Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Morse potential in DNA molecule – An experiment proposal


We rely on the helicoidal Peyrard-Bishop model for DNA dynamics. Interaction between nucleotides at a same site belonging to different strands is modelled by a Morse potential energy. This potential depends on two parameters that are different for AT and CG pairs, which is a possible source for inhomogeneity. It was shown recently (Zdravković and Satarić 2011) that certain values of these parameters bring about a negligible influence of inhomogeneity on the solitonic dynamics. We propose an experiment that should be carried out in order to determine the values of both of these parameters.

This is a preview of subscription content, log in to check access.

Figure 1
Figure 2
Figure 3
Figure 4


  1. Allemand JF, Bensimon D, Lavery R and Croquette V 1998 Stretched and overwound DNA forms a Pauling-like structure with exposed bases. Proc. Natl. Acad. Sci. USA 95 14152–14157

  2. Bockelmann U, Essevaz-Roulet B and Heslot F 1997 Molecular Stick-Slip Motion Revealed by Opening DNA with Piconewton Forces. Phys. Rev. Lett. 79 4489–4492

  3. Bockelmann U, Essevaz-Roulet B and Heslot F 1998 DNA strand separation studied by single molecule force measurements. Phys. Rev. E 58 2386–2394

  4. Boland T and Ratner BD 1995 Direct measurement of hydrogen bonding in DNA nucleotide bases by atomic force microscopy. Proc. Natl. Acad. Sci. USA 92 5297–5301

  5. Bustamante C, Marko JF, Siggia ED and Smith S 1994 Entropic elasticity of lambda-phage DNA. Science 265 1599–1600

  6. Clausen-Schaumann H, Rief M, Tolksdorf C and Gaub HE 2000 Mechanical Stability of Single DNA Molecules. Biophys. J. 78 1997–2007

  7. Dauxois T 1991 Dynamics of breather modes in a nonlinear “helicoidal” model of DNA. Phys. Lett. A 159 390–395

  8. Galburt EA, Grill SW and Bustamante C 2009 Single molecule transcription elongation. Methods 48 323–332

  9. Hakim MB, Lindsay SM and Powell J 1984 The speed of sound in DNA. Biopolymers 23 1185–1192

  10. Lee GU, Chrisey LA and Colton RJ 1994 Direct measurement of the forces between complementary strands of DNA. Science 266 771–773

  11. Lionnet T, Joubaud S, Lavery R, Bensimon D and Croquette V 2006 Wringing Out DNA. Phys. Rev. Lett. 96 178102

  12. Moffitt JR, Chemla YR, Smith SB and Bustamante C 2008 Recent Advances in Optical Tweezers. Annu. Rev. Biochem. 77 205–228

  13. Mosconi F, Allemand JF, Bensimon D and Croquette V 2009 Measurement of the Torque on a Single Stretched and Twisted DNA Using Magnetic Tweezers. Phys. Rev. Lett. 102 078301

  14. Peyrard M 2004 Nonlinear dynamics and statistical physics of DNA. Nonlinearity 17 R1

  15. Smith SB, Finzi L and Bustamante C 1992 Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258 1122–1126

  16. Smith SB, Cui Y and Bustamante C 1996 Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules. Science 271 795–799

  17. Strick TR, Dessinges MN, Charvin G, Dekker NH, Allemand JF, Bensimon D and Croquette V 2003 Stretching of macromolecules and proteins. Rep. Prog. Phys. 66 1–45

  18. Strunz T, Oroszlan K, Schäfer R and Güntherodt H-J 1999 Dynamic force spectroscopy of single DNA molecules. Proc. Natl. Acad. Sci. USA 96 11277 -11282

  19. Tabi CB, Mohamadou A and Kofané TC 2009 Modulated Wave Packets in DNA and Impact of Viscosity. Chin. Phys. Lett. 26 068703

  20. Williams MC, Pant K, Rouzina I and Karpel RL 2004 Single molecule force spectroscopy studies of DNA denaturation by T4 gene 32 protein. Spectroscopy-Int. J. 18 203–211

  21. Yakushevich LV 1998 Nonlinear Physics of DNA. In: Wiley Series in Nonlinear Science (Chichester, UK: John Wiley and Sons Ltd.)

  22. Zdravković S and Satarić MV 2006 Single Molecule Unzippering Experiments on DNA and Peyrard-Bishop-Dauxois Model. Phys. Rev. E 73 021905

  23. Zdravković S and Satarić MV 2008a Solitonic speed in DNA. Phys. Rev. E 77 031906

  24. Zdravković S and Satarić MV 2008b Nonlinear Schrödinger equation and DNA dynamics. Phys. Lett. A 373 126–132

  25. Zdravković S and Satarić MV 2009a Parameter selection in a Peyrard-Bishop-Dauxois model for DNA dynamics. Phys. Lett. A 373 2739–2745

  26. Zdravković S and Satarić MV 2009b DNA dynamics - Experiment proposals. Phys. Lett. A 373 4453–4459

  27. Zdravković S and Satarić MV 2010 Stacking interaction in DNA molecule. J. Comput. Theor. Nanosci. 7 2031–2035

  28. Zdravković S and Satarić MV 2011 Transverse interaction in DNA molecule. BioSystems 105 10–13

Download references


We want to thank to Dejan Milutinovich for his technical help and to the unknown referee for his/her useful suggestions and directions for future research.

This research was supported by funds from Serbian Ministry of Education and Sciences, grants III45010 and OI171009.

Author information

Correspondence to Slobodan Zdravković.

Additional information

[Zdravković S and Satarić MV 2012 Morse potential in DNA molecule – An experiment proposal. J. Biosci. 37 1–4] DOI

Corresponding editor: Basuthkar J Rao

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Zdravković, S., Satarić, M.V. Morse potential in DNA molecule – An experiment proposal. J Biosci 37, 613–616 (2012). https://doi.org/10.1007/s12038-012-9232-4

Download citation


  • DNA molecule
  • experiment proposal
  • helicoidal Peyrard-Bishop model
  • micromanipulative experiments