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. 1998 Aug 1;26(15):3567–3571. doi: 10.1093/nar/26.15.3567

Solution studies of the dimerization initiation site of HIV-1 genomic RNA.

F Dardel 1, R Marquet 1, C Ehresmann 1, B Ehresmann 1, S Blanquet 1
PMCID: PMC147735  PMID: 9671820

Abstract

Dimerization of HIV-1 genomic RNA is an essential step of the viral cycle, initiated at a conserved stem-loop structure which forms a 'kissing complex' involving loop-loop interactions (dimerization initiation site, DIS). A 19mer RNA oligonucleotide (DIS-19) has been synthesized which forms a stable symmetrical dimer in solution at millimolar concentrations. Dimerization does not depend on addition of Mg2+. RNA ligation experiments unambiguously indicate that the formed dimer is a stable kissing complex under the NMR experimental conditions.1H NMR resonance assignments were obtained for DIS-19 at 290 K and pH 6.5. Analysis of the pattern of NOE connectivities reveals that the helix formed by loop-loop base pairing is stacked onto the two terminal stems. Non-canonical base pairs between two essential and conserved adenines are found at the junctions between the two intramolecular and the single intramolecular helices.

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Selected References

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

  1. Berkhout B., van Wamel J. L. Role of the DIS hairpin in replication of human immunodeficiency virus type 1. J Virol. 1996 Oct;70(10):6723–6732. doi: 10.1128/jvi.70.10.6723-6732.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Chang K. Y., Tinoco I., Jr Characterization of a "kissing" hairpin complex derived from the human immunodeficiency virus genome. Proc Natl Acad Sci U S A. 1994 Aug 30;91(18):8705–8709. doi: 10.1073/pnas.91.18.8705. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chang K. Y., Tinoco I., Jr The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement. J Mol Biol. 1997 May 30;269(1):52–66. doi: 10.1006/jmbi.1997.1021. [DOI] [PubMed] [Google Scholar]
  4. Clever J. L., Wong M. L., Parslow T. G. Requirements for kissing-loop-mediated dimerization of human immunodeficiency virus RNA. J Virol. 1996 Sep;70(9):5902–5908. doi: 10.1128/jvi.70.9.5902-5908.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Laughrea M., Jetté L. A 19-nucleotide sequence upstream of the 5' major splice donor is part of the dimerization domain of human immunodeficiency virus 1 genomic RNA. Biochemistry. 1994 Nov 15;33(45):13464–13474. doi: 10.1021/bi00249a035. [DOI] [PubMed] [Google Scholar]
  6. Marino J. P., Gregorian R. S., Jr, Csankovszki G., Crothers D. M. Bent helix formation between RNA hairpins with complementary loops. Science. 1995 Jun 9;268(5216):1448–1454. doi: 10.1126/science.7539549. [DOI] [PubMed] [Google Scholar]
  7. Marquet R., Paillart J. C., Skripkin E., Ehresmann C., Ehresmann B. Dimerization of human immunodeficiency virus type 1 RNA involves sequences located upstream of the splice donor site. Nucleic Acids Res. 1994 Jan 25;22(2):145–151. doi: 10.1093/nar/22.2.145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. McBride M. S., Panganiban A. T. The human immunodeficiency virus type 1 encapsidation site is a multipartite RNA element composed of functional hairpin structures. J Virol. 1996 May;70(5):2963–2973. doi: 10.1128/jvi.70.5.2963-2973.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Milligan J. F., Groebe D. R., Witherell G. W., Uhlenbeck O. C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 1987 Nov 11;15(21):8783–8798. doi: 10.1093/nar/15.21.8783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Muriaux D., Girard P. M., Bonnet-Mathonière B., Paoletti J. Dimerization of HIV-1Lai RNA at low ionic strength. An autocomplementary sequence in the 5' leader region is evidenced by an antisense oligonucleotide. J Biol Chem. 1995 Apr 7;270(14):8209–8216. doi: 10.1074/jbc.270.14.8209. [DOI] [PubMed] [Google Scholar]
  11. Paillart J. C., Berthoux L., Ottmann M., Darlix J. L., Marquet R., Ehresmann B., Ehresmann C. A dual role of the putative RNA dimerization initiation site of human immunodeficiency virus type 1 in genomic RNA packaging and proviral DNA synthesis. J Virol. 1996 Dec;70(12):8348–8354. doi: 10.1128/jvi.70.12.8348-8354.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Paillart J. C., Marquet R., Skripkin E., Ehresmann B., Ehresmann C. Mutational analysis of the bipartite dimer linkage structure of human immunodeficiency virus type 1 genomic RNA. J Biol Chem. 1994 Nov 4;269(44):27486–27493. [PubMed] [Google Scholar]
  13. Paillart J. C., Marquet R., Skripkin E., Ehresmann C., Ehresmann B. Dimerization of retroviral genomic RNAs: structural and functional implications. Biochimie. 1996;78(7):639–653. doi: 10.1016/s0300-9084(96)80010-1. [DOI] [PubMed] [Google Scholar]
  14. Paillart J. C., Skripkin E., Ehresmann B., Ehresmann C., Marquet R. A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 RNA. Proc Natl Acad Sci U S A. 1996 May 28;93(11):5572–5577. doi: 10.1073/pnas.93.11.5572. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Paillart J. C., Westhof E., Ehresmann C., Ehresmann B., Marquet R. Non-canonical interactions in a kissing loop complex: the dimerization initiation site of HIV-1 genomic RNA. J Mol Biol. 1997 Jul 4;270(1):36–49. doi: 10.1006/jmbi.1997.1096. [DOI] [PubMed] [Google Scholar]
  16. Skripkin E., Paillart J. C., Marquet R., Blumenfeld M., Ehresmann B., Ehresmann C. Mechanisms of inhibition of in vitro dimerization of HIV type I RNA by sense and antisense oligonucleotides. J Biol Chem. 1996 Nov 15;271(46):28812–28817. doi: 10.1074/jbc.271.46.28812. [DOI] [PubMed] [Google Scholar]
  17. Skripkin E., Paillart J. C., Marquet R., Ehresmann B., Ehresmann C. Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro. Proc Natl Acad Sci U S A. 1994 May 24;91(11):4945–4949. doi: 10.1073/pnas.91.11.4945. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Wallis N. G., Dardel F., Blanquet S. Heteronuclear NMR studies of the interactions of 15N-labeled methionine-specific transfer RNAs with methionyl-tRNA transformylase. Biochemistry. 1995 Jun 13;34(23):7668–7677. doi: 10.1021/bi00023a013. [DOI] [PubMed] [Google Scholar]

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