The present application of configurational statistics to model the nucleic acids or polynucleotides provides an essential first step in relating the subtle features of chemical architecture to the unique physical and biological properties of these macromolecules. Through a combination of molecular modeling, potential energy calculations, and statistical mechanical analyses it is possible to elucidate details of nucleic acid conformation and to provide a rational understanding of observed experimental phenomena. The primary objectives of the program are to classify and understand the complex array of nucleotide conformers, to comprehend the effects of primary chemical sequences on secondary and tertiary structure, and to elucidate pathway of conformational transitions. The combined computations should enhance our comprehension of both polynucleotide extension and flexibility offering new structural insight into conformation and the irregularities of various forms. The chain statistics studies may also provide a molecular basis for understanding the nature and flexibility of specifically constrained structures such as small closed circles, loops, knots, hairpins, bulges, and cruciforms.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Method to Extend Research in Time (MERIT) Award (R37)
Project #
2R37GM020861-15
Application #
3484353
Study Section
Biophysics and Biophysical Chemistry A Study Section (BBCA)
Project Start
1977-08-01
Project End
1993-07-31
Budget Start
1988-08-01
Budget End
1989-07-31
Support Year
15
Fiscal Year
1988
Total Cost
Indirect Cost
Name
Rutgers University
Department
Type
Schools of Arts and Sciences
DUNS #
038633251
City
New Brunswick
State
NJ
Country
United States
Zip Code
08901
Peckham, Heather E; Olson, Wilma K (2011) Nucleic-acid structural deformability deduced from anisotropic displacement parameters. Biopolymers 95:254-69
Xu, Fei; Olson, Wilma K (2010) DNA architecture, deformability, and nucleosome positioning. J Biomol Struct Dyn 27:725-39
Zheng, Guohui; Colasanti, Andrew V; Lu, Xiang-Jun et al. (2010) 3DNALandscapes: a database for exploring the conformational features of DNA. Nucleic Acids Res 38:D267-74
Xu, Fei; Colasanti, Andrew V; Li, Yun et al. (2010) Long-range effects of histone point mutations on DNA remodeling revealed from computational analyses of SIN-mutant nucleosome structures. Nucleic Acids Res 38:6872-82
Zheng, Guohui; Czapla, Luke; Srinivasan, A R et al. (2010) How stiff is DNA? Phys Chem Chem Phys 12:1399-406
Olson, Wilma K; Esguerra, Mauricio; Xin, Yurong et al. (2009) New information content in RNA base pairing deduced from quantitative analysis of high-resolution structures. Methods 47:177-86
Balasubramanian, Sreekala; Xu, Fei; Olson, Wilma K (2009) DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences. Biophys J 96:2245-60
Zheng, Guohui; Lu, Xiang-Jun; Olson, Wilma K (2009) Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures. Nucleic Acids Res 37:W240-6
Xin, Yurong; Olson, Wilma K (2009) BPS: a database of RNA base-pair structures. Nucleic Acids Res 37:D83-8