A.B. ('78), University of California - Berkeley M.Sc. ('83) University of Colorado - Boulder Ph.D. ('91) Pennsylvania State University - University Park

Biological Chemistry; Physical Chemistry

A principal focus of our group is to understand the mechanism of DNA repair by the light-driven enzyme, DNA photolyase. DNA is often damaged by UV radiation that is not otherwise absorbed by the ozone layer. Photolyase is a FAD-containing (flavo)protein that uses light to drive an ultrafast electron transfer reaction between the protein and the bound DNA lesion. The transferred electron repairs the damaged DNA by an unknown mechanism. We are using ultrafast laser and biochemical techniques to unravel this mechanism. We also explore the details of substrate binding using state of the art fluorescence reporter and two photon excitation techniques.

A second area of interest centers around the electronic properties of flavins in flavoproteins. The redox properties of flavoenzymes are known to be sensitive to electronic interactions between the flavin cofactor and the protein host. We are studying these interactions quantitatively using Stark spectroscopy.

Pauszek, R.F., III, Kodali, G. & Stanley, R.J. Excited State Electronic Structures of 5,10-Methenyltetrahydrofolate and 5,10-Methylenetetrahydrofolate Determined by Stark Spectroscopy. Journal of Physical Chemistry A 118, 8320-8328 (2014). http://pubs.acs.org/doi/abs/10.1021/jp501143u

Pauszek, R.F. & Stanley, R.J. A "How-To" Guide to the Stark Spectroscopy of Flavins and Flavoproteins. in Flavins and Flavoproteins: Methods and Protocols, Vol. 1146 (eds. Weber, S. & Schleicher, E.) 443-466 (2014).

Kodali, G. & Stanley, R.J. Excited State Chemistry of Flavoproteins. in Handbook of Flavins and Flavoproteins (eds. Hille, R., Miller, S. & Palfey, B.) (de Gruyter, Berlin, 2013).

Pauszek, R.F. et al. Excited State Charge Redistribution and Dynamics in the Donor-pi-Acceptor Flavin Derivative ABFL. Journal of Physical Chemistry B 117, 15684-15694 (2013). http://pubs.acs.org/doi/abs/10.1021/jp406420h

Narayanan, M., Kodali, G., Singh, V. R., Velvadapu, Venkata & Stanley, R. J. "Oxidation and Reduction Potentials of 8-vinyladenosine Measured by Cyclic Voltammetry: Implications for Photoinduced Electron Transfer Quenching of a Fluorescent Adenine Analog" Journal of Photochemistry and Photobiology, A: Chemistry 249, 9-14, (2012). http://dx.doi.org/10.1016/j.jphotochem.2012.08.018

Yu, X., Eymur, S., Singh, V., Yang, B., Tonga, M., Bheemaraju, A., Cooke, G., Subramani, C., Venkataraman, D., Stanley, R. J. & Rotello, V. M. "Flavin as a Photo-Active Acceptor for Efficient Energy and Charge Transfer in a Model Donor-Acceptor System" Physical Chemistry Chemical Physics 14, 6749-6754, (2012). http://pubs.acs.org/doi/abs/10.1021/jp406420h

Kodali, G., Narayanan, M., & Stanley, R. J. "The Excited State Electronic Properties of 6-methylisoxanthopterin (6-MI): An Expereimental and Theoretical Study" Journal of Physical Chemistry B 116, 2981-2189, (2012). http://pubs.acs.org/doi/abs/10.1021/jp2110083

Narayanan, M., Kodali, G., Xing, Y. J., & Stanley, R. J. "Differential Fluorescence Quenching of Fluorescent Nucleic Acid Base Analogues by Native Nucleic Acid Monophosphates." Journal of Physical Chemistry 114, 5953-5963, (2010). http://pubs.acs.org/doi/abs/10.1021/jp1011507

Narayanan, M., Kodali, G., Xing, Y. J., & Stanley, R. J. "Photoinduced Electron Transfer Occurs between 2-Aminopurine and the DNA Nucleic Acid Monophosphates: Results from Cyclic Voltammetry and Fluorescence Quenching" Journal of Physical Chemistry B 114, 10573-10580, (2010). http://pubs.acs.org/doi/abs/10.1021/jp102355v

Kodali, G., Kistler, K. A., Narayanan, M., Matsika, S. & Stanley, R. J. "Change in Electronic Structure upon Optical Excitation of 8-Vinyladenosine: An Experimental and Theoretical Study" Journal of Physical Chemistry A 114, 256-267, (2010). http://pubs.acs.org/doi/abs/10.1021/jp908055h

Kodali, G., Siddiqui, S. U., & Stanley, R. J. "Charge Redistribution in Oxidized and Semiquinone E. coli DNA Photolyase upon Photoexcitation: Stark Spectroscopy Reveals a Rationale for the Position of Trp382." Journal of American Chemical Society 131, 4795-4807, (2009). http://pubs.acs.org/doi/abs/10.1021/ja809214r

Yang, K. & Stanley, R. J. "The extent of DNA deformation in DNA photolyase-substrate complexes: A solution state fluorescence study." Photochemistry & Photobiology 84, 741-749, (2008). DOI: 10.1111/j.1751-1097.2007.00251.x

Siddiqui, M. S. U., Kodali, B. & Stanley, R. J. "The electronic transition dipole moment directions of reduced flavin in stretched poly(vinyl alcohol) films. " Journal of Physical Chemistry B 112, 119-126, (2008). http://pubs.acs.org/doi/abs/10.1021/jp075830e

Kodali, G., Kistler, K. A. Matsika, S. & Stanley, R. J. "2-Aminopurine Excited State Electronic Structure Measured by Stark Spectroscopy" Journal of Physical Chemistry B 112, 1789-1795, (2008). http://pubs.acs.org/doi/abs/10.1021/jp076374x

Yang, K., Matsika, S. & Stanley, R. J. "6MAP, a fluorescent adenine analogue, is a probe of base flipping by DNA photolyase." Journal of Physical Chemistry B 111, 10615-10625, (2007). http://pubs.acs.org/doi/abs/10.1021/jp071035p

Yang, K. & Stanley, R. J. "Differential Distortion of Substrate Occurs When It Binds to DNA Photolyase: A 2-Aminopurine Study." Biochemistry 45, 11239-11245, (2006). http://pubs.acs.org/doi/abs/10.1021/bi060408u

Stanley, R. J. "Cyclobutylthymidine dimer repair by DNA photolyase in real time." ACS Symposium Series 935, 137-144, (2006). http://pubs.acs.org/doi/abs/10.1021/bk-2006-0935.ch009

Franzen, S., Jasaitis, A., Belyea, J., Brewer, S. H., Casey, R., MacFarlane, A. W. IV., Stanley, R. J., Vos, M. H. & Martin, J.-L. "Hydrophobic Distal Pocket Affects NO-Heme Geminate Recombination Dynamics in Dehaloperoxidase and H64V Myoglobin." Journal of Physical Chemistry B 110, 14483-14493, (2006). http://pubs.acs.org/doi/abs/10.1021/jp056790m

Stanley, R. J., Hou, Z., Yang, A. & Hawkins, M. E. "The Two-Photon Excitation Cross Section of 6MAP, a Fluorescent Adenine Analogue. " Journal of Physical Chemistry B 109, 3690-3695, (2005). http://pubs.acs.org/doi/abs/10.1021/jp0455982

Siddiqui, M. S. U. & Stanley, R. J. "A cryogenic optical waveguide spectrometer for the measurement of low-temperature absorption spectra of dilute biological samples. " Analytical Biochemistry 337, 121-129, (2005). http://www.sciencedirect.com/science/article/pii/S0003269704008498