Femtosecond Stimulated Raman Spectroscopy of the Cyclobutane Thymine Dimer Repair Mechanism: A Computational Study
- Authors:
-
- Department of Chemistry, 1102 Natural Sciences II, University of California, Irvine, California 92697-2025, United States
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2A, 12489 Berlin, Germany
- Publication Date:
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1160169
- Resource Type:
- Published Article
- Journal Name:
- Journal of the American Chemical Society
- Additional Journal Information:
- Journal Name: Journal of the American Chemical Society Journal Volume: 136 Journal Issue: 42; Journal ID: ISSN 0002-7863
- Publisher:
- American Chemical Society
- Country of Publication:
- United States
- Language:
- English
Citation Formats
Ando, Hideo, Fingerhut, Benjamin P., Dorfman, Konstantin E., Biggs, Jason D., and Mukamel, Shaul. Femtosecond Stimulated Raman Spectroscopy of the Cyclobutane Thymine Dimer Repair Mechanism: A Computational Study. United States: N. p., 2014.
Web. doi:10.1021/ja5063955.
Ando, Hideo, Fingerhut, Benjamin P., Dorfman, Konstantin E., Biggs, Jason D., & Mukamel, Shaul. Femtosecond Stimulated Raman Spectroscopy of the Cyclobutane Thymine Dimer Repair Mechanism: A Computational Study. United States. https://doi.org/10.1021/ja5063955
Ando, Hideo, Fingerhut, Benjamin P., Dorfman, Konstantin E., Biggs, Jason D., and Mukamel, Shaul. Thu .
"Femtosecond Stimulated Raman Spectroscopy of the Cyclobutane Thymine Dimer Repair Mechanism: A Computational Study". United States. https://doi.org/10.1021/ja5063955.
@article{osti_1160169,
title = {Femtosecond Stimulated Raman Spectroscopy of the Cyclobutane Thymine Dimer Repair Mechanism: A Computational Study},
author = {Ando, Hideo and Fingerhut, Benjamin P. and Dorfman, Konstantin E. and Biggs, Jason D. and Mukamel, Shaul},
abstractNote = {},
doi = {10.1021/ja5063955},
journal = {Journal of the American Chemical Society},
number = 42,
volume = 136,
place = {United States},
year = {Thu Oct 09 00:00:00 EDT 2014},
month = {Thu Oct 09 00:00:00 EDT 2014}
}
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https://doi.org/10.1021/ja5063955
https://doi.org/10.1021/ja5063955
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Cited by: 29 works
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Works referenced in this record:
Ultrafast Deactivation Channel for Thymine Dimerization
journal, September 2007
- Boggio-Pasqua, Martial; Groenhof, Gerrit; Schäfer, Lars V.
- Journal of the American Chemical Society, Vol. 129, Issue 36
The Sugar Conformation Governs (6-4) Photoproduct Formation at the Dinucleotide Level
journal, January 2008
- Desnous, Céline; Babu, B. Ravindra; Moriou, Céline
- Journal of the American Chemical Society, Vol. 130, Issue 1
Electronic Excited States Responsible for Dimer Formation upon UV Absorption Directly by Thymine Strands: Joint Experimental and Theoretical Study
journal, August 2012
- Banyasz, Akos; Douki, Thierry; Improta, Roberto
- Journal of the American Chemical Society, Vol. 134, Issue 36
Density Functionals with Broad Applicability in Chemistry
journal, February 2008
- Zhao, Yan; Truhlar, Donald G.
- Accounts of Chemical Research, Vol. 41, Issue 2
A deoxyribozyme that harnesses light to repair thymine dimers in DNA
journal, December 2003
- Chinnapen, D. J. - F.; Sen, D.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 1
Kinetics of cyclobutane thymine dimer splitting by DNA photolyase directly monitored in the UV
journal, May 2011
- Thiagarajan, V.; Byrdin, M.; Eker, A. P. M.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 23
Cis−Syn Thymidine Dimer Repair by DNA Photolyase in Real Time
journal, June 2003
- MacFarlane IV, Alexander W.; Stanley, Robert J.
- Biochemistry, Vol. 42, Issue 28, p. 8558-8568
How Fissors Works: Observing Vibrationally Adiabatic Conformational Change through Femtosecond Stimulated Raman Spectroscopy
journal, May 2013
- Cina, Jeffrey A.; Kovac, Philip A.
- The Journal of Physical Chemistry A, Vol. 117, Issue 29
Mechanism of UV-induced Dewar lesion repair catalysed by DNA (6-4) photolyase
journal, January 2012
- Fingerhut, Benjamin P.; Heil, Korbinian; Kaya, Emine
- Chemical Science, Vol. 3, Issue 6
Time-resolved broadband Raman spectroscopies: A unified six-wave-mixing representation
journal, September 2013
- Dorfman, Konstantin E.; Fingerhut, Benjamin P.; Mukamel, Shaul
- The Journal of Chemical Physics, Vol. 139, Issue 12
Thermodynamics of the Photoenzymic Repair Mechanism Studied by Density Functional Theory
journal, October 2000
- Durbeej, Bo; Eriksson, Leif A.
- Journal of the American Chemical Society, Vol. 122, Issue 41
Substrate and Temperature Dependence of DNA Photolyase Repair Activity Examined with Ultrafast Spectroscopy
journal, October 1997
- Langenbacher, Thomas; Zhao, Xiaodong; Bieser, Gero
- Journal of the American Chemical Society, Vol. 119, Issue 43
Solvation dynamics through Raman spectroscopy: Hydration of Br 2 and Br 3 − , and solvation of Br 2 in liquid bromine
journal, May 2011
- Branigan, Edward T.; Halberstadt, N.; Apkarian, V. A.
- The Journal of Chemical Physics, Vol. 134, Issue 17
An AIMD Study of CPD Repair Mechanism in Water: Role of Solvent in Ring Splitting
journal, April 2011
- Hassanali, Ali A.; Zhong, Dongping; Singer, Sherwin J.
- The Journal of Physical Chemistry B, Vol. 115, Issue 14
Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs
journal, January 2006
- Jurečka, Petr; Šponer, Jiří; Černý, Jiří
- Physical Chemistry Chemical Physics, Vol. 8, Issue 17, p. 1985-1993
UV-induced DNA damage and repair: a review
journal, March 2002
- Sinha, Rajeshwar P.; Häder, Donat-P.
- Photochemical & Photobiological Sciences, Vol. 1, Issue 4
Broadband infrared and Raman probes of excited-state vibrational molecular dynamics: simulation protocols based on loop diagrams
journal, January 2013
- Dorfman, Konstantin E.; Fingerhut, Benjamin P.; Mukamel, Shaul
- Physical Chemistry Chemical Physics, Vol. 15, Issue 29
-Helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time-resolved IR spectroscopy
journal, February 2005
- Bredenbeck, J.; Helbing, J.; Kumita, J. R.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 7
Ultrafast Raman loss spectroscopy
journal, March 2009
- Umapathy, Siva; Lakshmanna, Adithya; Mallick, Babita
- Journal of Raman Spectroscopy, Vol. 40, Issue 3
Monitoring Nonadiabatic Dynamics of the RNA Base Uracil by UV Pump–IR Probe Spectroscopy
journal, May 2013
- Fingerhut, Benjamin P.; Dorfman, Konstantin E.; Mukamel, Shaul
- The Journal of Physical Chemistry Letters, Vol. 4, Issue 11
Reaction mechanisms of DNA photolyase
journal, December 2010
- Brettel, Klaus; Byrdin, Martin
- Current Opinion in Structural Biology, Vol. 20, Issue 6
Femtosecond Stimulated Raman Spectroscopy
journal, May 2007
- Kukura, Philipp; McCamant, David W.; Mathies, Richard A.
- Annual Review of Physical Chemistry, Vol. 58, Issue 1
Stochastic simulation of chemical exchange in two dimensional infrared spectroscopy
journal, July 2006
- Šanda, František; Mukamel, Shaul
- The Journal of Chemical Physics, Vol. 125, Issue 1
Structure and Function of DNA Photolyase and Cryptochrome Blue-Light Photoreceptors
journal, June 2003
- Sancar, Aziz
- Chemical Reviews, Vol. 103, Issue 6
Communication: Comment on the effective temporal and spectral resolution of impulsive stimulated Raman signals
journal, April 2011
- Mukamel, Shaul; Biggs, Jason D.
- The Journal of Chemical Physics, Vol. 134, Issue 16
Probing the Conical Intersection Dynamics of the RNA Base Uracil by UV-Pump Stimulated-Raman-Probe Signals; Ab Initio Simulations
journal, February 2014
- Fingerhut, Benjamin P.; Dorfman, Konstantin E.; Mukamel, Shaul
- Journal of Chemical Theory and Computation, Vol. 10, Issue 3
Self‐consistent molecular orbital methods. XVIII. Constraints and stability in Hartree–Fock theory
journal, April 1977
- Seeger, Rolf; Pople, John A.
- The Journal of Chemical Physics, Vol. 66, Issue 7
The path of chemical reactions - the IRC approach
journal, December 1981
- Fukui, Kenichi
- Accounts of Chemical Research, Vol. 14, Issue 12
Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions
journal, January 2006
- Zhao, Yan; Schultz, Nathan E.; Truhlar, Donald G.
- Journal of Chemical Theory and Computation, Vol. 2, Issue 2
Crystal structure of DNA photolyase from Escherichia coli
journal, June 1995
- Park, H.; Kim, S.; Sancar, A.
- Science, Vol. 268, Issue 5219
Thymine Dimerization in DNA Is an Ultrafast Photoreaction
journal, February 2007
- Schreier, W. J.; Schrader, T. E.; Koller, F. O.
- Science, Vol. 315, Issue 5812
Dynamics and Mechanism of DNA Repair in a Biomimetic System: Flavin–Thymine Dimer Adduct
journal, January 2012
- Kao, Ya-Ting; Song, Qin-Hua; Saxena, Chaitanya
- Journal of the American Chemical Society, Vol. 134, Issue 3
Femtosecond time-resolved Raman spectroscopy using stimulated Raman scattering
journal, December 1999
- Yoshizawa, Masayuki; Kurosawa, Makoto
- Physical Review A, Vol. 61, Issue 1
Thymine Dimerization in DNA Model Systems: Cyclobutane Photolesion Is Predominantly Formed via the Singlet Channel
journal, March 2009
- Schreier, Wolfgang J.; Kubon, Julia; Regner, Nadja
- Journal of the American Chemical Society, Vol. 131, Issue 14
Surviving the Sun: Repair and bypass of DNA UV lesions
journal, October 2011
- Yang, Wei
- Protein Science, Vol. 20, Issue 11
Transition State Theory
journal, October 1981
- Pechukas, P.
- Annual Review of Physical Chemistry, Vol. 32, Issue 1
Spectroscopic Tracking of Structural Evolution in Ultrafast Stilbene Photoisomerization
journal, November 2008
- Takeuchi, S.; Ruhman, S.; Tsuneda, T.
- Science, Vol. 322, Issue 5904
Dynamics and mechanism of cyclobutane pyrimidine dimer repair by DNA photolyase
journal, July 2011
- Liu, Z.; Tan, C.; Guo, X.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 36
The influence of polarization functions on molecular orbital hydrogenation energies
journal, January 1973
- Hariharan, P. C.; Pople, J. A.
- Theoretica Chimica Acta, Vol. 28, Issue 3
Light-driven enzymatic catalysis of DNA repair: a review of recent biophysical studies on photolyase
journal, February 2005
- Weber, Stefan
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1707, Issue 1
Quantum theory of time-resolved femtosecond stimulated Raman spectroscopy: Direct versus cascade processes and application to CDCl 3
journal, January 2011
- Zhao, Bin; Sun, Zhigang; Lee, Soo-Y.
- The Journal of Chemical Physics, Vol. 134, Issue 2
Structural Observation of the Primary Isomerization in Vision with Femtosecond-Stimulated Raman
journal, November 2005
- Kukura, P.
- Science, Vol. 310, Issue 5750
Structure and function of DNA photolyase
journal, January 1994
- Sancar, Aziz
- Biochemistry, Vol. 33, Issue 1
A QM/MM Investigation of Thymine Dimer Radical Anion Splitting Catalyzed by DNA Photolyase
journal, February 2009
- Masson, Fanny; Laino, Teodoro; Rothlisberger, Ursula
- ChemPhysChem, Vol. 10, Issue 2
Mapping GFP structure evolution during proton transfer with femtosecond Raman spectroscopy
journal, November 2009
- Fang, Chong; Frontiera, Renee R.; Tran, Rosalie
- Nature, Vol. 462, Issue 7270
Ultrafast Photoconversion of the Green Fluorescent Protein Studied by Accumulative Femtosecond Spectroscopy
journal, April 2009
- Langhojer, Florian; Dimler, Frank; Jung, Gregor
- Biophysical Journal, Vol. 96, Issue 7
Ring Opening of the Cyclobutane in a Thymine Dimer Radical Anion
journal, November 2007
- Chatgilialoglu, Chryssostomos; Guerra, Maurizio; Kaloudis, Panagiotis
- Chemistry - A European Journal, Vol. 13, Issue 32
Assessment of the Performance of the M05−2X and M06−2X Exchange-Correlation Functionals for Noncovalent Interactions in Biomolecules
journal, November 2008
- Hohenstein, Edward G.; Chill, Samuel T.; Sherrill, C. David
- Journal of Chemical Theory and Computation, Vol. 4, Issue 12
Structure and Function of Photolyase and in Vivo Enzymology: 50th Anniversary
journal, November 2008
- Sancar, Aziz
- Journal of Biological Chemistry, Vol. 283, Issue 47
Direct observation of thymine dimer repair in DNA by photolyase
journal, September 2005
- Kao, Y. -T.; Saxena, C.; Wang, L.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 45
Quantum theory of (femtosecond) time-resolved stimulated Raman scattering
journal, April 2008
- Sun, Zhigang; Lu, J.; Zhang, Dong H.
- The Journal of Chemical Physics, Vol. 128, Issue 14
Stability analysis for solutions of the closed shell Kohn–Sham equation
journal, June 1996
- Bauernschmitt, Rüdiger; Ahlrichs, Reinhart
- The Journal of Chemical Physics, Vol. 104, Issue 22
Theory of femtosecond stimulated Raman spectroscopy
journal, August 2004
- Lee, Soo-Y.; Zhang, Donghui; McCamant, David W.
- The Journal of Chemical Physics, Vol. 121, Issue 8
Coherent ultrafast torsional motion and isomerization of a biomimetic dipolar photoswitch
journal, January 2010
- Briand, Julien; Bräm, Olivier; Réhault, Julien
- Physical Chemistry Chemical Physics, Vol. 12, Issue 13
An AIMD Study of the CPD Repair Mechanism in Water: Reaction Free Energy Surface and Mechanistic Implications
journal, April 2011
- Hassanali, Ali A.; Zhong, Dongping; Singer, Sherwin J.
- The Journal of Physical Chemistry B, Vol. 115, Issue 14
Computational Study of Thymine Dimer Radical Anion Splitting in the Self-Repair Process of Duplex DNA
journal, March 2008
- Masson, Fanny; Laino, Teodoro; Tavernelli, Ivano
- Journal of the American Chemical Society, Vol. 130, Issue 11
Protein Dynamics Studied with Ultrafast Two-Dimensional Infrared Vibrational Echo Spectroscopy
journal, March 2012
- Thielges, Megan C.; Fayer, Michael D.
- Accounts of Chemical Research, Vol. 45, Issue 11
Sequential Proton Transfer Through Water Bridges in Acid-Base Reactions
journal, October 2005
- Mohammed, O. F.
- Science, Vol. 310, Issue 5745
Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules
journal, March 1972
- Hehre, W. J.; Ditchfield, R.; Pople, J. A.
- The Journal of Chemical Physics, Vol. 56, Issue 5, p. 2257-2261