Biophysical and atomic force microscopy characterization of the RNA from satellite tobacco mosaic virus

Nucleic Acids Research

Volumn 38, Issue 22, 2010, Pages 8284-8294

  Kuznetsov, Yuri G ^a   Dowell, Jeffrey J ^b   Gavira, José A ^b   Ng, Joseph D ^b   McPherson, Alexander ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF ALABAMA IN HUNTSVILLE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PHENOL; SATELLITE RNA; SINGLE STRANDED RNA;

AGAR GEL ELECTROPHORESIS; ARTICLE; ATOMIC FORCE MICROSCOPY; BIOPHYSICS; CIRCULAR DICHROISM; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; DEFECTIVE VIRUS; DIFFERENTIAL SCANNING CALORIMETRY; NONHUMAN; PRIORITY JOURNAL; RNA CONFORMATION; STRUCTURE ANALYSIS; VIRUS CHARACTERIZATION;

CALORIMETRY, DIFFERENTIAL SCANNING; CIRCULAR DICHROISM; ELECTROPHORESIS, AGAR GEL; MICROSCOPY, ATOMIC FORCE; NUCLEIC ACID CONFORMATION; RNA, VIRAL; TOBACCO MOSAIC SATELLITE VIRUS; VIRION;

SATELLITE TOBACCO MOSAIC VIRUS;

EID: 78650498964     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq662     Document Type: Article

References (46)

1. Francki, R.I. (1985) Plant virus satellites. Annu. Rev. Microbiol., 39, 151-174.
2. Kassanis, B. (1962) Properties and behaviour of a virus depending for its multiplication on another. J. Gen. Microbiol., 27, 477-488.
3. Pritsche, C. and Mayo, X. (1989) In Mandahar, C.L. (ed.), Plant Viruses, Vol. 1. CRC Press, Boca Raton, pp. 289-321.
4. Ban, N., Larson, S.B. and McPherson, A. (1995) Structural comparison of the plant satellite viruses. Virology, 214, 571-583.
5. Dodds, J.A. (1991) Structure and function of the genome of satellite tobacco mosaic virus. Can. J. Plant Pathol., 13, 192.
6. Valverde, R.A. and Dodds, J.A. (1986) Evidence for a satellite RNA associated naturally with the U5 strain and experimentally with the U1 strain of TMV. J. Gen. Virol., 67, 1875.
7. Valverde, R.A. and Dodds, J.A. (1987) Some properties of isometric virus particles which contain the satellite RNA of TMV. J. Gen. Virol., 68, 965.
8. Larson, S.B., Day, J., Greenwood, A. and McPherson, A. (1998) Refined structure of satellite tobacco mosaic virus at 1.8 A resolution. J. Mol. Biol., 277, 37-59.
9. Larson, S.B., Koszelak, S., Day, J., Greenwood, A., Dodds, J.A. and McPherson, A. (1993) Three-dimensional structure of satellite tobacco mosaic virus at 2.9A resolution. J. Mol. Biol., 231, 375-391. (Pubitemid 23188260)
10. Larson, S.B., Koszelak, S., Day, J., Greenwood, A., Dodds, J.A. and McPherson, A. (1993) Double-helical RNA in satellite tobacco mosaic virus. Nature, 361, 179-182.
11. Larson, S.B. and McPherson, A. (2001) Satellite tobacco mosaic virus RNA: structure and implications for assembly. Curr. Opin. Struct. Biol., 11, 59-65. (Pubitemid 32155553)
12. Fresco, J.R., Alberts, B.M. and Doty, P. (1960) Some molecular details of the secondary structure of ribonucleic acid. Nature, 188, 98-101.
13. Onoa, B. and Tinoco, I. Jr (2004) RNA folding and unfolding. Curr. Opin. Struct. Biol., 14, 374-379.
14. Spirin, B.A. (1963) Intra-organ lymphatic system of the human penis. Arkh. Anat. Gistol. Embriol., 44, 68-80.
15. Witz, J. and Stazielle, C. (eds), (1973) Viral RNAs. Marcel Dekker, New York.
16. Freddolino, P.L., Arkhipov, A.S., Larson, S.B., McPherson, A. and Schulten, K. (2006) Molecular dynamicds simulations of the complete Satellite Tobacco Mosaic Virus. Structure, 14, 1-13.
17. Zucker, M. and Stiegler, P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9, 133-148.
18. 0-end of satellite tobacco mosaic virus RNA. Nucleic Acids Res., 22, 2882-2886.
19. Dodds, J.A. (1991) Structure and function of the genome of satellite tobacco mosaic virus. Can. J. Plant Pathol., 13, 192-195.
20. Mirkov, T.E., Mathews, D.M., Du Plessis, D.H. and Dodds, J.A. (1989) Nucleotide sequence and translation of satellite tobacco mosaic virus RNA. Virology, 170, 139-146.
21. Day, J., Kuznetsov, Y.G., Larson, S.B., Greenwood, A. and McPherson, A. (2001) Biophysical studies on the RNA cores of satellite tobacco mosaic virus. Biophys. J., 80, 2364-2371. (Pubitemid 32401999)
22. Kuznetsov, Y.G., Daijogo, S., Zhou, J., Semler, B.L. and McPherson, A. (2005) Atomic force microscopy analysis of icosahedral virus RNA. J. Mol. Biol., 347, 41-52.
23. Koszelak, S., Dodds, J.A. and McPherson, A. (1989) Preliminary analysis of crystals of satellite tobacco mosaic virus. J. Mol. Biol., 209, 323-325.
24. Kuznetsov, Y.G., Larson, S.B., Day, J., Greenwood, A. and McPherson, A. (2001) Structural Transitions of STMV Particles. Virology, 284, 223-234.
25. Hayat, M.A. (2000) Principles and Techniques of Electron Microscopy: Biological Applications, 4th edn. University of Cambridge Press, Cambridge, UK.
26. Feldman, M.Y. (1967) Reaction of formaldehyde with nucleotides and ribonucleic acid. Biohim. Biophys. Acta, 149, 20-34.
27. Moller, K., Rinke, J., Ross, A., Buddle, G. and Brimacombe, R. (1977) The use of formaldehyde in RNA-protein cross linking studies with ribosomal subunits from E. coli. Eur. J. Biochem., 76, 175-187.
28. Kuznetsov, Y.G. and McPherson, A. (2006) Atomic force microscopy investigation of turnip yellow mosaic virus capsid disruption and RNA extrusion. Virology, 352, 329-337.
29. Binning, G. and Quate, C.F. (1986) Atomic force microscope. Phys. Rev. Lett., 56, 930-933.
30. Bustamante, C. and Keller, D. (1995) Scanning force microscopy in biology. Phys. Today, 48, 32-38.
31. Goldsbury, C.S., Scheuring, S. and Kreplak, L. (2009) Introduction to Atomic Force Microscopy in Biology, Vol. Curr. Protocols in Protein Science.
32. Jena, B.P. and Heinrich Horber, J.K. (eds), (2002) Atomic Force Microscopy in Cell Biology. Elsevier, Academic Press, NY.
33. Morris, V.J., Kirby, A.R. and Gunning, A.P. (2010) Atomic Force Microscopy for Biologists, 2nd edn. Imperial College Press, London.
34. Kuznetsov, Y.G., Malkin, A.J., Lucas, R.W., Plomp, M. and McPherson, A. (2001) Imaging of viruses by atomic force microscopy. J. Gen. Virol., 82, 2025-2034.
35. Kuznetsov, Y.G. and McPherson, A. (2006) Atomic force microscopy investigation of Turnip Yellow Mosaic Virus capsid disruption and RNA extrusion. Virology, 352, 329-337.
36. Kuznetsov, Y.G., Datta, S., Kothari, N.H., Greenwood, A., Fan, H. and McPherson, A. (2002) Atomic force microscopy investigation of fibroblasts infected with wild-type and mutant murine leukemia virus (MuLV). Biophys. J., 83, 3665-3674.
37. Kuznetsov, Y.G., Victoria, J., Low, G.A., Robinson, J.E.W., Fan, H. and McPherson, A. (2004) AFM Imaging of Retroviruses HIV and MuLV. SCANNING, 26, 209-216.
38. Kuznetsov, Y.G. and McPherson, A. (2006) Identification of DNA and RNA from retroviruses using ribonuclease A. Scanning, 28, 278-281.
39. Malkin, A.J., Plomp, M. and McPherson, A. (2004) In Lieberman, P.M. (ed.), Virus Structure and Imaging, DNA Viruses, Methods and Protocols. Humana Press, Totowa, New Jersey, pp. 85-108.
40. Hansma, H.G. and Hoh, J.H. (1994) Biomolecular imaging with the atomic force microscope. Annu. Rev. Biophys. Biomol. Struct., 23, 115-139.
41. Hansma, H.G. and Pietrasanta, L. (1998) Atomic force microscopy and other scanning probe microscopies. Curr. Opin. Chem. Biol., 2, 579-584.
42. Ko, T.P., Day, J., Greenwood, A. and McPherson, A. (1994) Structures of three crystal forms of the sweet protein thaumatin. Acta. Crystallogr. D. Biol. Crystallogr., 50, 813-825.
43. Kuznetsov Yu, G., Malkin, A.J. and McPherson, A. (1999) AFM studies on the mechanisms of nucleation and growth of macromolecular crystals. J. Cryst. Growth, 196, 489-502.
44. Yoffe, A.M., Prinsen, P., Gopal, A., Knobler, C.M., Gelbart, W.M. and Ben-Shul, A. (2008) Predicting the sizes of large RNA molecules. Proc. Natl Acad. Sci. USA, 105, 16153-16158.
45. McPherson, A. (2005) Micelle formation and crystallization as paradigms for virus assembly. Bioessays, 27, 447-458.
46. Devkota, B., Petrov, A.S., Lemieux, S., Boz, M.B., Tang, L., Schneemann, A., Johnson, J.E. and Harvey, S.C. (2009) Structural and electrostatic characterization of pariacoto virus: implications for viral assembly. Biopolymers, 91, 530-538.