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. 1982 Sep 25;10(18):5587–5598. doi: 10.1093/nar/10.18.5587

Stiffness of viroids and viroid-like RNA in solution.

D Riesner, J M Kaper, J W Randles
PMCID: PMC320908  PMID: 7145708

Abstract

The sedimentation coefficients of the potato spindle tuber viroid, four viroid-like RNAs from cadang-cadang-disease, circular RNA from velvet tobacco mottle virus, circular RNA from Solanum nodiflorum mottle virus and double stranded RNA5 from cucumber mosaic virus were measured in the analytical ultracentrifuge. The numbers of nucleotides of the RNA species varied between 246 and 670. The hydrodynamic models of rigid rods and flexible cylinders were applied for the interpretation of the sedimentation coefficients. Double-stranded RNA5 from cucumber mosaic virus with 335 basepairs fits the model of a rigid rod with an hydrated diameter of 29 A. Potato spindle tuber viroid and the four viroid-like RNA species of cadang-cadang-disease form a homologous series of flexible cylinders with a Kuhn's statistical length lambda-1 of 600 A. The circular RNA from the two viruses mentioned above are more flexibel than the viroids and viroid-like RNAs. The hydrodynamic interpretation is in accordance with thermodynamic data and secondary structure models. In two of the RNAs from cadang-cadang, cruciform structures would also be possible on the basis of the nucleotide sequence. The hydrodynamic data, however, favour clearly the extended structure over the cruciform.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Cohen G., Eisenberg H. Deoxyribonucleate solutions: sedimentation in a density gradient, partial specific volumes, density and refractive index increments, and preferential interactions. Biopolymers. 1968;6(8):1077–1100. doi: 10.1002/bip.1968.360060805. [DOI] [PubMed] [Google Scholar]
  2. Diaz-Ruiz J. R., Kaper J. M. Cucumber mosaic virus-associated RNA 5. III. Little nucleotide sequence homology between CARNA 5 and helper RNA. Virology. 1977 Jul 1;80(1):204–213. doi: 10.1016/0042-6822(77)90393-2. [DOI] [PubMed] [Google Scholar]
  3. Diaz-Ruiz J. R., Kaper J. M. Cucumber mosaic virus-associated RNA 5. VI. Characterization and denaturation-renaturation behavior of the double-stranded form. Biochim Biophys Acta. 1979 Sep 27;564(2):275–288. doi: 10.1016/0005-2787(79)90225-9. [DOI] [PubMed] [Google Scholar]
  4. Garcia de la Torre J. G., Bloomfield V. A. Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications. Q Rev Biophys. 1981 Feb;14(1):81–139. doi: 10.1017/s0033583500002080. [DOI] [PubMed] [Google Scholar]
  5. Gross H. J., Domdey H., Lossow C., Jank P., Raba M., Alberty H., Sänger H. L. Nucleotide sequence and secondary structure of potato spindle tuber viroid. Nature. 1978 May 18;273(5659):203–208. doi: 10.1038/273203a0. [DOI] [PubMed] [Google Scholar]
  6. Henco K., Sänger H. L., Riesner D. Fine structure melting of viroids as studied by kinetic methods. Nucleic Acids Res. 1979 Jul 11;6(9):3041–3059. doi: 10.1093/nar/6.9.3041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Kovacic R. T., van Holde K. E. Sedimentation of homogeneous double-strand DNA molecules. Biochemistry. 1977 Apr 5;16(7):1490–1498. doi: 10.1021/bi00626a038. [DOI] [PubMed] [Google Scholar]
  8. Langowski J., Henco K., Riesner D., Sänger H. L. Common structural features of different viroids: serial arrangement of double helical sections and internal loops. Nucleic Acids Res. 1978 May;5(5):1589–1610. doi: 10.1093/nar/5.5.1589. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Riesner D., Henco K., Rokohl U., Klotz G., Kleinschmidt A. K., Domdey H., Jank P., Gross H. J., Sänger H. L. Structure and structure formation of viroids. J Mol Biol. 1979 Sep 5;133(1):85–115. doi: 10.1016/0022-2836(79)90252-3. [DOI] [PubMed] [Google Scholar]
  10. Sanger H. L., Klotz G., Riesner D., Gross H. J., Kleinschmidt A. K. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc Natl Acad Sci U S A. 1976 Nov;73(11):3852–3856. doi: 10.1073/pnas.73.11.3852. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Sogo J. M., Koller T., Diener T. O. Potato spindle tuber viroid. X. Visualization and size determination by electron microscopy. Virology. 1973 Sep;55(1):70–80. doi: 10.1016/s0042-6822(73)81009-8. [DOI] [PubMed] [Google Scholar]

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