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

Balasubramanian S, Xu F, Olson WK. (2009) DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences. Biophys J. 96(6):2245-60.

Olson WK, Esguerra M, Xin Y, Lu XJ. (2009) New information content in RNA base pairing deduced from quantitative analysis of high-resolution structures. Methods. 47(3):177-86.

Xin Y, Olson WK. (2008) BPS: a database of RNA base-pair structures. Nucleic Acids Res. 37(Database issue):D83-8.

Karymov MA, Chinnaraj M, Bogdanov A, Srinivasan AR, Zheng G, Olson WK, Lyubchenko YL. (2008) Structure, dynamics, and branch migration of a DNA Holliday junction: a single-molecule fluorescence and modeling study. Biophys J. 95(9):4372-83.

Lu XJ, Olson WK. (2008) 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nat Protoc. 3(7):1213-27.

Czapla L, Swigon D, Olson WK. (2008) Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations. J Mol Biol. 382(2):353-70.

Tolstorukov MY, Choudhary V, Olson WK, Zhurkin VB, Park PJ. (2008) nuScore: a web-interface for nucleosome positioning predictions. Bioinformatics. 24(12):1456-8.

Banerjee A, Misra M, Pai D, Shih LY, Woodley R, Lu XJ, Srinivasan AR, Olson WK, Davé RN, Venanzi CA. (2007) Feature extraction using molecular planes for fuzzy relational clustering of a flexible dopamine reuptake inhibitor. J Chem Inf Model. 47(6):2216-27.

Tolstorukov MY, Colasanti AV, McCandlish DM, Olson WK, Zhurkin VB. (2007) A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning. J Mol Biol. 371(3):725-38.

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.