SIOC 中文
ACS
Adv search

Acta Chimica Sinica >

2012 , Vol. 0 >Issue 04: 411 - 422

DOI: https://doi.org/10.6023/A1105251

Full Papers

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

  • Wang Guixiu ,
  • Wang Jianping
Expand
  • Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190

Received date: 2011-05-25

  Revised date: 2011-09-05

  Online published: 2011-10-25

Supported by

This work was supported by the National Natural Science Foundation of China (Nos. 20727001, 30870591).

Fold

Abstract

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 . DOI: 10.6023/A1105251

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.  
Options
Outlines

/

〈 〉