Abstract
Among the nucleic acids, the single-stranded RNA molecules have the highest potential to form a large variety of structures and to undergo quite different structural transitions. The determination of their structure and structural transitions is a prerequisite for understanding their function in replication, transcription, translation, and regulation. In many cases the problem of RNA structure is particularly difficult for in addition to the secondary structure formed by Watson-Crick base pairs and possibly wobble base pairs, a complicated tertiary structure exists which cannot be described by a few prototypes of interactions.
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T.O. Diener, Viroids: Structure and function, Science, 205:859 (1979).
H.J. Gross, and D. Riesner, Viroids: a class of subviral pathogens, Angew. Chem. Int. Ed. 19:231 (1980).
H.L. Sänger, Biology, structure, functions, and possible origin of viroids, in: “Encyclopaedia of Plant Physiology, New Series”, vol 14B, B. Parthier and D. Boulter, ed., Springer, Berlin, Heidelberg, New York (1981).
D. Riesner, M. Colpan, T.C. Goodman, L. Nagel, J. Schumacher, G. Steger, and H. Hofmann, Dynamics and interaction of viroids, J. Biomolec. Struct. Dynamics, 1:669 (1983).
D. Riesner and H.J. Gross, Viroids, Ann. Rev. Biochem., 54:531 (1985).
D. Riesner, K. Henco, U. Rokohl, G. Klotz, A.K. Kleinschmidt, H. Domdey, P. Jank, H.J. Gross, and H.L. Sänger, Structure and structure formation of viroids, J. Mol. Biol., 133:85 (1978).
J.M. Sogo, T. Koller, and T.O. Diener, Potato spindle tuber viroid. X. Visualization and size determination by electron microscopy, Virology, 55:70 (1973).
H.L. Sänger, G. Klotz, D. Riesner, H.J. Gross, and A.K. Kleinschmidt, Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures, Proc. Nat. Acad. Sci. USA, 73:3852 (1976).
U. Wild, K. Ramm, H.L. Sänger, and D. Riesner, Loops in viroids, Eur. J. Biochem., 103:227 (1980).
D. Riesner, J.M. Kaper, and J.W. Randies, Stiffness of viroids and viroid-like RNA in solution, Nucl. Acids Res., 10:5587 (1982).
T.C. Goodman, L. Nagel, W. Rappold, G. Klotz, and D. Riesner, Viroid replication: Equilibrium association constants and comparative activity measurements for the viroid-polymerase interaction, Nucl. Acids Res., 12:6231 (1984).
H.J. Gross, H.L. Sänger, J. Schumacher, G. Steger, and D. Riesner, Viroids: Their structure and possible origin, in: “Endocytobiology”, vol. II, H.E.A. Schenk, W. Schwemmler, ed., de Gruyter, Berlin.
R. Nussinov and I. Tinoco, Small changes in free energy assignments for unpaired bases do not affect predicted secondary structures in single stranded RNA, Nucl. Acids Res., 10:341 (1982).
G. Steger, H. Hofmann, J. Förtsch, H.J. Gross, J.W. Randies, H.L. Sänger, and D. Riesner, Conformational transitions in viroids and virusoids: Comparison of results from energy minimization algorithm and from experimental data, J. Biomolec. Struct. Dynamics, 2:543 (1984).
D. Pörschke, O. C. Uhlenbeck, and F. H. Martin, Thermodynamics and kinetics of the helix-coil transition of oligomers containing GC base pairs, Biopolymers, 12:1313 (1973).
J. Gralla and D.M. Crothers, Free energy of imperfect nucleic acid helices, J. Mol Biol., 73:497 (1973).
J. Gralla and D.M. Crothers, Free energy of imperfect nucleic acid helices. III. Small internal loops resulting from mismatches, J. Mol. Biol., 78:301 (1973).
T.R. Fink and H. Krakauer, The enthalpy of the ‘bulge’ defect of imperfect nucleic acid helices, Biopolymers, 14:433 (1975).
T.R. Fink and D.M. Crothers, Free energy of imperfect nucleic acid helices. I. The bulge effect, J. Mol. Biol. 66:1 (1972).
J.R. Fresco, L.C. Klotz, and E.G. Richards, New spectroscopic approach to the determination of helical secondary structure in ribonucleic acids, Cold Spring Harb. Symp. Quant. Biol., 28:83 (1963).
S.M. Coutts, Thermodynamics and kinetics of GC base pairing in the isolated extra arm of serine-specific tRNA from yeast, Biochem. Biophys. Acta, 232:94 (1971).
I. Tinoco, O.C. Uhlenbeck, and M.D. Levine, Estimation of secondary structure in ribonucleic acids, Nature, 230:362 (1971).
J. Langowski, K. Henco, D. Riesner, and H. L. Sänger, Common structural features of different viroids: Serial arrangement of double helical sections and internal loops, Nucl. Acids Res., 5:1589 (1978).
R. Nussinov, G. Pieczenik, J.R. Griggs, and D.J. Kleitman, Algorithms for loop matchings, SIAM J. Appl. Math., 35:68 (1978).
R. Nussinov and A. Jacobson, Fast algorithm for predicting the secondary structure of single-stranded RNA, Proc. Natl. Acad. Sci. USA, 77:6309 (1980).
M. Zuker and P. Stiegler, Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information, Nucl. Acids Res., 9:133 (1981).
K. Henco, H.L. Sänger, D. Riesner, Fine structure melting of viroids as studied by kinetic methods, Nucl. Acids Res., 6:3041 (1979).
J.W. Randies, G. Steger, and D. Riesner, Structural transitions in viroid-like RNAs associated with cadang-cadang disease, velvet tobacco mottle virus, and Solanum nodiflorum mottle virus, Nucl. Acids Res., 10:5569 (1982).
F.M. Pohl, Einfache Temperatursprung-Methode im Sekunden-bis Stundenbereich und die reversible Denaturierung von Chymotrypsin, Eur. J. Biochem., 4:373 (1968).
M. Eigen and L. DeMaeyer, Theoretical basis of relaxation spectroscopy, in “Techniques of Organic Chemistry”, Vol. VIII/2, A. Weissberger, ed., John Wiley, New York (1963).
K. Henco, G. Steger, and D. Riesner, Melting curves on less than 1μg of nucleic acid, Anal. Biochem., 101:255 (1980).
D. Riesner, M. Colpan, and J.W. Randies, A microcell for the temperature-jump technique, Anal. Biochem., 121:186 (1982).
H.J. Gross, G. Krupp, H. Domdey, M. Raba, P. Jank, Ch. Lossow, H. Alberty, K. Ramm, and H.L. Sänger, Nucleotide sequence and secondary structure of citrus exocortis and chrysanthemum stunt viroid, Eur. J. Biochem., 121:249 (1982).
P. Palukaitis and R.H. Symons, Purification and characterization of the circular form of CSV, J. Gen. Virol., 46:477 (1980).
M. Colpan, J. Schumacher, W. Brüggemann, H.L. Sänger, and D. Riesner, Large-scale purification of viroid RNA using Cs2SO4 gradient centrifugation and HPLC., Anal. Biochem., 131:257 (1983).
G. Steger, H. Müller, and D. Riesner, Helix-coil transition in double-stranded viral RNA: fine resolution melting and ionic strength dependence, Biochem. Biophys. Acta, 606:274 (1980).
K. Henco, D. Riesner, and H.L. Sänger, Conformation of viroids, Nucl. Acids Res., 4:177 (1977).
R.H. Symons, ASBV — primary sequence and proposed secondary structure, Nucl. Acids Res., 9:6527 (1981).
J. Haseloff and R.H. Symons, Comparative sequence and structure of viroid-like RNAs of two plant viruses, Nucl. Acids Res. 10:3681 (1982).
W.M. Fitch, Random sequences, J. Mol. Biol. 163:171 (1983).
M. Schnölzer, B. Haas, K. Ramm, H. Hofmann, and H.L. Sänger, Correlation between structure and pathogenicity of PSTV, subm.
H.L. Sänger, Minimal infectious agents: the viroids, in: “The Microbe, Part I, Viruses”, B.W.J. Mahy and J.R. Pathison, ed., Cambridge University Press (1984).
J. Visvader and R.H. Symons, Eleven new sequence variants of CEV and the correlation of sequence with pathogenicity, Nucl. Acids Res. 13:2907 (1985).
T.O. Diener, Are viroids escaped introns?, Proc. Natl. Acad. Sci. USA, 78:5014 (1981).
D. Riesner, G. Steger, J. Schumacher, H.J. Gross, J.W. Randies, and H.L. Sänger, Structure and Function of viroids, Biophys. Struct. Mech., 9:145 (1983).
P. Keese and R.H. Symons, Domains in viroids: evidence of intermolecular rearrangements and their contribution to viroid evolution, Proc. Natl. Acad. Sci. USA, 78:5014 (1981).
T. Meshi, M. Ishikawa, Y. Watanabe, J. Yamaya, Y. Okada, T. Sano, and E. Shikata, The sequences necessary for the infectivity of hop stunt viroid cDNA clones, Mol. Gen. Genet., 200:199 (1985).
M. Tabler and H.L. Sänger, Cloned single-and double-stranded DNA copies of PSTV RNA and co-inoculated subgenomic DNA fragments are infectious, EMBO J., 3:3055 (1984).
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Steger, G., Rosenbaum, V., Riesner, D. (1986). Viroids: Structure Formation and Function. In: van Knippenberg, P.H., Hilbers, C.W. (eds) Structure and Dynamics of RNA. NATO ASI Series, vol 110. Springer, Boston, MA. https://doi.org/10.1007/978-1-4684-5173-3_26
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DOI: https://doi.org/10.1007/978-1-4684-5173-3_26
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