Regensburg 2007 – scientific programme

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CPP: Fachverband Chemische Physik und Polymerphysik

CPP 14: Biological Systems

CPP 14.8: Talk

Tuesday, March 27, 2007, 12:00–12:15, H47

Looping charged elastic rods — •Andrey Cherstvy and Ralf Everaers — Max-Planck-Institut für Physik Komplexer Systeme, Nöthnitzer Straße 38, D-01187 Dresden, Germany

Finding optimal shape of a charged elastic rod under external torque and forces, as a minimum of rod elastic [1] and electrostatic (el) energy, is a complicated problem [2]. We calculate el energy of DNA loops and planar untwisted DNA rings [3]. We sum Debye-Hueckel el potentials between charges on bent/looped rod. Equilibrium loop shape [4] is unchanged by el interactions and loops have no self-contacts. DNA charges are modeled as straight or helical arrays. For large loops the excess el energy of DNA bending is well described by OSF theory of rod el persistence length. For small loops (eg. DNA wrapped around histones or DNA bent by lac-repressor [2]) the OSF assumptions are violated and el energies obtained are larger. For large rings the actual el excess energy is larger than OSF prediction due to a final penalty of approaching two DNA ends into a contact upon cyclization. For small circles, as there are not so many charges to sum over, the OSF underestimates el energy, especially at low salt. Our results are relevant to description of tight DNA looping in DNA-proteins complexes [2,5] and to cyclization of short DNAs [6] as a function of added salt.

[1] A.E.H. Love, Dover, NY (1944). [2] D. Swigon, et al., PNAS 103 9879 (2006). [3] A.G. Cherstvy and R. Everaers, in preparation. [4] J. Coyne, IEEE J. Ocean. Ing., 15 72 (1990). [5] A.G. Cherstvy at al., JPCB, 109 2962 (2005). [6] L. Czapla, et al., J. Chem. Th. Comput. 2 685 (2006) and refs. therein.