Article: A model coupling vibrational and rotational motion for the DNA molecule

We investigate a mechanical model for the DNA molecule using an extension of the Peyrard and Bishop model. In the present model, there are two chains of oscillators linked by a Morse potential, which represent the hydrogen bonds. The rotational and vibrational motions of each base pair are considered and the coupling for these motions are introduced by a nonlinear combination of them in the Morse potential. In this context, thermodynamics and structural properties are discussed.

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References

1.

Ruggiero . Parameters describing the H bond in DNA. Phys Rev A. 1991; 44(12):8435-8436. DOI: 10.1103/physreva.44.8435. View

2.

Vladescu I, McCauley M, Rouzina I, Williams M . Mapping the phase diagram of single DNA molecule force-induced melting in the presence of ethidium. Phys Rev Lett. 2005; 95(15):158102. DOI: 10.1103/PhysRevLett.95.158102. View

3.

Ambjornsson T, Banik S, Krichevsky O, Metzler R . Sequence sensitivity of breathing dynamics in heteropolymer DNA. Phys Rev Lett. 2006; 97(12):128105. DOI: 10.1103/PhysRevLett.97.128105. View

4.

Grinza P, Mossa A . Topological origin of the phase transition in a model of DNA denaturation. Phys Rev Lett. 2004; 92(15):158102. DOI: 10.1103/PhysRevLett.92.158102. View

5.

Ambjornsson T, Banik S, Krichevsky O, Metzler R . Breathing dynamics in heteropolymer DNA. Biophys J. 2007; 92(8):2674-84. PMC: 1831711. DOI: 10.1529/biophysj.106.095935. View

6.

Altan-Bonnet G, Libchaber A, Krichevsky O . Bubble dynamics in double-stranded DNA. Phys Rev Lett. 2003; 90(13):138101. DOI: 10.1103/PhysRevLett.90.138101. View

7.

Englander S, Kallenbach N, Heeger A, Krumhansl J, Litwin S . Nature of the open state in long polynucleotide double helices: possibility of soliton excitations. Proc Natl Acad Sci U S A. 1980; 77(12):7222-6. PMC: 350474. DOI: 10.1073/pnas.77.12.7222. View

8.

Kudritskaya Z, Danilov V . Quantum mechanical study of bases interactions in various associates in atomic dipole approximation. J Theor Biol. 1976; 59(2):303-18. DOI: 10.1016/0022-5193(76)90172-7. View

9.

Watson J, Crick F . Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature. 1953; 171(4356):737-8. DOI: 10.1038/171737a0. View

10.

De Luca J, Drigo Filho E, Ponno A, Ruggiero J . Energy localization in the Peyrard-Bishop DNA model. Phys Rev E Stat Nonlin Soft Matter Phys. 2004; 70(2 Pt 2):026213. DOI: 10.1103/PhysRevE.70.026213. View

11.

Zdravkovic S, Sataric M . Single-molecule unzippering experiments on DNA and Peyrard-Bishop-Dauxois model. Phys Rev E Stat Nonlin Soft Matter Phys. 2006; 73(2 Pt 1):021905. DOI: 10.1103/PhysRevE.73.021905. View

12.

Peyrard , BISHOP . Statistical mechanics of a nonlinear model for DNA denaturation. Phys Rev Lett. 1989; 62(23):2755-2758. DOI: 10.1103/PhysRevLett.62.2755. View

A Model Coupling Vibrational and Rotational Motion for the DNA Molecule