Raman characterization of Avocado Sunblotch viroid and its response to external perturbations and self-cleavage

BMC Biophysics

Volumn 7, Issue 1, 2014, Pages

  Hui Bon Hoa, Gaston ^a   Kaddour, Hussein ^b   Vergne, Jacques ^b   Kruglik, Sergei G ^b,c   Maurel, Marie Christine ^b  

^a INSERM   (France)

^b SORBONNE UNIVERSITÉ   (France)

^c CNRS   (France)

Author keywords

D2O perturbation; Raman spectroscopy; RNA conformation; Self cleavage activity; Temperature unfolding; Viroid

Indexed keywords

EID: 84913583784     PISSN: 20461682     EISSN: None     Source Type: Journal    
DOI: 10.1186/2046-1682-7-2     Document Type: Article

References (48)

1. Rocheleau L, Pelchat M. The subviral RNA database: a toolbox for viroids, the hepatitis delta virus and satellite RNAs research. BMC Microbiol 2006, 6:24. 10.1186/1471-2180-6-24, 1413538, 16519798.
2. Scott WG, Finch JT, Klug A. The crystal structure of an all-RNA hammerhead ribozyme - a proposed mechanism for RNA catalytic cleavage. Cell 1995, 81:991-1002. 10.1016/S0092-8674(05)80004-2, 7541315.
3. Scott WG, Murray JB, Arnold JRP, Stoddard BL, Klug A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science 1996, 274:2065-2069. 10.1126/science.274.5295.2065, 8953035.
4. Khvorova A, Lescoute A, Westhof E, Jayasena SD. Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat Struct Biol 2003, 10:708-712. 10.1038/nsb959, 12881719.
5. Kaddour H, Vergne J, Hervé G, Maurel M-C. High-pressure analysis of a hammerhead ribozyme from Chrysanthemum chlorotic mottle viroid reveals two different populations of self-cleaving molecule. FEBS J 2011, 278:3739-3747. 10.1111/j.1742-4658.2011.08291.x, 21824288.
6. Chen JH, Yajima R, Chadalavada DM, Chase E, Bevilacqua PC, Golden BL. A 1.9 angstrom crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage. Biochemistry 2010, 49:6508-6518. 10.1021/bi100670p, 20677830.
7. Daros JA, Marcos JF, Hernandez C, Flores R. Replication of avocado sunblotch viroid - evidence for a symmetrical pathway with 2 rolling circles and hammerhead ribozyme processing. Proc Natl Acad Sci U S A 1994, 91:12813-12817. 10.1073/pnas.91.26.12813, 45530, 7809126.
8. Gora-Sochacka A. Viroids: unusual small pathogenic RNAs. Acta Biochim Pol 2004, 51:587-607.
9. Hutchins CJ, Keese P, Visvader JE, Rathjen PD, McInnes JL, Symons RH. Comparison of multimeric plus and minus forms of viroids and virusoids. Plant Mol Biol 1985, 4:293-304. 10.1007/BF02418248, 24310879.
10. Wild U, Ramm K, Sanger HL, Riesner D. Loops in viroids - accessibility to transfer-RNA anticodon binding. Eur J Biochem 1980, 103:227-235. 10.1111/j.1432-1033.1980.tb04307.x, 6153976.
11. Ding B, Itaya A. Viroid: A useful model for studying the basic principles of infection and RNA biology. Mol Plant Microbe Interact 2007, 20:7-20. 10.1094/MPMI-20-0007, 17249418.
12. Chen Y, Eldho NV, Dayie TK, Carey PR. Probing adenine rings and backbone linkages using base specific isotope-edited Raman spectroscopy: application to group II intron ribozyme domain V. Biochemistry 2010, 49:3427-3435. 10.1021/bi902117w, 2863103, 20225830.
13. Ohnishi K, Ohshima M, Furuichi N. Evolution from possible primitive tRNA-viroids to early poly-tRNA-derived mRNAs: a new approach from the poly-tRNA theory. Genome Inform 2005, 16:94-103.
14. Gong B, Chen JH, Bevilacqua PC, Golden BL, Carey PR. Competition between Co(NH(3))(6)(3+) and Inner Sphere Mg(2+) Ions in the HDV Ribozyme. Biochemistry 2009, 48:11961-11970. 10.1021/bi901091v, 2795014, 19888753.
15. Wartell RM, Harrell JT. Characteristics and variations of B-type DNA conformations in solution - a quantitative analysis of Raman band intensities of 8 DNAs. Biochemistry 1986, 25:2664-2671. 10.1021/bi00357a056, 3718971.
16. Fanconi B, Tomlinso B, Nafie LA, Small W, Peticolas WL. Polarized laser Raman studies of biological polymers. J Chem Phys 1969, 51:3993-4005. 10.1063/1.1672620, 5350182.
17. Erfurth SC, Kiser EJ, Peticolas WL. Determination of backbone structure of nucleic acids and nucleic-acid oligomers by laser Raman scattering. Proc Natl Acad Sci U S A 1972, 69:938-941. 10.1073/pnas.69.4.938, 426599, 4502943.
18. Small EW, Peticolas WL. Conformational dependence of Raman scattering intensities from polynucleotides. 3. Order-disorder changes in helical structures. Biopolymers 1971, 10:1377-1416. 10.1002/bip.360100811, 5094578.
19. Small EW, Peticolas WL. Conformational dependence of Raman scattering intensities from polynucleotides. Biopolymers 1971, 10:69-88. 10.1002/bip.360100107, 5544945.
20. Thomas GJ, Hartman KA, Medeiros GC. Raman studies of nucleic acids. 6. Conformational structures of transfer RNAfMet, transfer RNAVal and transfer RNA2Phe. Biochim Biophys Acta 1972, 277:71-79. 10.1016/0005-2787(72)90353-X, 4559804.
21. Thomas GJ, Livramento J. Kinetics of hydrogen-deuterium exchange in adenosine 5′-monophosphate, adenosine 3′/5′-monophosphate, and poly(riboadenylic acid) determined by laser Raman spectroscopy. Biochemistry 1975, 14:5210-5218. 10.1021/bi00694a030, 172119.
22. Thomas GJ, Wang AHJ. Laser Raman spectroscopy of nucleic acids. Nucleic Acids Mol Biol 1988, 2:1-30.
23. Nishimura Y, Tsuboi M. Local conformations and polymorphism of DNA duplexes as revealed by their Raman spectra. Advances in Spectroscopy. Vol. 13. Spectroscopy of Biological Systems 1986, 177-232. New York: Wiley, Clark RJ, Hester AE.
24. Tsuboi M, Benevides JM, Thomas GJ. Raman Tensors and their application in structural studies of biological systems. P Jpn Acad B - Phys 2009, 85:83-97.
25. Tsuboi M, Takahashi S, Muraishi S, Kajiura T, Nishimura S. Raman spectrum of a transfer RNA. Science 1971, 174:1142-1144. 10.1126/science.174.4014.1142, 4943907.
26. Hobro AJ, Rouhi M, Blanch EW, Conn GL. Raman and Raman optical activity (ROA) analysis of RNA structural motifs in Domain I of the EMCV IRES. Nucleic Acids Res 2007, 35:1169-1177. 10.1093/nar/gkm012, 1851652, 17264119.
27. Hobro AJ, Rouhi M, Conn GL, Blanch EW. Raman and Raman optical activity (ROA) analysis of RNA structural motifs. Vib Spectrosc 2008, 48:37-43.
28. Lord RC, Thomas GJ. Raman spectral studies of nucleic acids and related molecules. I. Ribonucleic acid derivatives. Spectrochim Acta A 1967, 23:2551.
29. Aylward NN, Koenig JL. Laser excited Raman spectra of poly(cytidylic acid). Macromolecules 1970, 3:583.
30. Lafleur L, Rice J, Thomas GJ. Raman studies of nucleic acids. 7. PolyA-PolyU and PolyG-PolyC. Biopolymers 1972, 11:2423-2437. 10.1002/bip.1972.360111205, 4649726.
31. Erfurth SC, Peticolas WL. Melting and premelting phenomenon in DNA by laser Raman scattering. Biopolymers 1975, 14:247-264. 10.1002/bip.1975.360140202, 1174661.
32. Brown EB, Peticolas WL. Conformational geometry and vibrational frequencies of nucleic-acid chains. Biopolymers 1975, 14:1259-1271. 10.1002/bip.1975.360140614, 1164547.
33. Thomas GJ, Benevides JM, Prescott B. Biomolecular Stereodynamics, vol. IV 1986, 227. NY: Adenine Press Guilderland, Sarma S, Sarma A.
34. Yu NT. Ph. D. Thesis 1969, 02139 11. Cambridge, Massachussets: Department of Chemistry, MIT.
35. Benevides JM, Weiss MA, Thomas GJ. Raman studies of nucleic-acids. 41. Design of the helix-turn helix motif - nonlocal effects of quaternary structure in DNA recognition investigated by laser Raman spectroscopy. Biochemistry 1991, 30:4381-4388. 10.1021/bi00232a003, 2021630.
36. Medeiros GC, Thomas GJ. Raman studies of nucleic acids. 4. Vibrational spectra and associative interactions of aqueous inosine derivatives. Biochim Biophys Acta 1971, 247:449-462. 10.1016/0005-2787(71)90031-1, 5125629.
37. Valdemaras R. Interactions of cyclic AMP and its dibutyryl analogue with model membrane: X-ray diffraction and Raman spectroscopy study using cubic liquid-crystalline phases of monoolein. Biophys Chem 2001, 90:75-87. 10.1016/S0301-4622(01)00133-8, 11321676.
38. Weaver JL, Williams RW. Raman spectroscopic measurement of base stacking in solutions of adenosine, AMP, ATP, and oligoadenylates. Biochemistry 1988, 27:8899-8903. 10.1021/bi00425a005, 3233211.
39. Fujimoto N, Toyama A, Takeuchi H. Effects of hydrogen bonding on the UV resonance Raman bands of the adenine ring and its C8-deuterated analog. J Mol Struct 1998, 447:61-69.
40. Thomas GJ, Hartman KA. Raman studies of nucleic acids. 8. Estimation of RNA secondary structure from Raman scattering by phosphate group vibrations. Biochim Biophys Acta 1973, 312:311-322. 10.1016/0005-2787(73)90376-6, 4579230.
41. Hartman KA, McDonald-Ordzie PE, Kaper JM, Prescott B, Thomas GJJ. Studies of virus structure by laser Raman spectroscopy. 4. Turnip yellow mosaic-virus and capsids. Biochemistry 1978, 17:2118-2123. 10.1021/bi00604a015, 352393.
42. Nishimura Y, Tsuboi M, Nakano T, Higuchi S, Sato T, Shida T, Uesugi S, Ohtsuka E, Ikehara M. Raman diagnosis of nucleic-acid structure - sugar-puckering and glycosidic conformation in the guanosine moiety. Nucleic Acids Res 1983, 11:1579-1588. 10.1093/nar/11.5.1579, 325817, 6186993.
43. Hernandez B, Baumruk V, Leulliot N, Gouyette C, Huynh-Dinh T, Ghomi M. Thermodynamic and structural features of ultrastable DNA and RNA hairpins. J Mol Struct 2003, 651:67-74.
44. Razumas V, Niaura G, Talaikyte Z, Vagonis A, Nylander T. Interactions of cyclic AMP and its dibutyryl analogue with model membrane: X-ray diffraction and Raman spectroscopic study using cubic liquid-crystalline phases of monoolein. Biophys Chem 2001, 90:75-87. 10.1016/S0301-4622(01)00133-8, 11321676.
45. Daros JA, Flores R. Arabidopsis thaliana has the enzymatic machinery for replicating representative viroid species of the family Pospiviroidae. Proc Natl Acad Sci U S A 2004, 101:6792-6797. 10.1073/pnas.0401090101, 404124, 15096616.
46. Duguid J, Bloomfield VA, Benevides J, Thomas GJ. Raman spectral studies of nucleic acids. 44. Raman spectroscopy of DNA-metal complexes. 1. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd. Biophys J 1993, 65:1916-1928. 10.1016/S0006-3495(93)81263-3, 1225927, 8298021.
47. Zhelyaskov V, Yue KT. A Raman study of the binding of Fe(III) to ATP and AMP. Biochem J 1992, 287:561-566. 1133201, 1445215.
48. Tatischeff I, Larquet E, Falcón-Pérez JM, Turpin P-Y, Kruglik SG. Fast characterization of cell-derived extracellular vesicles by nanoparticles tracking analysis, cryo-electron microscopy, and Raman tweezers microspectroscopy. J Extracellular Vesicles 2012, 1:19179.