.1016/j.physa.2014.10.029
Abstract
We study the role of cations on the stability of double stranded DNA (dsDNA) molecules.It is known that the two strands of double stranded DNA(dsDNA) have negative charge due to phosphate group. Cations in the form of salt in the solution, act as shielding agents thereby reducing the repulsion between these strands. We study several heterogeneous DNA molecules. We calculate the phase diagrams for DNA molecules in thermal as well as in force ensembles using Peyrard-Bishop-Dauxois (PBD) model. The dissociation and the stacking energies are the two most important factors that play an important role in the DNA stability. With suitable modifications in the model parameters we investigate the role of cation concentration on the stability of different heterogeneous DNA molecules. The objective of this work is to understand how these cations modify the strength of different pairs or bases along the strand. The phase diagram for the force ensemble case (a dsDNA is pulled from an end) is compared with the experimental results.
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- 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
- Pulling short DNA molecules having defects on different locations
- Base pair fluctuations in helical models for nucleic acids
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- Mesoscopic helical models for DNA
- Twist-stretch relations in nucleic acids
- DNA Unzipping Transition
- Statistical method for A-RNA and B-DNA