Anharmonic Vibrations of Nucleobases: III, Structural Basis of Oneand Two-Dimensional Infrared Spectra for DNA Stacking Dimers

doi:10.6023/A1105251

Acta Chimica Sinica ›› 2012, Vol. 0 ›› Issue (04): 411-422.DOI: 10.6023/A1105251 Previous Articles Next Articles

Full Papers

核酸碱基的非谐性振动: III, DNA 叠加二聚体的一维和二维红外光谱

王桂秀, 王建平

中国科学院化学研究所分子反应动力学国家重点实验室北京分子科学国家实验室北京 100190

投稿日期:2011-05-25 修回日期:2011-09-05 发布日期:2011-10-25
通讯作者: 王建平
基金资助:
国家自然科学基金(Nos. 20727001, 30870591)资助项目.

Anharmonic Vibrations of Nucleobases: III, Structural Basis of Oneand Two-Dimensional Infrared Spectra for DNA Stacking Dimers

Wang Guixiu, Wang Jianping

Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190

Received:2011-05-25 Revised:2011-09-05 Published:2011-10-25
Supported by:
This work was supported by the National Natural Science Foundation of China (Nos. 20727001, 30870591).

In this work, DNA base monomers, 15 B-form stacking dimers and two G-quadruplex stacking dimers were studied by quantum chemical computations. Detailed anharmonic vibrational analysis was carried out to reveal vibrational signatures for structural aspect of the base monomers and dimers. It was found that from isolated base monomers to stacking dimers, particularly those containing guanine, the interaction between the C＝O stretching is very strong, as depicted by the significant changes of their vibrational frequencies and anharmonicities. Such changes can be manifested well in simulated 1D IR and 2D IR spectra. Delocalization degree of the C＝O vibrational modes in stacking dimers, represented by the potential energy distribution and the contribution to the diagonal anharmonicity composition from the vibrators, was found to have significant variations in comparison with isolated bases, which resulted from the influences of the C＝O stretching and the nearby vibrations of stacking bases.

Key words: quantum chemical computation, B-form DNA stacking dimers, G-quadruplex stacking dimers, anharmonic vibration, anharmonicity

Cite this article

Wang Guixiu, Wang Jianping. Anharmonic Vibrations of Nucleobases: III, Structural Basis of Oneand Two-Dimensional Infrared Spectra for DNA Stacking Dimers[J]. Acta Chimica Sinica, 2012, 0(04): 411-422.

Export EndNote|Reference Manager|ProCite|BibTeX|RefWorks

share this article

References

1 Nowak, M. J.; Lapinski, L.; Kwiatkowski, J. S.; Leszczynski, J. J. Phys. Chem. 1996, 10, 3527.

2 Szczepaniak, K.; Szczesniak, M. M.; Person, W. B. J. Phys. Chem. A 2000, 104, 3852.

3 Szczesniak, M.; Szczepaniak, K.; Kwiatkowski, J. S.; KuBulat, K.; Person, W. B. J. Am. Chem. Soc. 1988, 110, 8319.

4 Szczesniak, M.; Nowak, M. J.; Rostkowska, H.; Szczepaniak, K.; Person, W. B.; Shugar, D. J. Am. Chem. Soc. 1983, 105, 5969.

5 Szczepaniak, K.; Szczesniak, M.; Person, W. B. Chem. Phys. Lett. 1988, 153, 39.

6 Sheina, G. G.; Stepanian, S. G.; Radchenko, E. D.; Blagoi, Y. P. J. Mol. Struct. 1987, 158, 275.

7 Szczepaniak, K.; Szczesniak, M. J. Mol. Struct. 1987, 156, 29.

8 Schoone, K.; Maes, G.; Adamowicz, L. J. Mol. Struct. 1999, 480-481, 505.

9 Nir, E.; Janzen, C.; Imhof, P.; Kleinermanns, K.; de Vries, M. S. J. Chem. Phys. 2001, 115, 4604.

10 .Mons, M.; Dimicoli, I.; Piuzzi, F.; Tardivel, B.; Elhanine, M. J. Phys. Chem. A 2002, 106, 5088.

11 Seefeld, K.; Brause, R.; H?ber, T.; Kleinermanns, K. J. Phys. Chem. A 2007, 111, 6217.

12 Kyogoku, Y.; Lord, R. C.; Rich, A. J. Am. Chem. Soc. 1967, 89, 496.

13 Rozenberg, M.; Jung, C.; Shoham, G. Spectrochim. Acta A 2005, 61, 733.

14 Adam, S.; Liquier, J.; Taboury, J. A.; Taillandier, E. Biochemistry 1986, 25, 3220.

15 Plützer, C.; Hünig, I.; Kleinermanns, K.; Nir, E.; de Vries, M. S. ChemPhysChem 2003, 4, 838.

16 Nir, E.; Plützer, C.; Kleinermanns, K.; de Vries, M. S. Eur. Phys. J. 2002, 20, 317.

17 Fritzsche, H. J. Mol. Struct. 1991, 242, 245.

18 Ouali, M.; Gousset, H.; Geinguenaud, F.; Liquier, J.; Gabarro-Arpa, J.; Bret, M. L.; Taillandier, E. Nucleic Acids Res. 1997, 25, 4816.

19 Liquier, J.; Taillandier, E. Infrared Spectroscopy of Biomolecules, Eds.; Mantsch, H. H.; Chapman, D., John Wiley & Sons Inc., New York, 1996, pp. 131～158.

20 Maevsky, A. A.; Sukhorukov, B. I. Nucleic Acids Res. 1980, 8, 3029.

21 Zanni, M. T.; Asplund, M. C.; Hochstrasser, R. M. J. Chem. Phys. 2001, 114, 4579.

22 Hamm, P.; Lim, M.; Hochstrasser, R. M. J. Phys. Chem. B 1998, 102, 6123.

23 Asplund, M. C.; Zanni, M. T.; Hochstrasser, R. M. Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 8219.

24 Wang, J. Chin. Sci. Bull. 2006, 52, 1221.

25 Scheurer, C.; Piryatinski, A.; Mukamel, S. J. Am. Chem. Soc. 2001, 123, 3114.

26 Golonzka, O.; Khalil, M.; Demird?ven, N.; Tokmakoff, A. Phys. Rev. Lett. 2001, 86, 2154.

27 Zanni, M. T.; Gnanakaran, S.; Stenger, J.; Hochstrasser, R. M. J. Phys. Chem. B 2001, 105, 6520.

28 Massari, A. M.; Finkelstein, I. J.; McClain, B. L.; Goj, A.; Wen, X.; Bren, K. L.; Loring, R. F.; Fayer, M. D. J. Am. Chem. Soc. 2005, 127, 14279.

29 Asbury, J. B.; Steinel, T.; Stromberg, C.; Gaffney, K. J.; Piletic, I. R.; Fayer, M. D. J. Chem. Phys. 2003, 119, 12981.

30 Gnanakaran, S.; Hochstrasser, R. M. J. Am. Chem. Soc. 2001, 123, 12886.

31 Kim, Y. S.; Wang, J.; Hochstrasser, R. M. J. Phys. Chem. B 2005, 109, 7511.

32 Moran, A.; Mukamel, S. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 506.

33 Vorobyev, D. Y.; Kuo, C.-H.; Kuroda, D. G.; Scott, J. N.; Vanderkooi, J. M.; Hochstrasser, R. M. J. Phys. Chem. B 2010, 114, 2944.

34 Krummel, A. T.; Mukherjee, P.; Zanni, M. T. J. Phys. Chem. B 2003, 107, 9165.

35 Krummel, A. T.; Zanni, M. T. J. Phys. Chem. B 2006, 110, 13991.

36 Wang, J.; Cai, K.; Ma, X. ChemPhysChem 2009, 10, 2242.

37 Barone, V. J. Chem. Phys. 2005, 122, 014108.

38 Barone, V.; Festa, G.; Grandi, A.; Rega, N.; Sanna, N. Chem. Phys. Lett. 2004, 388, 279.

39 Biczysko, M.; Panek, P.; Barone, V. Chem. Phys. Lett. 2009, 475, 105.

40 Wang, G.; Ma, X.; Wang, J. Chin. J. Chem. Phys. 2009, 22, 563.

41 Wang, G.; Zhao, J.; Wang, J. Sci. Chin. Ser. B 2011, 54, 1590.

42 Watson, J. D.; Crick, F. H. C. Nature 1953, 171, 737.

43 Suzuki, M.; Amano, N.; Kakinuma, J.; Tateno, M. J. Mol. Biol. 1997, 274, 421.

44 Bommarito, S.; Peyret, N.; Jr, J. S. Nucleic Acids Res. 2000, 28, 1929.

45 Desfran?ois, C.; Carles, S.; Schermann, J. P. Chem. Rev. 2000, 100, 3943.

46 Mao, L.; Wang, Y.; Liu, Y.; Hu, X. J. Mol. Biol. 2004, 336, 787.

47 Matta, C. F.; Castillo, N.; Boyd, R. J. J. Phys. Chem. B 2006, 110, 563.

48 Hobza, J.; Sponer, J. J. Am. Chem. Soc. 2002, 124, 11802.

49 ?poner, J.; Leszczyński, J.; Hobza, P. J. Phys. Chem. 1996, 100, 5590.

50 ?poner, J.; Leszczynski, J.; Hobza, P. Biopolymers 2002, 61, 3.

51 Hobza, J.; Sponer, J. Chem. Rev. 1999, 99, 3247.

52 Lee, C.; Park, K.-H.; Kim, J.-A.; Hahn, S.; Cho, M. J. Chem. Phys. 2006, 125, 114510.

53 Lee, C.; Park, K.-H.; Cho, M. J. Chem. Phys. 2006, 125, 114508.

54 Lee, C.; Cho, M. J. Chem. Phys. 2006, 125, 114509.

55 McCarthy, W.; Plokhotnichenko, A. M.; Radchenko, E. D.; Smets, J.; Smith, D. M. A.; Stepanian, S. G.; Adamowicz, L. J. Phys. Chem. A 1997, 101, 7208.

56 Reha, D.; Kabelá?, M.; Ryjá?ek, F.; Sponer, J.; Sponer, J. E.; Elstner, M.; Suhai, S.; Hobza, P. J. Am. Chem. Soc. 2002, 124, 3366.

57 Czyznikowska, Z.; Zalesny, R.; Ziólkowski, M.; Gora, R. W.; Cysewski, P. Chem. Phys. Lett. 2007, 450, 132.

58 Wang, J. J. Phys. Chem. B 2008, 112, 4790.

59 Tsuzuki, S.; Honda, K.; Azumi, R. J. Am. Chem. Soc. 2002, 124, 1220.

60 Fang, C.; Wang, J.; Kim, Y. S.; Charnley, A. K.; Barber-Armstrong, W.; Smith, A. B.; Decatur, S. M.; Hochstrasser, R. M. J. Phys. Chem. B 2004, 108, 10415.

61 Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A., D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A., G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision B. 05, Gaussian, Inc., Pittsburgh, PA, 2003.

62 Keniry, M. A.; Strahan, G. D.; Owen, E. A.; Shafer, R. Eur. J. Biochem. 1995, 233, 631.

63 Rutledge, L. R.; Durst, H. F.; Wetmore, S. D. Phys. Chem. Chem. Phys. 2008, 10, 2801.

64 Rutledge, L. R.; Campbell-Verduyn, L. S.; Wetmore, S. D. Chem. Phys. Lett. 2007, 444, 167.

65 Helios, K.; Wysokiński, R.; Zierkiewicz, W.; Proniewicz, L. M.; Michalska, D. J. Phys. Chem. B 2009, 113, 8158.

66 Wang, J.; Hochstrasser, R. M. J. Phys. Chem. B 2006, 110, 3798.

核酸碱基的非谐性振动: III, DNA 叠加二聚体的一维和二维红外光谱

Anharmonic Vibrations of Nucleobases: III, Structural Basis of Oneand Two-Dimensional Infrared Spectra for DNA Stacking Dimers

PDF

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 0

Recommended Articles

Metrics

Comments