Polarized Raman spectroscopy of double-stranded RNA from bacteriophage φ6: Local Raman tensors of base and backbone vibrations

Biophysical Journal

Volumn 72, Issue 6, 1997, Pages 2748-2762

  Benevides, James M ^a   Tsuboi, Masamichi ^a,b   Bamford, Jaana K H ^a   Thomas Jr , George J ^a  

^a UNIVERSITY OF MISSOURI KANSAS CITY   (United States)

^b IWAKI MEISEI UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA;

ARTICLE; BACTERIOPHAGE; BASE PAIRING; NUCLEOTIDE SEQUENCE; POLARIZATION; RAMAN SPECTROMETRY;

EID: 0030977447     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78917-3     Document Type: Article

References (44)

1. Arnott, S., D. W. Hukins, and S. D. Dover. 1972. Optimized parameters for RNA double-helices. Biochem. Biophys. Res. Commun. 48:1392-1399.
2. Benevides, J. M., D. Lemeur, and G. J. Thomas, Jr. 1984. Molecular conformations and 8-CH exchange rates of purine ribo-and deoxyribonucleotides: investigation by Raman spectroscopy. Biopolymers. 23:1011-1024.
3. 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 residue orientations. J. Am. Chem. Soc. 115: 5351-5359.
4. Benevides, J. M., M. A. Weiss, and G, J. Thomas, Jr. 1994a. An altered specificity mutation in the λ repressor induces global reorganization of the protein-DNA interface. J. Biol. Chem. 269:10869-10878.
5. Benevides, J. M., G. Kukolj, C. Autexier, K. L. Aubrey, M. S. DuBow, and G. J. Thomas, Jr. 1994b. Secondary structure and interaction of phage D108 Ner repressor with a 61-base-pair operator: evidence for altered protein and DNA structures in the complex. Biochemistry. 33: 10701-10710.
6. Brandes, R., A. Rupprecht, and D. R. Kearns. 1989. Interaction of water with oriented DNA in the A-and B-form conformations. Biophys. J. 56:683-691.
7. Guan, Y., and G. J. Thomas, Jr. 1996a. Vibrational analysis of nucleic acids. IV. Normal modes of the DNA phosphodiester structure modeled by diethyl phosphate. Biopolymers. 39:813-835.
8. Guan, Y., and G. J. Thomas, Jr. 1996b. Vibrational analysis of nucleic acids. V. Force field and conformation dependent modes of the phosphodiester backbone modeled by diethyl phosphate. Biophys. J. 71: 2802-2814.
9. Higgs, P. W. 1953. The vibration spectra of helical molecules. Infrared and Raman selection rules, intensities and approximate frequencies. Proc. R. Soc. Lond. (Biol). A220:472-485.
10. Lafleur, L., J. Rice, and G. J. Thomas, Jr. 1972. Raman studies of nucleic acids. VII. poly(A)•poly(U) and poly(G)•poly(C). Biopolymers. 11: 2423-2437.
11. Lamba, O. P., A. H.-J. Wang, and G. J. Thomas, Jr. 1989. Low-frequency dynamics and Raman scattering of crystals of B-, A-and Z-DNA and fibers of C-DNA. Biopolymers. 28:677-678.
12. Li, T., Z. Chen, J. E. Johnson, and G. J. Thomas, Jr. 1990. Structural studies of bean pod mottle virus, capsid and RNA in crystal and solution states by laser Raman spectroscopy. Biochemistry. 29:5018-5026.
13. Li, T., D. H. Bamford, J. K. H. Bamford, and G. J. Thomas, Jr. 1993a. Structural studies of the enveloped dsRNA bacteriophage φ6 of Pseudomonas syringae by Raman spectroscopy. I. The virion and its membrane envelope. J. Mol. Biol. 230:461-472.
14. Li, T., J. E. Johnson, and G. J. Thomas, Jr. 1993b. Raman dynamic probe of hydrogen exchange in bean pod mottle virus: base-specific retardation of exchange in packaged ssRNA. Biophys. J. 65:1963-1972.
15. Li, Y., G. J. Thomas, Jr., M. Fuller, and J. King. 1981. Investigations of bacteriophage P22 by laser Raman spectroscopy. Prog. Clin. Biol. Res. 64:271-283.
16. Lord, R. C., and G. J. Thomas, Jr. 1967. Raman spectral studies of nucleic acids and related molecules. I. Ribonucleic acid derivatives. Spectrochim. Acta. 23A:2551-2591.
17. Mindich, L., and D. H. Bamford. 1988. Lipid containing bacteriophages. In The Bacteriophages, Vol. 2. R. Calendar, editor. Plenum Press, New York. 475-516.
18. Miura, T., and G. J. Thomas, Jr. 1995. Structure and dynamics of interstrand guanine association in quadruplex telomeric DNA. Biochemistry. 34:9645-9653.
19. Nishimura, Y., and M. Tsuboi. 1986. Local conformations and polymorphism of DNA duplexes as revealed by their Raman spectra. In Spectroscopy of Biological Systems. Vol. 13. R. J. H. Clark and R. E. Hester, editors. Wiley-Interscience, New York. 177-232.
20. Olkkonen, V. M., P. M. Ojala, and D. H. Bamford. 1991. Generation of infectious nucleocapsids by in vitro assembly of the shell protein onto the polymerase complex of the dsRNA bacteriophage φ6. J. Mol. Biol 218:569-581.
21. Overman, S. A., M. Tsuboi, and G. J. Thomas. Jr. 1996. Subunit orientation in the filamentous virus Ff (fd, f1, M13). J. Mol. Biol. 259:331-336.
22. Prescott, B., W. Steinmetz, and G. J. Thomas, Jr. 1984. Characterization of DNA secondary structure by Raman spectroscopy. Biopolymers. 23: 235-256.
23. Reilly, K. E., and G. J. Thomas, Jr. 1994. Hydrogen exchange dynamics of the P22 virion determined by time-resolved Raman spectroscopy: effects of chromosome packaging on the kinetics of nucleotide exchanges. J. Mol. Biol. 241:68-82.
24. Steitz, T. A. 1990. Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding. Q. Rev. Biophys. 23:205-280.
25. Susi, H., S. Ard, and J. M. Purcell. 1973. Vibrational spectra of nucleic acid constituents. II. Planar vibrations of cytosine. Spectrochim. Acta. 29A: 725-733.
26. Thomas, G. J., Jr. 1970. Raman spectral studies of nucleic acids. III. Laser-excited spectra of ribosomal RNA. Biochim. Biophys. Acta. 213: 417-423.
27. Thomas, G. J., Jr., and J. M. Benevides. 1985. An A-helix structure for poly(dA-dT) · poly(dA-dT). Biopolymers. 24:1101-1105.
28. 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. 68:1073-1088.
29. Thomas, G. J., Jr. 1986. Applications of Raman spectroscopy in structural studies of viruses, nucleoproteins and their constituents. In Spectroscopy of Biological Systems, Vol. 13. R. J. H. Clark and R. E. Hester, editors. John Wiley and Sons, New York. 233-309.
30. Thomas, G. J., Jr., and M. Tsuboi. 1993. Raman spectroscopy of nucleic acids and their complexes. Adv. Biophys. Chem. 3:1-70.
31. Tsuboi, M., T. Ikeda, and T. Ueda. 1991. Raman microscopy of a small uniaxial crystal: tetragonal aspartame. J. Raman Spectrosc. 22:619-626.
32. Tsuboi, M., Y. Nishimura, A. Y. Hirakawa, and W. L. Peticolas. 1987. Resonance Raman spectroscopy and normal modes of the nucleic acid bases. In Biological Applications of Raman Spectroscopy: Resonance Raman Spectra of Polyenes and Aromatics, Vol. 2. T. G. Spiro, editor. Wiley-Interscience, New York. 109-179.
33. Tsuboi, M., S. A. Overman, and G. J. Thomas, Jr. 1996. Orientation of tryptophan-26 in coat protein subunits of the filamentous virus Ff by polarized Raman microspectroscopy. Biochemistry. 35:10403-10410.
34. Tsuboi, M., S. Takahashi, and I. Harada. 1973. Infrared and Raman spectra of nucleic acids: vibrations in the base residues. In Physico-Chemical Properties of Nucleic Acids, Vol. 1. J. Duchesne, editor. Academic Press, New York. 92-145.
35. -1 vibration and its orientation in a biopolymer. J. Raman Spectrosc. 26:745-749.
36. Tsuboi, M., T. Ueda, K. Ushizawa, Y. Sasatake, A. Ono, M. Kainosho, and Y. Ishido. 1994. Assignments of the deoxyribose vibrations: isotopic thymidine. Bull. Chem. Soc. Jpn. 67:1483-1484.
37. Tuma, R., J. H. K. Bamford, D. H. Bamford, M. P. Russell, and G. J. Thomas, Jr. 1996a. Structure, interactions and dynamics of PRD1 virus. I. Coupling of subunit folding and capsid assembly. J. Mol. Biol. 257:87-101.
38. Tuma, R., J. H. K. Bamford, D. H. Bamford, and G. J. Thomas, Jr. 1996b. Structure, interactions and dynamics of PRD1 virus. II. Organization of the viral membrane and DNA. J. Mol. Biol. 257:102-115.
39. Tuma, R., P. E. Prevelige, and G. J. Thomas, Jr. 1996c. Structural transitions in the scaffolding and coat proteins of P22 virus during assembly and disassembly. Biochemistry. 35:4619-4627.
40. Ueda, T., K. Ushizawa, and M. Tsuboi. 1993. Depolarization of Raman scattering from some nucleotides of RNA and DNA. Biopolymers. 33:1791-1802.
41. Ueda, T., K. Ushizawa, and M. Tsuboi. 1996. Local Raman tensors of cytidine and their orientations in poly(rI) · poly(rC). J. Mol. Struct. 379:171-187.
42. Urabe, H., H. Hayashi, Y. Tominaga, Y. Nishimura, K. Kubota, and M. Tsuboi. 1985. Collective vibrational modes in molecular assembly of DNA and its application to biological systems. Low frequency Raman spectroscopy. J. Chem. Phys. 82:531-535.
43. Ushizawa, K., T. Ueda, and M. Tsuboi. 1996a. Polarized micro Raman spectroscopic studies of nucleic acid: local Raman tensors in inosine-5′-monophosphoric acid and the orientation of hypoxanthine residue in poly(rI) · poly(rC) fiber. Nucleosides Nucleotides. 15:569-584.
44. Ushizawa, K., T. Ueda, and M. Tsuboi. 1996b. Raman scattering tensors of thymidine. J. Mol. Struct. (in press).