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. 1987 Sep 11;15(17):7045–7052. doi: 10.1093/nar/15.17.7045

Nucleotide sequence and secondary structure of apple scar skin viroid.

J Hashimoto 1, H Koganezawa 1
PMCID: PMC306191  PMID: 3658673

Abstract

The complete nucleotide sequence of apple scar skin viroid(ASSV) has been established, and a probable secondary structure is proposed. A single-stranded circular ASSV RNA consists of 330 nucleotides and can assume the rodlike conformation with extensive base-pairing characteristic of all the known viroids. ASSV shows low sequence homologies with other viroids and lacks the central conserved region. These indicate that ASSV should be allocated to a separate viroid group. However, homologous sequences with potato spindle tuber viroid(PSTV) in ASSV occur in limited and scattered regions of both viroids. These homologous regions fall within the particular domains in the viroid domain model which has been previously proposed by Keese and Symons(Proc. Natl. Acad. Sci. USA. 82, 4582-4586, 1985).

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Selected References

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

  1. Bodkin D. K., Knudson D. L. Assessment of sequence relatedness of double-stranded RNA genes by RNA-RNA blot hybridization. J Virol Methods. 1985 Jan;10(1):45–52. doi: 10.1016/0166-0934(85)90087-4. [DOI] [PubMed] [Google Scholar]
  2. Diener T. O. Are viroids escaped introns? Proc Natl Acad Sci U S A. 1981 Aug;78(8):5014–5015. doi: 10.1073/pnas.78.8.5014. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Diener T. O. Viroid processing: a model involving the central conserved region and hairpin I. Proc Natl Acad Sci U S A. 1986 Jan;83(1):58–62. doi: 10.1073/pnas.83.1.58. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. 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]
  5. Gross H. J., Krupp G., Domdey H., Raba M., Jank P., Lossow C., Alberty H., Ramm K., Sänger H. L. Nucleotide sequence and secondary structure of citrus exocortis and chrysanthemum stunt viroid. Eur J Biochem. 1982 Jan;121(2):249–257. doi: 10.1111/j.1432-1033.1982.tb05779.x. [DOI] [PubMed] [Google Scholar]
  6. Gubler U., Hoffman B. J. A simple and very efficient method for generating cDNA libraries. Gene. 1983 Nov;25(2-3):263–269. doi: 10.1016/0378-1119(83)90230-5. [DOI] [PubMed] [Google Scholar]
  7. Haseloff J., Symons R. H. Comparative sequence and structure of viroid-like RNAs of two plant viruses. Nucleic Acids Res. 1982 Jun 25;10(12):3681–3691. doi: 10.1093/nar/10.12.3681. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hoopes B. C., McClure W. R. Studies on the selectivity of DNA precipitation by spermine. Nucleic Acids Res. 1981 Oct 24;9(20):5493–5504. doi: 10.1093/nar/9.20.5493. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Keese P., Symons R. H. Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution. Proc Natl Acad Sci U S A. 1985 Jul;82(14):4582–4586. doi: 10.1073/pnas.82.14.4582. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Loening U. E. The fractionation of high-molecular-weight ribonucleic acid by polyacrylamide-gel electrophoresis. Biochem J. 1967 Jan;102(1):251–257. doi: 10.1042/bj1020251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Ohno T., Takamatsu N., Meshi T., Okada Y. Hop stunt viroid: molecular cloning and nucleotide sequence of the complete cDNA copy. Nucleic Acids Res. 1983 Sep 24;11(18):6185–6197. doi: 10.1093/nar/11.18.6185. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Randles J. W., Rillo E. P., Diener T. O. The viroidlike structure and cellular location of anomalous RNA associated with the cadang-cadang disease. Virology. 1976 Oct 1;74(1):128–139. doi: 10.1016/0042-6822(76)90135-5. [DOI] [PubMed] [Google Scholar]
  13. Reddy R. Compilation of small RNA sequences. Nucleic Acids Res. 1986;14 (Suppl):r61–r72. doi: 10.1093/nar/14.suppl.r61. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Riesner D., Gross H. J. Viroids. Annu Rev Biochem. 1985;54:531–564. doi: 10.1146/annurev.bi.54.070185.002531. [DOI] [PubMed] [Google Scholar]
  15. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Schumacher J., Sänger H. L., Riesner D. Subcellular localization of viroids in highly purified nuclei from tomato leaf tissue. EMBO J. 1983;2(9):1549–1555. doi: 10.1002/j.1460-2075.1983.tb01622.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Visvader J. E., Forster A. C., Symons R. H. Infectivity and in vitro mutagenesis of monomeric cDNA clones of citrus exocortis viroid indicates the site of processing of viroid precursors. Nucleic Acids Res. 1985 Aug 26;13(16):5843–5856. doi: 10.1093/nar/13.16.5843. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Zuker M., Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981 Jan 10;9(1):133–148. doi: 10.1093/nar/9.1.133. [DOI] [PMC free article] [PubMed] [Google Scholar]

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