Fast dynamics of supercoiled DNA revealed by single-molecule experiments

The dynamics of supercoiled DNA play an important role in various cellular processes such as transcription and replication that involve DNA supercoiling. We present experiments that enhance our understanding of these dynamics by measuring the intrinsic response of single DNA molecules to sudden changes in tension or torsion. The observed dynamics can be accurately described by quasistatic models, independent of the degree of supercoiling initially present in the molecules. In particular, the dynamics are not affected by the continuous removal of the plectonemes. These results set an upper bound on the hydrodynamic drag opposing plectoneme removal, and thus provide a quantitative baseline for the dynamics of bare DNA.

[1]  Leroy F. Liu,et al.  Transcription generates positively and negatively supercoiled domains in the template , 1988, Cell.

[2]  T. Baker,et al.  In vitro assembly of a prepriming complex at the origin of the Escherichia coli chromosome. , 1987, The Journal of biological chemistry.

[3]  U. Bockelmann,et al.  Rotational drag on DNA: a single molecule experiment. , 2002, Physical review letters.

[4]  N R Cozzarelli,et al.  Effect of supercoiling on the juxtaposition and relative orientation of DNA sites. , 1996, Biophysical journal.

[5]  T. Strick,et al.  Behavior of supercoiled DNA. , 1998, Biophysical journal.

[6]  JAMES C. Wang,et al.  DNA axial rotation and the merge of oppositely supercoiled DNA domains in Escherichia coli: effects of DNA bends. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Y. Tsao,et al.  Transcription-driven supercoiling of DNA: Direct biochemical evidence from in vitro studies , 1989, Cell.

[8]  Michelle D. Wang,et al.  Estimating the persistence length of a worm-like chain molecule from force-extension measurements. , 1999, Biophysical journal.

[9]  F. Brochard-Wyart,et al.  Polymer Chains Under Strong Flow: Stems and Flowers , 1995, Turkish Journal of Physics.

[10]  Z. Wang,et al.  Long-range effects in a supercoiled DNA domain generated by transcription in vitro. , 1997, Journal of molecular biology.

[11]  S. Quake,et al.  Relaxation of a single DNA molecule observed by optical microscopy. , 1994, Science.

[12]  R. Dickman,et al.  Recoiling DNA molecule: simulation and experiment , 2002, physics/0203087.

[13]  C. Levinthal,et al.  ON THE UNWINDING OF DNA. , 1956, Proceedings of the National Academy of Sciences of the United States of America.

[14]  P. Cluzel,et al.  Evidence for the universal scaling behaviour of a freely relaxing DNA molecule , 1996 .

[15]  A. Bensimon,et al.  The Elasticity of a Single Supercoiled DNA Molecule , 1996, Science.

[16]  T. Strick,et al.  Twisting DNA: single molecule studies , 2004 .

[17]  F S Pavone,et al.  Three-dimensional magneto-optic trap for micro-object manipulation. , 2001, Optics letters.

[18]  Cyril Claudet,et al.  Magneto-optical tweezers built around an inverted microscope. , 2005, Applied optics.

[19]  A. Nordheim,et al.  Transcription-induced conformational change in a topologically closed DNA domain. , 1991, Nucleic acids research.

[20]  M. Feingold.  Single-molecule studies of DNA and DNA-protein interactions , 2001 .

[21]  J. Howard,et al.  The force exerted by a single kinesin molecule against a viscous load. , 1994, Biophysical journal.

[22]  D. Prieve,et al.  Hindered diffusion of colloidal particles very near to a wall: Revisited , 2000 .

[23]  J. Champoux.  DNA topoisomerases: structure, function, and mechanism. , 2001, Annual review of biochemistry.

[24]  S. Halford,et al.  Protein motion from non‐specific to specific DNA by three‐dimensional routes aided by supercoiling , 2003, The EMBO journal.

[25]  G. Giaever,et al.  Supercoiling of intracellular DNA can occur in eukaryotic cells , 1988, Cell.

[26]  J. Wang,et al.  Supercoiling of the DNA template during transcription. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Fisher Lm.  DNA supercoiling and gene expression. , 1984 .

[28]  F. Leng,et al.  Potent stimulation of transcription-coupled DNA supercoiling by sequence-specific DNA-binding proteins , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[29]  P. Nelson.  Transport of torsional stress in DNA. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[30]  T Schlick,et al.  Dynamics of site juxtaposition in supercoiled DNA. , 2001, Proceedings of the National Academy of Sciences of the United States of America.