Berlin 2005 – scientific programme

Parts | Days | Selection | Search | Downloads | Help

AKB: Biologische Physik

AKB 45: Single Molecule Biophysics

AKB 45.1: Invited Talk

Monday, March 7, 2005, 14:30–15:00, TU H2013

Coupled dynamics of DNA-breathing and binding of proteins that selectively bind to single-stranded DNA — •Ralf Metzler and Tobias Ambjörnsson — NORDITA, Blegdamsvej 17, DK-2100 Copenhagen OE

Under physiological conditions, the double-helix is the thermodynamically stable configuration of DNA. A long-standing puzzle had been why the presence of selectively single-stranded DNA binding proteins (SSBs) does not lead to full DNA-denaturation, as SSB binding is thermodynamically favorable. By detailed single-molecule studies, it was corroborated quantitatively that for the gp32-SSB there exists a kinetic block for SSB-binding: below the melting temperature of DNA, that is, the lifetime of a bubble is shorter than the typical binding time of an SSB, counteracting the expected helix-destabilization through the SSBs. We derived a dynamical model to quantify the coupled dynamics between a fluctuating DNA-bubble and SSBs that attempt to bind to it. Depending on the system parameters (temperature, external force, SSB binding rate and strength, SSB size), the presence of SSBs leads to enhanced bubble lifetime. Effectively, the bubble free energy is lowered, or even full denaturation caused by SSBs.