Faculty of Engineering and Natural Sciences

SEMINAR ANNOUNCEMENT

     

DNA Melting and Supercoils

Alkan Kabakçıoğlu
Department of Physics, Koç University

Abstract:
The physics of DNA melting (separation of the two strands upon increasing temperature) has been of interest since 60's with some new theoretical developments lately. After reviewing the basics and the existing literature, I will discuss a model we recently developed for circular DNA rings, by taking into account the twisting of the two strains around each other. Guided by recent single-molecule experiments on DNA strands, we propose that the torsional stress induced by locally denatured regions enforces formation of supercoils whose"writhe" absorbs the "linking number" expelled by loops. We find that, when the entropy exponent for a loop is smaller than two, the denaturation transition does not take place. Otherwise a first-order denaturation transition is predicted in contrast with earlier models. We also find a topology-induced drop in the melting temperature in agreement with recent experiments. Time permitting, I will also present recent results on a mesoscopic DNA model we recently developed, which is capable of simulating long-time dynamics of DNA chains ~1000 bps.

Bio:
1999 Ph.D.  - MIT, Dept of Physics, Condensed Matter Theory 1999-2001 Postdoc - Weizmann Institute of Science, Physics of Complex Systems 2003-2005 Postdoc - University of Padova, Dept of Physics 2005-present Koç University Current research: Biopolymers, phase transitions in complex systems,  intra-cellular interaction networks                       
                      
Wednesday, 24 March 2010,  FENS L035,  13:40
                 

[start_dates] => Array ( [0] => 2010-03-24 00:00:00 ) [end_dates] => Array ( [0] => 2010-03-24 00:00:00 ) [where] => [headline] => [comments_count] => 0 [created] => 1269295200 [error] => [errorcode] => 0 ) --> A. Kabakçıoğlu; "DNA Melting and Supercoils", March 24 | Faculty of Engineering and Natural Sciences
A. Kabakçıoğlu; "DNA Melting and Supercoils", March 24
  • FENS
  • A. Kabakçıoğlu; "DNA Melting and Supercoils", March 24

You are here

Faculty of Engineering and Natural Sciences

SEMINAR ANNOUNCEMENT

     

DNA Melting and Supercoils

Alkan Kabakçıoğlu
Department of Physics, Koç University

Abstract:
The physics of DNA melting (separation of the two strands upon increasing temperature) has been of interest since 60's with some new theoretical developments lately. After reviewing the basics and the existing literature, I will discuss a model we recently developed for circular DNA rings, by taking into account the twisting of the two strains around each other. Guided by recent single-molecule experiments on DNA strands, we propose that the torsional stress induced by locally denatured regions enforces formation of supercoils whose"writhe" absorbs the "linking number" expelled by loops. We find that, when the entropy exponent for a loop is smaller than two, the denaturation transition does not take place. Otherwise a first-order denaturation transition is predicted in contrast with earlier models. We also find a topology-induced drop in the melting temperature in agreement with recent experiments. Time permitting, I will also present recent results on a mesoscopic DNA model we recently developed, which is capable of simulating long-time dynamics of DNA chains ~1000 bps.

Bio:
1999 Ph.D.  - MIT, Dept of Physics, Condensed Matter Theory 1999-2001 Postdoc - Weizmann Institute of Science, Physics of Complex Systems 2003-2005 Postdoc - University of Padova, Dept of Physics 2005-present Koç University Current research: Biopolymers, phase transitions in complex systems,  intra-cellular interaction networks                       
                      
Wednesday, 24 March 2010,  FENS L035,  13:40