By John N. Abelson, Melvin I. Simon, David M.J. Lilley, James E. Dahlberg

To appreciate the constitution and dynamics of DNA and its interactions with ligands, an entire research of its confirmational flexibility is needed. This quantity and its significant other, quantity 211 of Methods of Enzymology, collate in a single resource the entire tools and methods had to accomplish that objective

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Additional info for DNA Structures Part B: Chemical and Electrophoretic Analysis of DNA

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Most other authors have not made such a correction for residual writhe, relying instead on the approximate calculation of LeBret, 26 according to which molecules below a critical size (roughly 1000 bp) have zero writhe. The result is to make our value of C about 25% larger than that found by other authors for analysis of the same data sets. Taylor and Hagerman 4 have misrepresented our calculation in stating that it is based on an extrapolation of the writhe variance to the long chain limit. The value of C can also be determined from data such as those reported by Shore and Baldwin3 on the dependence of cyclization rate on DNA chain length over an interval of a full helical turn.

2o S. D. Levene and D. M. Crothers, J. Mol. Biol. 189, 73 (1986). 21 S. D. Levene and D. M. Crothers, J. Mol. Biol. 189, 61 (1986). 2z N. Metropolis, A. W. Rosembluth, M. N. Rosembluth, A. H. Teller, and E. Teller, J. Chem. Phys. 21, 1087 (1953). 23 p. j. Hagerman and V. A. Ramadevi, J. Mol. Biol. 212, 351 (1990). 18 GEL ELECTROPHORESIS AND TOPOLOGICAL METHODS [1] the DNA molecule. Repeated application of standard rotation matrices generates a trajectory for the helix a x i s . 24 Thermal motion is modeled by allowing the orientation of the helix axis to fluctuate through random small rotations about the x, y, and z axes at each base pair treated independently.

Crothers, Proc. Natl. Acad. Sci. A. 85, 1763 (1988). 36 S. Diekmann, Nucleic Acids. Res. 15, 247 (1987). 37 C. R. Calladine, H. R. Drew, and M. J. McCall, J. Mol. Biol. 201, 127 (1988). 38 S. D. Levene and B. H. Zimm, Science 245, 396 (1989). 39 N. C. Stellwagen, Biochemistry 22, 6186 (1983). [2] ANALYZING D N A CURVATURE IN POLYACRYLAMIDE GELS 33 fragment results in reduced mobility. 4°,4~This structural origin of a migration anomaly in a polyacrylamide gel can be separated easily from curved DNA by running a gel in the presence of ethidium bromide: while the anomaly due to the four-way junction increases, the anomaly due to curved DNA is strongly reduced.

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