Abstract
Nucleic acids are the very essence of life, containing the genetic potential of all organisms. However, the sheer size of nucleic acids makes them susceptible to a variety of environmental insults. Of these, ultraviolet-induced damage to nucleic acids has received extensive attention due to its role in disease. The primary step in ultraviolet-induced damage is the absorption of light and the subsequent electronic and structural dynamics on the excited-state potential energy surface. In this chapter, we will review the use of Raman and resonance Raman spectroscopy as a means of obtaining excited-state structural dynamics. Specifically, the application of Raman and resonance Raman spectroscopy to determine the excited-state structural dynamics of nucleic acids and their components will be discussed
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Zaug AJ, Been MD, Cech TR (1986) Nature 324: 429.
Chakraborty C. (2007) Curr. Drug Targets 8: 469.
Watson JD, Crick FHC (1953) Nature 171: 737.
Saenger W (1984) Principles of nucleic acid structure, Springer-Verlag, New York, p 556.
Blancafort L, Cohen B, Hare PM, Kohler B, Robb MA (2005) J Phys Chem A 109: 4431.
Cohen B, Crespo-Hernandez CE, Kohler B (2004) Faraday Discuss 127: 137.
Cohen B, Hare PM, Kohler B (2003) J Am Chem Soc 125: 13594.
Crespo-Hernandez CE, Cohen B, Hare PM, Kohler B (2004) Chem Rev 104: 1977.
Crespo-Hernandez CE, Cohen B, Kohler B (2006) Nature 441: E8.
Crespo-Hernandez CE, Cohen B, Kohler B (2005) Nature 436: 1141.
Hare PM, Crespo-Hernandez CE, Kohler B (2007) Proc Natl Acad Sci USA 104: 435.
Malone RJ, Miller AM, Kohler B (2003) Photochem Photobiol 77: 158.
Pecourt JML, Peon J, Kohler B (2001) J Am Chem Soc 123: 10370.
Gustavsson T, Banyasz A, Lazzarotto E, Markovitsi D, Scalmani G, Frisch MJ, Barone V, Improta R (2006) J Am Chem Soc 128: 607.
Gustavsson T, Sarkar N, Lazzarotto E, Markovitsi D, Barone V, Improta R (2006) J Phys Chem B 110: 12843.
Gustavsson T, Sarkar N, Lazzarotto E, Markovitsi D, Improta R (2006) Chem Phys Lett 429: 551.
Gustavsson T, Sharonov A, Markovitsi D (2002) Chem Phys Lett 351: 195.
Markovitsi D, Talbot F, Gustavsson T, Onidas D, Lazzarotto E, Marguet S (2006) Nature 441: E7.
Onidas D, Markovitsi D, Marguet S, Sharonov A, Gustavsson T (2002) J Phys Chem B 106: 11367.
Santoro F, Barone V, Gustavsson T, Improta R (2006) J Am Chem Soc 128: 16312.
Sharonov A, Gustavsson T, Carre V, Renault E, Markovitsi D (2003) Chem Phys Lett 380: 173.
Sharonov A, Gustavsson T, Marguet S, Markovitsi D (2003) Photochem Photobiol Sci 2: 362.
He YG, Wu CY, Kong W (2004) J Phys Chem A 108: 943.
He YG, Wu CY, Kong W (2003) J Phys Chem A 107: 5145.
Fulscher MP, SerranoAndres L, Roos BO (1997) J Am Chem Soc 119: 6168.
Lorentzon J, Fulscher MP, Roos BO (1995) J Am Chem Soc 117: 9265.
Fulscher MP, Roos BO (1995) J Am Chem Soc 117: 2089.
Jean JM, Krueger BP (2006) J Phys Chem B 110: 2899.
Durbeej B, Eriksson LA (2002) J. Photochem Photobiol A-Chem 152: 95.
Zhang RB, Eriksson LA (2006) J Phys Chem B 110: 7556.
Canuel C, Elhanine M, Mons M, Piuzzi F, Tardivel B, Dimicoli I (2006) Phys Chem Chem Phys 8: 3978.
Blancafort L (2006) J Am Chem Soc 128: 210.
Chen H, Li SH (2006) J Chem Phys 124: 154315.
Serrano-Andres L, Merchan M, Borin AC (2006) Chem – Eur J 12: 6559.
Zendlova L, Hobza P, Kabelac M (2006) ChemPhysChem 7: 439.
Pancur T, Schwalb NK, Renth F, Temps F (2005) Chem Phys 313: 199.
Merchan M, Gonzalez-Luque R, Climent T, Serrano-Andres L, Rodriuguez E, Reguero M, Pelaez D (2006) J Phys Chem B 110: 26471.
Gustavsson T, Banyasz A, Lazzarotto E, Markovitsi D, Scalmani G, Frisch MJ, Barone V, Improta R (2006) J Am Chem Soc 128: 607.
Langer H, Doltsinis NL (2003) Phys Chem Chem Phys 5: 4516.
Langer H, Doltsinis NL (2004) Phys Chem Chem Phys 6: 2742.
Marian CM. (2007) J Phys Chem A 111: 1545.
Sobolewski AL, Domcke W (2004) Phys Chem Chem Phys 6: 2763.
Sobolewski AL, Domcke W, Hattig C (2005) Proc Natl Acad Sci USA 102: 17903.
Ismail N, Blancafort L, Olivucci M, Kohler B, Robb MA (2002) J Am Chem Soc 124: 6818.
Merchan M, Serrano-Andres L (2003) J Am Chem Soc 125: 8108.
Matsika S. (2004) J Phys Chem A 108: 7584.
Perun S, Sobolewski AL, Domcke W (2006) J Phys Chem A 110: 13238.
Zgierski MZ, Patchkovskii S, Fujiwara T, Lim EC (2005) J Phys Chem A 109: 9384.
Chen H, Li SH (2006) J Phys Chem A 110: 12360.
Perun S, Sobolewski AL, Domcke W (2005) Chem Phys 313: 107.
Schultz T, Samoylova E, Radloff W, Hertel IV, Sobolewski AL, Domcke W (2004) Science 306: 1765.
Abo-Riziq A, Grace L, Nir E, Kabelac M, Hobza P, de Vries MS (2005) Proc Natl Acad Sci USA 102: 20.
Perun S, Sobolewski AL, Domcke W (2006) J Phys Chem A 110: 9031.
Markwick PRL, Doltsinis NL, Schlitter J (2007) J Chem Phys 126: 045104.
Markwick PRL, Doltsinis NL (2007) J Chem Phys 126: 175102.
Canuel C, Mons M, Piuzzi F, Tardivel B, Dimicoli I, Elhanine M (2005) J Chem Phys 122: 074316.
Kang H, Lee KT, Jung B, Ko YJ, Kim SK (2002) J Am Chem Soc 124: 12958.
Mulkidjanian AY, Cherepanov DA, Galperin MY (2003) BMC Evol Biol 3: 12.
Ruzsicska BP, Lemaire DGE (1995) CRC handbook of organic photochemistry and photobiology, CRC Press, New York, p 1289.
Cadet J, Anselmino C, Douki T, Voituriez L (1992) J Photochem Photobiol B-Biol 15: 277.
Cadet J, Sage E, Douki T (2005) Mutat Res Funda Molec Mech Mutag 571: 3.
Dodonova NY. (1993) J Photochem Photobiol B-Biol 18: 111.
Gorner H. (1994) J Photochem Photobiol B-Biol 26: 117.
Szacilowski K, Macyk W, Drzewiecka-Matuszek A, Brindell M, Stochel G (2005) Chem Rev 105: 2647.
Eller MS, Ostrom K, Gilchrest BA (1996) Proc Natl Acad Sci USA 93: 1087.
Gorner H. (1991) J Photochem Photobiol B-Biol 10: 91.
Mitchell D (1995) In: Horspool W, Song P (ed) CRC handbook of organic photochemistry and photobiology, CRC Press, New York, p 1326.
Baik MH, Silverman JS, Yang IV, Ropp PA, Szalai VA, Yang WT, Thorp HH (2001) J Phys Chem B 105: 6437.
Kanvah S, Schuster GB (2006) Pure Appl Chem 78: 2297.
Yavin E, Boal AK, Stemp EDA, Boon EM, Livingston AL, O’Shea VL, David SS, Barton JK (2005) Proc Natl Acad Sci USA 102: 1023546.
Crespo-Hernandez CE, Cohen B, Hare PM, Kohler B (2004) Chem Rev 104: 1977.
Sobolewski AL, Domcke W (2002) Eur Phys J D 20: 369.
Mishra SK, Shukla MK, Mishra PC (2000) Spectroc Acta Pt A-Molec Biomolec Spectr 56: 1355.
Mennucci B, Toniolo A, Tomasi J (2001) J Phys Chem A 105: 4749.
Broo A (1998) J Phys Chem A 102: 526.
Holmen A, Broo A, Albinsson B, Norden B (1997) J Am Chem Soc 119: 12240.
Wilson E, Decius J, Cross P (1955) Molecular vibrations, McGraw-Hill, New York.
Myers AB (1997) Acc Chem Res 30: 519.
Myers AB (1997) J Raman Spectrosc 28: 389.
Lee SY, Heller EJ (1979) J Chem Phys 71: 4777.
Kelley AM (1999) J Phys Chem A 103: 6891.
Myers AB, Mathies RA (1987) In: Spiro TG (ed) Biological Applications of Raman Spectroscopy, Wiley-Interscience, New York, p 1.
Myers AB (1995) In: Myers AB, Rizzo TR (ed) Laser Techniques in Chemistry, Wiley, New York, p 325.
Mukamel S (1995) Principles of nonlinear optical spectroscopy, Oxford University Press, New York.
Islampour R, Dehestani M, Lin SH (2000) Mol Phys 98: 98101.
Hizhnyakov V, Tehver I (1997) J Raman Spectrosc 28: 403.
Gu Y, Champion PM (1990) Chem Phys Lett 171: 254.
Mahapatra S, Chakrabarti N, Sathyamurthy N (1999) Int Rev Phys Chem 18: 235.
Page JB, Tonks DL (1981) J Chem Phys 75: 5694.
Fraga E, Loppnow GR (1998) J Phys Chem B 102: 7659.
Webb MA, Kwong CM, Loppnow GR (1997) J Phys Chem B 101: 5062.
Loppnow GR, Fraga E (1997) J Am Chem Soc 119: 896.
Mathies R, Oseroff AR, Stryer L (1976) Proc Natl Acad Sci USA 73: 1.
Tsuboi M, Nishimura Y, Hirakawa A, Peticolas W (1987) In: Spiro TG (ed) Biological Applications of Raman Spectroscopy, vol 2. Wiley-Interscience, New York, p 109.
Benevides JM, Overman SA, Thomas GJ (2005) J Raman Spectrosc 36: 279.
Lagant P, Elass A, Dauchez M, Vergoten G, Peticolas WL (1992) Spectroc Acta Pt A-Molec Biomolec Spectr 48: 1323.
Mathlouthi M, Seuvre AM, Koenig JL (1984) Carbohydr Res 134: 23.
Wojcik MJ (1990) J Mol Struct 219: 305.
Florian J, Hrouda V (1993) Spectroc Acta Pt A-Molec Biomolec Spectr 49: 921.
Person W, Szczepaniak K (1993) Vib Spect Struct 20: 239.
Shanker R, Yadav RA, Singh IS (1994) Spectroc Acta Pt A-Molec Biomolec Spectr 50: 1251.
Tsuboi M, Ueda T, Ushizawa K, Sasatake Y, Ono A, Kainosho M, Ishido Y (1994) Bull Chem Soc Jpn 67: 1483.
Aamouche A, Ghomi M, Coulombeau C, Grajcar L, Baron MH, Jobic H, Berthier G (1997) J Phys Chem A 101: 1808.
Zhang SL, Michaelian KH, Loppnow GR (1998) J Phys Chem A 102: 461.
Rastogi VK, Singh C, Jain V, Palafox MA (2000) J Raman Spectrosc 31: 1005.
Nowak MJ (1989) J Mol Struct 193: 35.
Graindourze M, Smets J, Zeegershuyskens T, Maes G (1990) J Mol Struct 222: 345.
Person W, Szczepaniak K, Szczepaniak MDB,JE (1993) NATO ASI Ser C 406: 141.
Les A, Adamowicz L, Nowak MJ, Lapinski L (1992) Spectroc Acta Pt A-Molec Biomolec Spectr 48: 1385.
Szczepaniak K, Szczesniak MM, Person WB (2000) J Phys Chem A 104: 3852.
Colarusso P, Zhang KQ, Guo BJ, Bernath PF (1997) Chem Phys Lett 269: 39.
Susi H, Ard JS (1974) Spectroc Acta Pt A-Molec Biomolec Spectr A 30: 1843.
Lagant P, Vergoten G, Efremov R, Peticolas WL (1994) Spectroc Acta Pt A-Molec Biomolec Spectr 50: 961.
Rush T, Peticolas WL (1995) J Phys Chem 99: 14647.
Aida M, Kaneko M, Dupuis M, Ueda T, Ushizawa K, Ito G, Kumakura A, Tsuboi M (1997) Spectroc Acta Pt A-Molec Biomolec Spectr 53: 393.
Yarasi S, Billinghurst BE, Loppnow GR (2007) J Raman Spectrosc 38: 1117.
Peticolas WL, Rush T (1995) J Comput Chem 16: 1261.
Lagant P, Vergoten G, Peticolas WL (1999) J Raman Spectrosc 30: 1001.
Yarasi S, Brost P, Loppnow GR (2007) J Phys Chem A 111:5130.
Yarasi S, Brost P, Loppnow GR (2007 In preparation) To be submitted J Am Chem Soc.
Barnes AJ, Stuckey MA, Legall L (1984) Spectroc Acta Pt A-Molec Biomolec Spectr 40: 419.
Szczesniak M, Nowak MJ, Rostkowska H, Szczepaniak K, Person WB, Shugar D (1983) J Am Chem Soc 105: 5969.
Wojcik MJ, Rostkowska H, Szczepaniak K, Person WB (1989) Spectroc Acta Pt A-Molec Biomolec Spectr 45: 499.
Susi H, Ard JS (1971) Spectrochimica Acta Part A-Molecular Spectroscopy A 27: 1549.
Lewis TP, Miles HT, Becker ED (1984) J Phys Chem 88: 3253.
Chinsky L, Huberthabart M, Laigle A, Turpin PY (1983) J Raman Spectrosc 14: 322.
Nishimura Y, Tsuboi M, Kato S, Morokuma K (1981) J Am Chem Soc 103: 1354.
Chin S, Scott I, Szczepaniak K, Person WB (1984) J Am Chem Soc 106: 3415.
Letellier R, Ghomi M, Taillandier E (1987) Eur Biophys J Biophys Lett 14: 423.
Csaszar P, Harsanyi L, Boggs JE (1988) Int J Quantum Chem 33: 1.
Broo A, Pearl G, Zerner MC (1997) J Phys Chem A 101: 2478.
Ilich P, Hemann CF, Hille R (1997) J Phys Chem B 101: 10923.
Gaigeot MP, Sprik M (2003) J Phys Chem B 107: 10344.
Ghomi M, Letellier R, Taillandier E, Chinsky L, Laigle A, Turpin PY (1986) J Raman Spectrosc 17: 249.
Matsika S (2005) J Phys Chem A 109: 7538.
Matsika S (2004) J Phys Chem A 108: 7584.
Billinghurst BE, Loppnow GR (2006) J Phys Chem A 110: 2353.
Peticolas WL, Strommen DP, Lakshminarayanan V (1980) J Chem Phys 73: 4185.
Suen W, Spiro TG, Sowers LC, Fresco JR (1999) Proc Natl Acad Sci USA 96: 4500.
Toyama A, Takeuchi H, Harada I (1991) J Mol Struct 242: 87.
Fraga E, Billinghurst BE, Oladepo S, Loppnow GR (2007) In Preparation.
Billinghurst BE, Yeung R, Loppnow GR (2006) J Phys Chem A 110: 6185.
Budavari S (ed) (1989) The Merck Index : An Encyclopedia of Chemicals, Drugs, and Biologicals, Merck. Rathway, NJ: 11th ed.
Nishimura Y, Tsuboi M, Kubasek WL, Bajdor K, Peticolas WL (1987) J Raman Spectrosc 18: 221.
Tsuboi M, Komatsu M, Hoshi J, Kawashima E, Sekine T, Ishido Y, Russell MP, Benevides JM, Thomas GJ (1997) J Am Chem Soc 119: 2025.
Purrello R, Molina M, Wang Y, Smulevich G, Fossella J, Fresco JR, Spiro TG (1993) J Am Chem Soc 115: 760.
Pezolet M, Yu TJ, Peticolas WL (1975) J Raman Spectrosc 3: 55.
Blazej DC, Peticolas WL (1977) Proc Natl Acad Sci USA 74: 742639.
Nishimura Y, Hirakawa AY, Tsuboi M (1977) Chem Lett 907.
Nishimura Y, Tsuboi M, Kubasek WL, Bajdor K, Peticolas WL (1987) J Raman Spectrosc 18: 221.
Peticolas WL, Blazej DC (1979) Chem Phys Lett 63: 604.
Kubasek WL, Hudson B, Peticolas WL (1985) Proc Natl Acad Sci USA 82: 2369.
Blazej DC, Peticolas WL (1980) J Chem Phys 72: 3134.
Turpin PY, Peticolas WL (1985) J Phys Chem 89: 5156.
Peticola.Wl (1973) J Opt Soc Am 63: 477.
Blazej DC, Peticolas WL (1977) Proc Natl Acad Sci USA 74: 2639.
Fodor SPA, Rava RP, Hays TR, Spiro TG (1985) J Am Chem Soc 107: 1520.
Perno JR, Grygon CA, Spiro TG (1989) J Phys Chem 93: 5672.
Spiro TG (1974) Acc Chem Res 7: 339.
Behringer J (1975) Mol Spectrosc 3: 163.
Johnson BB, Peticolas WL (1976) Annu Rev Phys Chem 27: 465.
Tang J, Albrecht A (1970) Raman Spectrosc 2: 33.
Peticola Wl, Nafie L, Stein P, Fanconi B (1970) J Chem Phys 52: 1576.
Friedman JM, Hochstrasser RM (1973) Chem Phys 1: 457.
Warshel A, Karplus M (1972) J Am Chem Soc 94: 5612.
Inagaki F, Tasumi M, Miyazawa T (1974) J Mol Spectrosc 50: 286.
Garozzo M, Galluzzi F (1976) J Chem Phys 64: 1720.
Stein P, Miskowski V, Woodruff WH, Griffin JP, Werner KG, Gaber BP, Spiro TG (1976) J Chem Phys 64: 2159.
Nafie LA, Pastor RW, Dabrowiak JC, Woodruff WH (1976) J Am Chem Soc 98: 8007.
Mingardi M, Siebrand W (1975) J Chem Phys 62: 1074.
Shelnutt JA, Oshea DC, Yu NT, Cheung LD, Felton RH (1976) J Chem Phys 64: 1156.
Johnson BB, Nafie LA, Peticolas WL (1977) Chem Phys 19: 303.
Yarasi S, Yeung R, Loppnow GR (2007 In preparation for submission to) J Phys Chem A.
Kundu L, Loppnow GR (2007) Photochem Photobiol 83: 600.
Peticolas WL (1995) Methods Enzymol 246: 389.
Erfurth SC, Peticolas WL (1975) Biopolymers 14: 247.
Fodor SPA, Spiro TG (1986) J Am Chem Soc 108: 3198.
Mukerji I, Shiber MC, Fresco JR, Spiro TG (1996) Nucleic Acids Res 24: 5013.
Mukerji I, Shiber MC, Spiro TG, Fresco JR (1995) Biochemistry (NY) 34: 14300.
Chan SS, Austin RH, Mukerji I, Spiro TG (1997) Biophys J 72: 1512.
Grygon CA, Spiro TG (1990) Biopolymers 29: 707.
Schreier WJ, Schrader TE, Koller FO, Gilch P, Crespo-Hernandez CE, Swaminathan VN, Carell T, Zinth W, Kohler B (2007) Science 315: 625.
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Loppnow, G.R., Billinghurst, B.E., Oladepo, S.A. (2008). Excited-State Structural Dynamics of Nucleic Acids and Their Components. In: Shukla, M.K., Leszczynski, J. (eds) Radiation Induced Molecular Phenomena in Nucleic Acids. Challenges and Advances In Computational Chemistry and Physics, vol 5. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-8184-2_9
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