Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature.

The validity of a theoretical nearest-neighbor model based on conformational energy calculations, for translating the deterministic fluctuations of DNA base sequences in superstructural elements, is tested on the electrophoretic data of 450 multimeric, duplex oligonucleotides with different sequence, periodicity, and complexity, corresponding to all the experimental data so far published. An accurate semiempirical linear relation between the gel electrophoretic retardation and the dispersion of the theoretical curvature was found which allows a prediction of electrophoretic anomalies of DNA tracts, e.g., the cyclic permutation gel assays, with great confidence. Such a pattern of agreement allows the interpretation of the gel electrophoresis retardation as due to an increase of activation energy required in straightening the DNA axis.

[1]  Paul J. Hagerman,et al.  Sequence-directed curvature of DNA , 1986, Nature.

[2]  A. Palleschi,et al.  A theoretical model of DNA curvature. , 1988, Biophysical chemistry.

[3]  Edward N. Trifonov,et al.  Estimation of wedge components in curved DNA , 1987, Nature.

[4]  R. Dickerson,et al.  Base sequence and helix structure variation in B and A DNA. , 1983, Journal of molecular biology.

[5]  A. Palleschi,et al.  Periodical polydeoxynucleotides and DNA curvature. , 1989, Biochemistry.

[6]  Hen-Ming Wu,et al.  The locus of sequence-directed and protein-induced DNA bending , 1984, Nature.

[7]  Hen-Ming Wu,et al.  DNA bending at adenine · thymine tracts , 1986, Nature.

[8]  D. Crothers,et al.  Cooperativity in A-tract structure and bending properties of composite TnAn blocks. , 1989, Biochemistry.

[9]  E. Trifonov,et al.  Sequence-dependent deformational anisotropy of chromatin DNA. , 1980, Nucleic acids research.

[10]  A. Lakshminarayanan,et al.  Stereochemistry of nucleic acids and polynucleotides III. Electronic charge distribution , 1971, Biopolymers.

[11]  A. R. Srinivasan,et al.  Base sequence effects in double helical DNA. I. Potential energy estimates of local base morphology. , 1987, Journal of biomolecular structure & dynamics.

[12]  J. Griffith,et al.  Visualization of the bent helix in kinetoplast DNA by electron microscopy , 1986, Cell.

[13]  D. Crothers,et al.  Calibration of DNA curvature and a unified description of sequence-directed bending. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Stephen C. Harvey,et al.  Computer graphics program to reveal the dependence of the gross three- dimensional structure of the B-DNA double helix on primary structure , 1986, Nucleic Acids Res..

[15]  A. Palleschi,et al.  A theoretical model of the sequence dependent superstructures of DNA , 1989 .