The three-dimensional spatial arrangements of double helical DNA deformed along various supercoiled trajectories will be generated mathematically and then analyzed the detailed molecular level. The extent to which the regular linear duplex can be forced to bend and twist will then be monitored by semiempirical potential energy calculations. Bond lengths, valence angles, and torsion angles will be kept within normally prescribed limits, and steric and electrostatic interactions of nonbonded atoms and groups will be estimated with standard functions. Of particular interest will be the long-range effects associated with close contacts of sequentially distant chain residues. Long-range ionic effects will be examined using a newly modified Coulombia potential that reproduces the electrostatic interactions between charges on the surface of a dielectric cylinder immersed in salt water. The stabilities of various three-dimensional forms (e.g., toroidal, interwound, circular, etc.) will be compared and the detailed conformational variations of the standard double helical secondary structure examined. The relative contributions of bending and twisting to the total energy will be computed directly and compared with elastic models of supercoiling. The ability of the potential energy functions to account for macroscopic properties of the supercoils will be tested using established statistical mechanical procedures. Various secondary structural forms (e.g., A-, B-, Z-DNA) will be deformed along the superhelical trajectories in an attempt to understand the supercoil-induced conformational transitions of the DNA duplex.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Rutgers University
Schools of Arts and Sciences
New Brunswick
United States
Zip Code
Xu, Fei; Zheng, Hongning; Clauvelin, Nicolas et al. (2017) Parallels between DNA and collagen - comparing elastic models of the double and triple helix. Sci Rep 7:12802
Nizovtseva, Ekaterina V; Todolli, Stefjord; Olson, Wilma K et al. (2017) Towards quantitative analysis of gene regulation by enhancers. Epigenomics 9:1219-1231
Todolli, Stefjord; Perez, Pamela J; Clauvelin, Nicolas et al. (2017) Contributions of Sequence to the Higher-Order Structures of DNA. Biophys J 112:416-426
Nizovtseva, Ekaterina V; Clauvelin, Nicolas; Todolli, Stefjord et al. (2017) Nucleosome-free DNA regions differentially affect distant communication in chromatin. Nucleic Acids Res 45:3059-3067
Perez, Pamela J; Olson, Wilma K (2016) Insights into Genome Architecture Deduced from the Properties of Short Lac Repressor-mediated DNA Loops. Biophys Rev 8:135-144
Lu, Xiang-Jun; Bussemaker, Harmen J; Olson, Wilma K (2015) DSSR: an integrated software tool for dissecting the spatial structure of RNA. Nucleic Acids Res 43:e142
Clauvelin, N; Lo, P; Kulaeva, O I et al. (2015) Nucleosome positioning and composition modulate in silico chromatin flexibility. J Phys Condens Matter 27:064112
Wei, Juan; Czapla, Luke; Grosner, Michael A et al. (2014) DNA topology confers sequence specificity to nonspecific architectural proteins. Proc Natl Acad Sci U S A 111:16742-7
Yusufaly, Tahir I; Li, Yun; Singh, Gautam et al. (2014) Arginine-phosphate salt bridges between histones and DNA: intermolecular actuators that control nucleosome architecture. J Chem Phys 141:165102
Clauvelin, Nicolas; Olson, Wilma K; Tobias, Irwin (2014) Effect of the boundary conditions and influence of the rotational inertia on the vibrational modes of an elastic ring. J Elast 115:193-224

Showing the most recent 10 out of 66 publications