Wilma K. Olson Professor Rutgers University Department of Chemistry Wright-Rieman Labs. Busch Campus Piscataway. NJ 08854 (732) 445-3993 FAX - 5958 olson@rutchem.rutgers.edu

Biopolymer conformation and properties

The primary research goal of our research group is to understand the three-dimensional structure and the structure-dependent properties of the nucleic acids in terms of their constituent chemical architecture. Problems of current interest include: (1) new computational methods to generate and analyze constrained configurations such as the loops and hairpins of RNA. the cruciform junctions of DNA. and the closed. superhelical arrangements of the double helix; (2) computer simulation of the DNA helix to random coil transition; (3) improved procedures to analyze local structural morphology and to model the effects of base sequence and electrostatics on macromolecular flexibility; (4) new computational models of protein-nucleic acid interactions.

Selected Publications

Swigon D. Coleman BD. Olson WK. (2006) Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation. Proc Natl Acad Sci U S A. 103(26):9879-84.

Liu G. Geurts AM. Yae K. Srinivasan AR. Fahrenkrug SC. Largaespada DA. Takeda J. Horie K. Olson WK. Hackett PB. (2005)Target-site preferences of Sleeping Beauty transposons. J Mol Biol. 346(1):161-73.

Ge. W.. Schneider. B.. and Olson. W. K. (2005) Knowledge-based elastic potentials for docking drugs or proteins with nucleic Acids. Biophys. J. 88:1166-1190.

Zhurkin. V. B.. Tolstorukov. M. Y.. Xu. F.. Colasanti. A. V.. and Olson. W. K. (2005) Sequence-dependent Variability of B DNA: An Update on Bending and Curvature in DNA Conformation and Transcription. Takashi O.. Ed.. Landes Bioscience/Eurekah.com. Georgetown. TX. Chapter 2.

Matsumoto. A.. Tobias. I.. and Olson. W. K. (2005) Normal mode analysis of circular DNA at the base pair level. II. Large-scale Configurational Transformation of a Naturally Curved Molecule. J. Chem. Theor. Comp. 1:130-142.

Matsumoto. A.. Tobias. I.. and Olson. W. K. (2005) Normal mode analysis of circular DNA at the base pair level. I. Comparison of Computed Motions with Predicted Behavior of an Ideal Elastic Rod. J. Chem. Theor. Comp. 1:117-129.

Olson. W. K.. Swigon. D.. and Coleman. B. D. (2004) Implications of the dependence of the elastic properties of DNA on nucleotide sequence. Phil. Trans. Roy. Soc. 362:1403-1422.

Coleman. B D.. Olson. W K.. and Swigon. D (2003) Theory of sequence-dependent DNA elasticity. J. Chem. Phys.118(15):7127-7140.

Lu. X‑J and Olson. WK. (2003) 3DNA: A software package for the analysis. rebuilding. and visualization of three-dimensional nucleic acid structure. Nucleic Acids Res. 31(17):5108-5121.

Kosikov. KM.. Gorin. AA.. Lu. X-J. Olson. WK.. and Manning. GS. (2002) Bending of DNA by asymmetric charge neutralization: All-atom energy simulations. J. Am. Chem. Soc.124(17):4838-4847.

Matsumoto. A and Olson. WK. (2002) Sequence‑dependent motions of DNA: A normal mode analysis at the base‑pair level. Biophys. J. 83:22-41.

Wang. L. Srinivasan. A. R.. Hingerty. BE.. Olson. WiK.. and Broyde. S (2002) Accurate representation of B-DNA double helical structure with implicit solvent and counterions. Biophys. J. 83:382-406.

Ruan. Q. Zhuang. P. Li. S. Perlow. R. Srinivasan. A. R.. Lu. X.-J.. Broyde. S. Olson. K.. and Geacintov. NE. (2001) Base sequence effects in bending by bulky carcinogen-DNA adducts: Experimental and computational analysis. Biochemistry 40:10458-10472.

Olson. WK.. Lu. X‑J. Westbrook. J. Bansal. M. Burley. SK.. Dickerson. RE.. Gerstein. M. Harvey. SC.. Heinemann. U. Neidle. S. Shakked. Z. Suzuki. M. Tung. C‑S. Sklenar. H. Westhof. E. Wolberger. C. and Berman. HM. (2001) A standard reference frame for the description of nucleic acid base‑pair geometry. J. Mol. Biol. 313:229-237.

Lu. X.-J.. Shakked. Z.. Olson. W.K. (2000) A-form conformational motifs in ligand-bound DNA structures. J. Mol. Biol. 300(4):819-840.

Olson. W.K.. Zhurkin. V.B. (2000). Modeling DNA deformations. Curr. Opin. Struct. Biol. 10(3):286-297.

Katritch. V.. Bustamante. C.. Olson W.K. (2000). Pulling chromatin fibers: computer simulations of direct physical micromanipulations J. Mol. Biol. 295(1):29-40.

Martino. J.A.. Katritch. V.. Olson. W.K. (2000). Influence of nucleosome structure on the three-dimensional folding of idealized minichromosomes. Structure 7(8):1009-1022.