Biophysical Chemistry

Temple University Department of Chemistry

Publications

1.             Yang, K. & Stanley, R.J. The extent of DNA deformation in DNA photolyase-substrate complexes: A solution state fluorescence study. Photochemistry and Photobiology 84, 741-749 (2008).

2.             Siddiqui, M.S.U., Kodali, G. & 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).

3.             Kodali, G., Siddiqui, M.S.U. & Stanley, R.J. Excited state electronic structures of oxidized and semiquinone E. coli CPD photolyase as measured by Stark spectroscopy. Journal of the American Chemical Society submitted (2008).

4.             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).

5.             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).

6.             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).

7.             Stanley, R.J. Cyclobutylthymidine dimer repair by DNA photolyase in real time. ACS Symposium Series 935, 137-144 (2006).

8.             Franzen, S., Jasaitis, A., Belyea, J., Brewer, S.H., Casey, R., MacFarlane, A.W.I., 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).

9.             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).

10.           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).

11.            MacFarlane IV, A.W. & Stanley, R.J. Cis-Syn Thymidine Dimer Repair by DNA Photolyase in Real Time. Biochemistry 42, 8558-8568 (2003).

12.           Hopkins, N. & Stanley, R.J. Measurement of the Electronic Properties of the Flavoprotein Old Yellow Enzyme (OYE) and the OYE:p-Cl Phenol Charge-Transfer Complex Using Stark Spectroscopy. Biochemistry 42, 991-999 (2003).

13.           Franzen, S. & Stanley, R.J. A theoretical explanation for quantum yield failure in bacterial photosynthetic reaction centers. Chemical Physics 276, 115-127 (2002).

14.           Christine, K.S., MacFarlane IV, A.W., Yang, K. & Stanley, R.J. Cyclobutylpyrimidine Dimer Base Flipping by DNA Photolyase. Journal of Biological Chemistry 277, 38339-38344 (2002).

15.           Stanley, R.J. & Siddiqui, M.S. A Stark Spectroscopic Study of N(3)-Methyl, N(10)-Isobutyl-7,8-Dimethylisoalloxazine in Nonpolar Low-Temperature Glasses: Experiment and Comparison with Calculations. Journal of Physical Chemistry A 105, 11001-11008 (2001).

16.           Stanley, R.J. Advances in flavin and flavoprotein optical spectroscopy. Antioxidants & Redox Signaling 3, 847-866 (2001).

17.           MacFarlane IV, A.W. & Stanley, R.J. Evidence of Powerful Substrate Electric Fields in DNA Photolyase: Implications for Thymidine Dimer Repair. Biochemistry 40, 15203-15214 (2001).

18.           Stanley, R.J. & MacFarlane IV, A.W. Ultrafast Excited State Dynamics of Oxidized Flavins: Direct Observations of Quenching by Purines. J. Phys. Chem. A 104, 6899-6906 (2000).

19.           Stanley, R.J. & Macfarlane IV, A.W. Direct Measurements of Ultrafast Excited State Quenching of Isoalloxazine by Adenine in FAD. in Proceedings of the 13th International Congress on Flavins and Flavoproteins (ed. Weber, R.) (Konstanz, Germany, 1999).

20.          Stanley, R.J. & MacFarlane, A.W.I. Subpicosecond ultrafast dynamics of excited-state flavins. Book of Abstracts, 218th ACS National Meeting, New Orleans, Aug. 22-26, HYS-362 (1999).

21.           Stanley, R.J. & Jang, H. Dipole moments and polarizabilities of flavins explored using Stark-effect spectroscopy. Flavins Flavoproteins 1999, Proc. Int. Symp., 13th, 41-44 (1999).

22.           Stanley, R.J. & Jang, H. Electronic Structure Measurements of Oxidized Flavins and Flavin Complexes using Stark-Effect Spectroscopy. J. Phys. Chem. A 103, 8976-8984 (1999).

23.           Oh, D.H., Stanley, R.J., Lin, M., Hoeffler, W.K., Boxer, S.G., Berns, M.W. & Bauer, E.A. Two-photon excitation of 4'-hydroxymethyl-4,5',8-trimethylpsoralen. Photochem. Photobiol. 65, 91-95 (1997).

24.           King, B.A., Stanley, R.J. & Boxer, S.G. Excited State Energy Transfer Pathways in Photosynthetic Reaction Centers. 2. Heterodimer Special Pair. J. Phys. Chem. B 101, 3644-3648 (1997).

25.           Stanley, R.J., King, B. & Boxer, S.G. Excited State Energy Transfer Pathways in Photosynthetic Reaction Centers. 1. Structural Symmetry Effects. J. Phys. Chem. 100, 12052-12059 (1996).

26.           Stanley, R.J., Swent, R.L. & Smith, T.I. Synchronization of a femtosecond modelocked Ti:sapphire laser to the Stanford SCA/FEL. Opt. Commun. 115, 87-92 (1995).

27.           Stanley, R.J. & Castleman, A.W., Jr. Cluster ion-dip spectroscopy. Adv. Ser. Phys. Chem. 4, 689-729 (1995).

28.          Stanley, R.J. & Boxer, S.G. Oscillations in the Spontaneous Fluorescence from Photosynthetic Reaction Centers. J. Phys. Chem. 99, 859-63 (1995).

29.           Lao, K., Franzen, S., Steffen, M., Lambright, D., Stanley, R. & Boxer, S.G. Effects of applied electric fields on the quantum yields for the initial electron transfer steps in bacterial photosynthesis. II. Dynamic Stark effect. Chem. Phys. 197, 259-75 (1995).

30.          Stanley, R.J. & Castleman, A.W., Jr. Ion dip spectroscopy of phenol-d (PhOD) and phenol-d hydrate-d2 [PhOD(D2O)1]. J. Chem. Phys. 98, 796-9 (1993).

31.           Lao, K., Franzen, S., Stanley, R.J., Lambright, D.G. & Boxer, S.G. Effects of applied electric fields on the quantum yields of the initial electron-transfer steps in bacterial photosynthesis. 1. Quantum yield failure. J. Phys. Chem. 97, 13165-71 (1993).

32.           Wei, S., Purnell, J., Buzza, S.A., Stanley, R.J. & Castleman, A.W., Jr. Femtosecond multiphoton ionization of ammonia clusters. J. Chem. Phys. 97, 9480-2 (1992).

33.           Boxer, S.G., Franzen, S., Lao, K., Lockhart, D.J., Stanley, R., Steffen, M. & Stocker, J.W. Electric field effects on the quantum yields and kinetics of fluorescence and transient intermediates in bacterial reaction centers. NATO ASI Ser., Ser. A 237, 271-82 (1992).

34.           Stanley, R.J. & Castleman, A.W., Jr. Cluster ion dip spectroscopy of hydrogen-bonded phenol-(water)n clusters, n = 0-4. J. Chem. Phys. 94, 7744-56 (1991).

35.           Stanley, R.J., Cook, M. & Castleman, A.W., Jr. Unimolecular dissociation rate constants: chlorobenzene cations revisited by using a new method. J. Phys. Chem. 94, 3668-74 (1990).

36.           Stanley, R.J. & Castleman, A.W., Jr. Ion dip spectroscopy of van der Waals clusters. J. Chem. Phys. 92, 5770-5 (1990).

37.           Castleman, A.W., Jr., Echt, O., Morgan, S., Dao, P.D. & Stanley, R.J. Unimolecular dissociation of cluster ions following multiphoton ionization and subsequent proton transfer reaction. Ber. Bunsen-Ges. Phys. Chem. 89, 281-4 (1985).

38.          Echt, O., Morgan, S., Dao, P.D., Stanley, R.J. & Castleman, A.W., Jr. Multiphoton ionization of ammonia clusters with a tunable laser. Ber. Bunsen-Ges. Phys. Chem. 88, 217-19 (1984).

39.           Echt, O., Morgan, S., Dao, P.D., Stanley, R.J. & Castleman, A.W., Jr. Multiphoton ionization of ammonia clusters (NH3)n and unimolecular dissociation of ammonia cluster ions. Contrib. - Symp. At. Surf. Phys., 246-51 (1984).

40.          Stanley, R.J., Echt, O. & Castleman, A.W., Jr. Resonance-enhanced             multiphoton ionization (2 + 1) of the ~B and ~C' states of ammonia. Appl.          Phys. B   B32, 35-8 (1983).

 

Selected Presentations by the Group

1.              Stanley, R.J., Kodali, G., Siddiqui, S., Hou, Z. & Narayanan, M. Light-driven enzymatic DNA repair: What's hot and what's not. Abstracts of Papers, 234th ACS National Meeting, Boston, MA, United States, August 19-23, 2007, PHYS-689 (2007).

2.             Kodali, G. & Stanley, R.J. Electronic properties of 2-aminopurine as measured by Stark spectroscopy. Abstracts of Papers, 232nd ACS National Meeting, San Francisco, CA, United States, Sept. 10-14, 2006, PHYS-514 (2006).

3.             Yearsley, D.M., McIntire, W.S. & Stanley, R.J. FAD Synthetase is slightly promiscuous. Abstracts, 37th Middle Atlantic Regional Meeting of the American Chemical Society, New Brunswick, NJ, United States, May 22-25, 2005, GENE-325 (2005).

4.             Yang, K. & Stanley, R.J. Extent of DNA deformation in DNA photolyase-substrate complexes: A solution state fluorescence study. Abstracts of Papers, 230th ACS National Meeting, Washington, DC, United States, Aug. 28-Sept. 1, 2005, BIOL-038 (2005).

5.             Stanley, R.J., Hou, Z., Narayaran, M. & Kodali, G. Intermediates in Light-driven DNA Repair by Photolyase. Abstracts, 37th Middle Atlantic Regional Meeting of the American Chemical Society, New Brunswick, NJ, United States, May 22-25, 2005, GENE-648 (2005).

6.             Kodali, G., Siddiqui, M.S. & Stanley, R.J. A Stark Spectroscopic Study of Semiquinone FAD in DNA Photolyase. Abstracts, 37th Middle Atlantic Regional Meeting of the American Chemical Society, New Brunswick, NJ, United States, May 22-25, 2005, GENE-399 (2005).

7.             Stanley, R.J. & MacFarlane, A.W. Mechanistic insights into light-driven DNA repair by photolyase. Abstracts of Papers, 228th ACS National Meeting, Philadelphia, PA, United States, August 22-26, 2004, AGFD-050 (2004).

8.             Yang, K. & Stanley, R.J. Sequence specificity in base flipping by DNA photolyase. Abstracts, 36th Middle Atlantic Regional Meeting of the American Chemical Society, Princeton, NJ, United States, June 8-11, 354 (2003).

9.             Stanley, R.J. & MacFarlane, A.W. Light-driven enzymatic DNA repair in real time. Abstracts, 36th Middle Atlantic Regional Meeting of the American Chemical Society, Princeton, NJ, United States, June 8-11, 173 (2003).

10.           Stanley, R.J., Christine, K.S., Yang, K. & MacFarlane, A.W.I.V. Cyclobutylpyrimidine dimer base flipping by DNA photolyase. Abstracts of Papers, 225th ACS National Meeting, New Orleans, LA, United States, March 23-27, 2003, PHYS-508 (2003).

11.            Siddiqui, M.S., Narayanan, M. & Stanley, R.J. A new optical waveguide low-temperature absorption spectrometer to facilitate stark spectroscopy of flavoproteins. Abstracts, 36th Middle Atlantic Regional Meeting of the American Chemical Society, Princeton, NJ, United States, June 8-11, 355 (2003).

12.            Moravcevic, K. & Stanley, R.J. Reconstitution of DNA photolyase with a FAD analog: Does adenine matter? Abstracts, 36th Middle Atlantic Regional Meeting of the American Chemical Society, Princeton, NJ, United States, June 8-11, 356 (2003).

13.            Stanley, R.J. & MacFarlane, A.W.I.V. Subpicosecond ultrafast dynamics of excited-state flavins. Book of Abstracts, 218th ACS National Meeting, New Orleans, Aug. 22-26, PHYS-362 (1999).

14.            Stanley, R.J. & MacFarlane, A.W.I.V. Direct measurements of ultrafast excited state quenching of isoalloxazine by adenine in FAD. Flavins and Flavoproteins 1999, Proceedings of the International Symposium, 13th, Konstanz, Germany, Aug. 29-Sept. 4, 1999, 99-102 (1999).

15. Stanley, R.J. & Jang, H. Dipole moments and polarizabilities of flavins explored using Stark-effect spectroscopy. Flavins and Flavoproteins 1999, Proceedings of the International Symposium, 13th, Konstanz, Germany, Aug. 29-Sept. 4, 1999, 41-44 (1999).

Selected Invited Addresses

1990 - Gordon Conference on Molecular and Ionic Clusters: "Solvation Effects on Spectroscopy and Dynamics," Volterra, Italy.

1996 - Chemistry Department Seminar Series,  University of Rochester, Rochester, New York.

1997 - Chemistry Department Seminar Series,  The Pennsylvania State University,  University Park, Pennsylvania.

1999 - Chemistry Department Seminar Series, "Stark Spectroscopy of Flavins", University of Pennsylvania.

2000 - Chemistry Department Seminar Series, "Stark Spectroscopy of Flavins", University of Massachusetts, Amherst MA.

2001 - Chemistry Department Seminar Series, "Charge Transfer Interactions in Flavoproteins: A Dipole's Perspective",  Carnegie Mellon University, Pittsburgh PA

2001 - Chemistry Department Seminar Series, "Charge Transfer Interactions in Flavoproteins: A Dipole's Perspective",  North Carolina State University, Raleigh, NC

2002 - "Substrate Electric Fields in DNA Repair", Department of Chemistry, Mount Holyoke College, South Hadley, MA.

2003 - Department of Chemistry Seminar Series, University of Missouri, St. Louis MO

2003 - Department of Chemistry Seminar Series, University of Missouri, Columbia MO

2003 - Physical Chemistry Colloquium, Pennsylvania State University, University Park PA

2003 - 36th Middle Atlantic Regional ACS Meeting,  Princeton, NJ

2003 - 225th ACS National Meeting, New Orleans, LA

2005 - "Mechanistic Insights into Light-Driven DNA Repair by DNA Photolyase" 14^th Annual Conference on Flavins and Flavoproteins, Shonan Village, Japan, April 2005

2005 - "Intermediates in the light-driven repair reaction by DNA Photolyase" , Mid-Atlantic    Regional Meeting of the American Chemistry Society, Rutgers University.

2005 - "Intermediates in the ultrafast repair of DNA by DNA photolyase", Zhanjia Hou, Goutham Kodali, Madhavan Narayanan, Kongsheng Yang, and Robert J. Stanley, Femtochemistry VII, Washington DC, July.

2006 - "DNA photolyase: an unsolved mystery of substrate suicide or Substrate electric fields and their effect on electron transfer", Robert J. Stanley and Goutham Kodali, American Society of Photobiology, Rio Del Mar, Puerto Rico, July.

2006 - "Photolyase: Binding of sun-burnt DNA and light-driven ultrafast repair", University of Kentucky, Lexington KY

2007 - "Photolyase: Binding of sun-burnt DNA and light-driven ultrafast repair", Drexel University, Department of Chemistry, Philadelphia, PA.

2007 - "Photolyase: Binding of sun-burnt DNA and light-driven ultrafast repair", Temple University, Department of Biology, Philadelphia PA.

2007 - "Light-driven enzymatic DNA repair: What's hot and what's not."Stanley, R.J., Kodali, G., Siddiqui, S., Hou, Z. & Narayanan, M. 234th ACS National Meeting, Boston, MA.

 

Temple University Department of Chemistry