Skip to main content
PMC home page
RNA logoLink to RNA
. 1999 May;5(5):646–655. doi: 10.1017/s1355838299982195

The folding of large RNAs studied by hybridization to arrays of complementary oligonucleotides.

M Sohail 1, S Akhtar 1, E M Southern 1
PMCID: PMC1369792  PMID: 10334335

Abstract

Folding pathways of large RNAs are poorly understood. We have addressed this question by hybridizing in vitro transcripts, which varied in size, to an array of antisense oligonucleotides. All transcripts included a common sequence and all but one shared the same start-point; the other had a small deletion of the 5' end. Minimal free energy calculations predicted quite different folds for these transcripts. However, hybridization to the array showed predominant features that were shared by transcripts of all lengths, though some oligonucleotides that hybridized strongly to the short transcripts gave weak interaction with longer transcripts. A full-length RNA fragment that had been denatured by heating and allowed to cool slowly gave the same hybridization result as a shorter transcript. Taken together, these results support theories that RNA folding creates local stable states that are trapped early in the transcription or folding process. As the transcript elongates, interactions are added between regions that are transcribed early and those transcribed late. The method here described helps in identifying regions in the transcripts that take part in long-range interactions.

Full Text

The Full Text of this article is available as a PDF (1.3 MB).

Selected References

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

  1. Batey R. T., Doudna J. A. The parallel universe of RNA folding. Nat Struct Biol. 1998 May;5(5):337–340. doi: 10.1038/nsb0598-337. [DOI] [PubMed] [Google Scholar]
  2. Boyle J., Robillard G. T., Kim S. H. Sequential folding of transfer RNA. A nuclear magnetic resonance study of successively longer tRNA fragments with a common 5' end. J Mol Biol. 1980 Jun 5;139(4):601–625. doi: 10.1016/0022-2836(80)90051-0. [DOI] [PubMed] [Google Scholar]
  3. Brion P., Westhof E. Hierarchy and dynamics of RNA folding. Annu Rev Biophys Biomol Struct. 1997;26:113–137. doi: 10.1146/annurev.biophys.26.1.113. [DOI] [PubMed] [Google Scholar]
  4. Cate J. H., Gooding A. R., Podell E., Zhou K., Golden B. L., Kundrot C. E., Cech T. R., Doudna J. A. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 1996 Sep 20;273(5282):1678–1685. doi: 10.1126/science.273.5282.1678. [DOI] [PubMed] [Google Scholar]
  5. Drmanac S., Kita D., Labat I., Hauser B., Schmidt C., Burczak J. D., Drmanac R. Accurate sequencing by hybridization for DNA diagnostics and individual genomics. Nat Biotechnol. 1998 Jan;16(1):54–58. doi: 10.1038/nbt0198-54. [DOI] [PubMed] [Google Scholar]
  6. Dumas J. P., Ninio J. Efficient algorithms for folding and comparing nucleic acid sequences. Nucleic Acids Res. 1982 Jan 11;10(1):197–206. doi: 10.1093/nar/10.1.197. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Gaspin C., Westhof E. An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints. J Mol Biol. 1995 Nov 24;254(2):163–174. doi: 10.1006/jmbi.1995.0608. [DOI] [PubMed] [Google Scholar]
  8. Ho S. P., Bao Y., Lesher T., Malhotra R., Ma L. Y., Fluharty S. J., Sakai R. R. Mapping of RNA accessible sites for antisense experiments with oligonucleotide libraries. Nat Biotechnol. 1998 Jan;16(1):59–63. doi: 10.1038/nbt0198-59. [DOI] [PubMed] [Google Scholar]
  9. Kim S. H., Suddath F. L., Quigley G. J., McPherson A., Sussman J. L., Wang A. H., Seeman N. C., Rich A. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science. 1974 Aug 2;185(4149):435–440. doi: 10.1126/science.185.4149.435. [DOI] [PubMed] [Google Scholar]
  10. Konings D. A., Gutell R. R. A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs. RNA. 1995 Aug;1(6):559–574. [PMC free article] [PubMed] [Google Scholar]
  11. Kramer F. R., Mills D. R. Secondary structure formation during RNA synthesis. Nucleic Acids Res. 1981 Oct 10;9(19):5109–5124. doi: 10.1093/nar/9.19.5109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Lauber E., Guilley H., Richards K., Jonard G., Gilmer D. Conformation of the 3'-end of beet necrotic yellow vein benevirus RNA 3 analysed by chemical and enzymatic probing and mutagenesis. Nucleic Acids Res. 1997 Dec 1;25(23):4723–4729. doi: 10.1093/nar/25.23.4723. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Matson R. S., Rampal J. B., Coassin P. J. Biopolymer synthesis on polypropylene supports. I. Oligonucleotides. Anal Biochem. 1994 Mar;217(2):306–310. doi: 10.1006/abio.1994.1123. [DOI] [PubMed] [Google Scholar]
  14. Michel F., Westhof E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol. 1990 Dec 5;216(3):585–610. doi: 10.1016/0022-2836(90)90386-Z. [DOI] [PubMed] [Google Scholar]
  15. Milner N., Mir K. U., Southern E. M. Selecting effective antisense reagents on combinatorial oligonucleotide arrays. Nat Biotechnol. 1997 Jun;15(6):537–541. doi: 10.1038/nbt0697-537. [DOI] [PubMed] [Google Scholar]
  16. Moras D. A major leap toward the tertiary structure of large RNAs. RNA. 1997 Feb;3(2):111–113. [PMC free article] [PubMed] [Google Scholar]
  17. Nussinov R., Jacobson A. B. Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6309–6313. doi: 10.1073/pnas.77.11.6309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Robertus J. D., Ladner J. E., Finch J. T., Rhodes D., Brown R. S., Clark B. F., Klug A. Structure of yeast phenylalanine tRNA at 3 A resolution. Nature. 1974 Aug 16;250(467):546–551. doi: 10.1038/250546a0. [DOI] [PubMed] [Google Scholar]
  19. Schuster P., Stadler P. F., Renner A. RNA structures and folding: from conventional to new issues in structure predictions. Curr Opin Struct Biol. 1997 Apr;7(2):229–235. doi: 10.1016/s0959-440x(97)80030-9. [DOI] [PubMed] [Google Scholar]
  20. Scott W. G., Finch J. T., Klug A. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell. 1995 Jun 30;81(7):991–1002. doi: 10.1016/s0092-8674(05)80004-2. [DOI] [PubMed] [Google Scholar]
  21. Southern E. M., Case-Green S. C., Elder J. K., Johnson M., Mir K. U., Wang L., Williams J. C. Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids. Nucleic Acids Res. 1994 Apr 25;22(8):1368–1373. doi: 10.1093/nar/22.8.1368. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Tinoco I., Jr, Borer P. N., Dengler B., Levin M. D., Uhlenbeck O. C., Crothers D. M., Bralla J. Improved estimation of secondary structure in ribonucleic acids. Nat New Biol. 1973 Nov 14;246(150):40–41. doi: 10.1038/newbio246040a0. [DOI] [PubMed] [Google Scholar]
  23. Tinoco I., Jr, Kieft J. S. The ion core in RNA folding. Nat Struct Biol. 1997 Jul;4(7):509–512. doi: 10.1038/nsb0797-509. [DOI] [PubMed] [Google Scholar]
  24. Toulmé J. J., Tinévez R. L., Brossalina E. Targeting RNA structures by antisense oligonucleotides. Biochimie. 1996;78(7):663–673. doi: 10.1016/s0300-9084(96)80012-5. [DOI] [PubMed] [Google Scholar]
  25. Wodicka L., Dong H., Mittmann M., Ho M. H., Lockhart D. J. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat Biotechnol. 1997 Dec;15(13):1359–1367. doi: 10.1038/nbt1297-1359. [DOI] [PubMed] [Google Scholar]
  26. Zarrinkar P. P., Williamson J. R. Kinetic intermediates in RNA folding. Science. 1994 Aug 12;265(5174):918–924. doi: 10.1126/science.8052848. [DOI] [PubMed] [Google Scholar]
  27. Zuker M. On finding all suboptimal foldings of an RNA molecule. Science. 1989 Apr 7;244(4900):48–52. doi: 10.1126/science.2468181. [DOI] [PubMed] [Google Scholar]
  28. de Saizieu A., Certa U., Warrington J., Gray C., Keck W., Mous J. Bacterial transcript imaging by hybridization of total RNA to oligonucleotide arrays. Nat Biotechnol. 1998 Jan;16(1):45–48. doi: 10.1038/nbt0198-45. [DOI] [PubMed] [Google Scholar]

Articles from RNA are provided here courtesy of The RNA Society

RESOURCES