Statistical-Mechanical Analysis of Enzymatic Topological Transformations in DNA Molecules

There are two classes of enzymes, DNA topoisomerases and site-specific recombinases, which change DNA topology. Many details of the enzyme action remain unknown, and therefore different models of the reactions require critical testing. A great help in such testing comes from computer simulation. The computational approach, described in the review, allows simulating the distribution of the reaction products for a chosen model of the enzyme action. Comparing the simulated distribution with corresponding experimental data serves as a model test. The major principles and assumptions of the approach, which is based on the simulation of an equilibrium set of DNA conformations, are discussed. The general consideration is illustrated by two specific examples, models of type II DNA topoisomerases and tyrosine family of site-specific recombination.

[1]  R. Hoess,et al.  Interaction of the bacteriophage P1 recombinase Cre with the recombining site loxP. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[2]  J. Roca,et al.  The capture of a DNA double helix by an ATP-dependent protein clamp: A key step in DNA transport by type II DNA topoisomerases , 1992, Cell.

[3]  J. Roca,et al.  DNA transport by a type II DNA topoisomerase: Evidence in favor of a two-gate mechanism , 1994, Cell.

[4]  M Frank-Kamenetskii,et al.  Conformational and thermodynamic properties of supercoiled DNA. , 1992, Journal of molecular biology.

[5]  P. Sadowski,et al.  Cre Induces an Asymmetric DNA Bend in Its Target loxP Site* , 2003, Journal of Biological Chemistry.

[6]  A. Vologodskii,et al.  Probability of the site juxtaposition determines the rate of protein-mediated DNA looping. , 2007, Biophysical journal.

[7]  F. Guo,et al.  Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[8]  K. Klenin,et al.  Computation of writhe in modeling of supercoiled DNA. , 2000, Biopolymers.

[9]  H. Frisch,et al.  Thermodynamics and equilibrium sedimentation analysis of the close approach of DNA molecules and a molecular ordering transition , 1981, Biopolymers.

[10]  N R Cozzarelli,et al.  Probability of DNA knotting and the effective diameter of the DNA double helix. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[11]  K. Klenin,et al.  Effect of excluded volume on topological properties of circular DNA. , 1988, Journal of biomolecular structure & dynamics.

[12]  F. B. Fuller.  The writhing number of a space curve. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[13]  N R Cozzarelli,et al.  The effect of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling. , 1997, Nucleic acids research.

[14]  B. Andrews,et al.  Isolation of intermediates in the binding of the FLP recombinase of the yeast plasmid 2-micron circle to its target sequence. , 1987, Journal of molecular biology.

[15]  D. Stigter,et al.  Interactions of highly charged colloidal cylinders with applications to double‐stranded DNA , 1977 .

[16]  L. Iype,et al.  Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping. , 2000, Molecular cell.

[17]  N. Cozzarelli,et al.  Mechanism of topology simplification by type II DNA topoisomerases , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[18]  M. Jayaram,et al.  A general model for site-specific recombination by the integrase family recombinases. , 1999, Nucleic acids research.

[19]  R. Hoess,et al.  Mechanism of strand cleavage and exchange in the Cre-lox site-specific recombination system. , 1985, Journal of molecular biology.

[20]  A. Vologodskii.  Monte Carlo Simulation of DNA Topological Properties , 2007 .

[21]  A. Vologodskii.  Simulation of Equilibrium and Dynamic Properties of Large DNA Molecules , 2006 .

[22]  Quan Du,et al.  Protein-induced local DNA bends regulate global topology of recombination products. , 2007, Journal of molecular biology.

[23]  N. Grindley,et al.  Mechanisms of site-specific recombination. , 2003, Annual review of biochemistry.

[24]  A. Vologodskii,et al.  Symmetric DNA sites are functionally asymmetric within Flp and Cre site-specific DNA recombination synapses. , 2002, Journal of molecular biology.

[25]  D. Filman,et al.  A structural basis for allosteric control of DNA recombination by λ integrase , 2005, Nature.

[26]  J. Berger,et al.  Structural basis for gate-DNA recognition and bending by type IIA topoisomerases , 2007, Nature.

[27]  J. Wang,et al.  DNA transport by a type II topoisomerase: direct evidence for a two-gate mechanism. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[28]  D. Rolfsen.  Knots and Links , 2003 .

[29]  P. Sadowski,et al.  FLP protein of 2 mu circle plasmid of yeast induces multiple bends in the FLP recognition target site. , 1990, Journal of molecular biology.

[30]  J. Schellman,et al.  Flexibility of DNA , 1974, Biopolymers.

[31]  R. Wade,et al.  Comparative kinetic analysis of FLP and cre recombinases: mathematical models for DNA binding and recombination. , 1998, Journal of molecular biology.

[32]  Marc Le Bret,et al.  Monte carlo computation of the supercoiling energy, the sedimentation constant, and the radius of gyration of unknotted and knotted circular DNA , 1980, Biopolymers.

[33]  A. Flammini,et al.  Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topoisomerases , 2007, Nucleic acids research.

[34]  H. Chan,et al.  Topological information embodied in local juxtaposition geometry provides a statistical mechanical basis for unknotting by type-2 DNA topoisomerases. , 2006, Journal of molecular biology.

[35]  N. Cozzarelli,et al.  Modeling of long‐range electrostatic interactions in DNA , 1995, Biopolymers.

[36]  D N Gopaul,et al.  Structure and mechanism in site-specific recombination. , 1999, Current opinion in structural biology.

[37]  J. Wang,et al.  Moving one DNA double helix through another by a type II DNA topoisomerase: the story of a simple molecular machine , 1998, Quarterly Reviews of Biophysics.

[38]  H. Nash,et al.  Bending and supercoiling of DNA at the attachment site of bacteriophage lambda. , 1990, Trends in biochemical sciences.

[39]  R. Hoess,et al.  Studies on the properties of P1 site-specific recombination: Evidence for topologically unlinked products following recombination , 1983, Cell.

[40]  A. V. Lukashin,et al.  Statistical mechanics and topology of polymer chains , 1975, Nature.

[41]  V. Anshelevich,et al.  Torsional and bending rigidity of the double helix from data on small DNA rings. , 1985, Journal of biomolecular structure & dynamics.

[42]  Nicholas R. Cozzarelli,et al.  Roles of supercoiled DNA structure in DNA transactions , 1992, Current Biology.

[43]  D. Filman,et al.  A structural basis for allosteric control of DNA recombination by lambda integrase. , 2005, Nature.

[44]  M. Frank-Kamenetskii,et al.  Topological interaction between polymer chains , 1975 .

[45]  B. Sauer,et al.  Stoichiometry of the Cre recombinase bound to the lox recombining site. , 1992, Nucleic acids research.