Vibrational analysis of nucleic acids. V. Force field and conformation- dependent modes of the phosphodiester backbone modeled by diethyl phosphate

Biophysical Journal

Volumn 71, Issue 5, 1996, Pages 2802-2814

  Guan, Yifu ^a   Thomas Jr , George J ^a  

^a UNIVERSITY OF MISSOURI KANSAS CITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHEMICAL STRUCTURE; DNA CONFORMATION; MODEL; NUCLEIC ACID ANALYSIS; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

EID: 0029970811     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(96)79474-2     Document Type: Article

References (27)

1. 8). Biochemistry. 35:5747-5755.
2. Benevides, J. M., M. Tsuboi, A. H.-J. Wang, and G. J. Thomas, Jr. 1993. Local Raman tensors of double-helical DNA in the crystal: a basis for determining DNA residues orientations. J. Am. Chem. Soc. 115: 5351-5359.
3. Bicknell-Brown, E., K. G. Brown, and W. B. Person. 1982. Conformation-dependent Raman bands of phospholipid surfaces. 3. Head group orthophosphate stretching vibrations. J. Raman Spectrosc. 12:180-189.
4. Duguid, J. G., V. A. Bloomfield, J. M. Benevides, and G. J. Thomas, Jr. 1996. DNA melting investigated by differential scanning calorimetry and Raman spectroscopy. Biophys. J. In press.
5. Durig, J. R., H. Nanaie, and G. A. Guirgis. 1991. Raman and infrared spectra, barriers to internal rotation, vibrational assignments and ab initio calculations on 2-fluoropropane. J. Raman Spectrosc. 22:155-168.
6. Erfurth, S. C., P. J. Bond, and W. L. Peticolas. 1975. Characterization of the A ↔ B transition of DNA in fibers and gels by laser Raman spectroscopy. Biopolymers. 14:1245-1257.
7. Erfurth, S. C., E. J. Kiser, and W. L. Peticolas. 1972. Determination of the backbone structure of nucleic acids and nucleic acid oligomers by laser Raman scattering. Proc. Natl. Acad. Sci. USA. 69:938-941.
8. Guan, Y., G. Choi, R. Glaser, and G. J. Thomas, Jr. 1995. Vibrational analysis of nucleic acids. 2. Ab initio calculation of the molecular force field and normal modes of dimethyl phosphate. J. Phys. Chem. 99: 12,054-12,062.
9. Guan, Y., and G. J. Thomas, Jr. 1996a. Vibrational analysis of nucleic acids. 3. Conformation-dependent Raman markers of the phosphodiester backbone modeled by dimethyl phosphate. J. Mol. Struct. 379:31-41.
10. Guan, Y., and G. J. Thomas, Jr. 1996b. Vibrational analysis of nucleicacids. 4. Normal modes of the DNA phosphodiester structure modeled by diethyl phosphate. Biopolymers. (in press).
11. 2-. Biophys. J. 66:225-235.
12. Hadzi, D., M. Hodoscek, J. Grdadolnik, and F. Avbelj. 1992. Intermolecular effects on phosphate frequencies in phospholipids - infrared study and ab initio model calculation. J. Mol. Struct. 266:9-19.
13. Kyogoku, Y., and Y. Iitaka. 1964. The crystal structure of barium diethyl phosphate. Acta Crystallogr. 21:49-57.
14. Liang, C., C. S. Ewig, T. R. Slouch, and A. T. Hagler. 1993. Ab initio studies of lipid model species. 1. Dimethyl phosphate and methyl propyl phosphate anions. J. Am. Chem. Soc. 115:1537-1545.
15. Prescott. B., W. Steinmetz, and G. J. Thomas, Jr. 1984. Characterization of DNA structures by laser Raman spectroscopy. Biopolymers. 23: 235-256.
16. Shaw, R. A., H. Wieser, R. Duller, and A. Rauk. 1990. Vibrational optical activity of (S)-1-d-ethanol. J. Am. Chem. Soc. 112:5401-5410.
17. Snyder, R. G., and G. Zerbi. 1957. Vibrational analysis of ten simple aliphatic ethers: spectra, assignments, valence force field and molecular conformations. Spectrochim. Acta. 23A:391-437.
18. Taga, K., K. Miyagai, N. Hirabayashi, T. Yoshida, and H. Okabayashi. 1991. Vibrational spectra and normal coordinate analysis of barium dimethyl, diethyl and ethyl methyl phosphates. J. Mol. Struct. 245:1-11.
19. Taillandier, E., and J. Liquier. 1992. Infrared spectroscopy of DNA. Methods Enzymol. 211:307-335.
20. Terpstra, P. A., C. Otto, G. M. J. Segers-Nolten, J. S. Kanger, and J. Greve. 1995. Raman depolarization ratios in RNA and DNA are sensitive for sugar-base coupling. Biospectroscopy. 1:255-263.
21. Thomas, G. J., Jr., J. M. Benevides, S. A. Overman, T. Ueda, K. Ushizawa, M. Saitoh, and M. Tsuboi. 1995. Polarized Raman spectra of oriented fibers of A DNA and B DNA: anisotropic and isotropic local Raman tensors of base and backbone vibrations. Biophys. J. 69:1073-1088.
22. Thomas, G. J., Jr., J. M. Benevides, and B. Prescott. 1986. DNA and RNA structure in crystals, fibers and solutions by Raman spectroscopy with applications to nucleoproteins. Biomol. Stereodynam. 4:227-253.
23. Thomas, G. J., Jr., G. C. Medeiros, and K. A. Hartman. 1971. The dependence of Raman scattering on the conformation of ribosomal RNA. Biochem. Biophys. Res. Commun. 44:587-592.
24. Thomas, G. J., Jr., and M. Tsuboi. 1993. Raman spectroscopy of nucleic acids and their complexes. Adv. Biophys. Chem. 3:1-70.
25. Thomas, G. J., Jr., and A. H.-J. Wang. 1988. Laser Raman spectroscopy of nucleic acids. In Nucleic Acids and Molecular Biology, Vol. 2. F. Eckstein and D. M. J. Lilley, editors. Springer-Verlag, Berlin. 1-30.
26. Wilson. E. B., Jr., J. C. Decius, and P. C. Cross. 1955. Molecular Vibrations. McGraw-Hill, New York.
27. Zhao, W., J. Bandekar, and S. Krimm, 1990. Vibrational studies of the disulfide group in proteins. 3. A simplified ab initio force field for diethyl disulfide and SS and CS stretch frequency-conformation correlations for diisobutyl disulfide. J. Mol. Struct. 238:43-54.