Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1996 Apr 15;24(8):1460–1464. doi: 10.1093/nar/24.8.1460

The binding mode of drugs to the TAR RNA of HIV-1 studied by electric linear dichroism.

C Bailly 1, P Colson 1, C Houssier 1, F Hamy 1
PMCID: PMC145822  PMID: 8628678

Abstract

For the first time, the interaction between a series of small molecules and the TAR RNA of HIV-1 has been investigated by electric linear dichroism (ELD). The compounds tested include the DNA intercalating drugs proflavine and ethidium bromide and an amsacrine-4-carboxamide DNA-threading intercalator as well as the AT-specific DNA minor groove binders netropsin, Hoechst 33258, berenil and DAPI. In all cases except for netropsin, negative reduced dichroism signals were measured in the drug absorption band. In agreement with previous studies, the results indicate that both classical and threading intercalation can occur with the TAR RNA. The ELD data show that the mode of binding of the drugs Hoechst 33258, berenil and DAPI to the TAR RNA is similar to their binding mode in GC-rich regions of DNA and likely involves intercalation into the A-form TAR RNA helix. The wide and shallow minor groove of the TAR RNA is apparently not accessible to DNA minor groove binding drugs such as netropsin. The ELD technique appears uniquely valuable as a means of investigating the interaction of drugs with the TAR RNA.

Full Text

The Full Text of this article is available as a PDF (67.3 KB).

Selected References

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

  1. Bailly C., Colson P., Houssier C., Wang H., Bathini Y., Lown J. W. Mode of DNA binding of bis-benzimidazoles and related structures studied by electric linear dichroism. J Biomol Struct Dyn. 1994 Aug;12(1):173–181. doi: 10.1080/07391102.1994.10508095. [DOI] [PubMed] [Google Scholar]
  2. Bailly C., Colson P., Hénichart J. P., Houssier C. The different binding modes of Hoechst 33258 to DNA studied by electric linear dichroism. Nucleic Acids Res. 1993 Aug 11;21(16):3705–3709. doi: 10.1093/nar/21.16.3705. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bailly C., Denny W. A., Mellor L. E., Wakelin L. P., Waring M. J. Sequence specificity of the binding of 9-aminoacridine- and amsacrine-4-carboxamides to DNA studied by DNase I footprinting. Biochemistry. 1992 Apr 7;31(13):3514–3524. doi: 10.1021/bi00128a028. [DOI] [PubMed] [Google Scholar]
  4. Bailly C., Hénichart J. P., Colson P., Houssier C. Drug-DNA sequence-dependent interactions analysed by electric linear dichroism. J Mol Recognit. 1992 Dec;5(4):155–171. doi: 10.1002/jmr.300050406. [DOI] [PubMed] [Google Scholar]
  5. Battigello J. M., Cui M., Roshong S., Carter B. J. Enediyne-mediated cleavage of RNA. Bioorg Med Chem. 1995 Jun;3(6):839–849. doi: 10.1016/0968-0896(95)00046-j. [DOI] [PubMed] [Google Scholar]
  6. Chen L., Frankel A. D. A peptide interaction in the major groove of RNA resembles protein interactions in the minor groove of DNA. Proc Natl Acad Sci U S A. 1995 May 23;92(11):5077–5081. doi: 10.1073/pnas.92.11.5077. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Churcher M. J., Lamont C., Hamy F., Dingwall C., Green S. M., Lowe A. D., Butler J. G., Gait M. J., Karn J. High affinity binding of TAR RNA by the human immunodeficiency virus type-1 tat protein requires base-pairs in the RNA stem and amino acid residues flanking the basic region. J Mol Biol. 1993 Mar 5;230(1):90–110. doi: 10.1006/jmbi.1993.1128. [DOI] [PubMed] [Google Scholar]
  8. Colson P., Bailly C., Houssier C. Electric linear dichroism as a new tool to study sequence preference in drug binding to DNA. Biophys Chem. 1996 Jan 16;58(1-2):125–140. doi: 10.1016/0301-4622(95)00092-5. [DOI] [PubMed] [Google Scholar]
  9. Colson P., Houssier C., Bailly C. Use of electric linear dichroism and competition experiments with intercalating drugs to investigate the mode of binding of Hoechst 33258, berenil and DAPI to GC sequences. J Biomol Struct Dyn. 1995 Oct;13(2):351–366. doi: 10.1080/07391102.1995.10508845. [DOI] [PubMed] [Google Scholar]
  10. Delling U., Roy S., Sumner-Smith M., Barnett R., Reid L., Rosen C. A., Sonenberg N. The number of positively charged amino acids in the basic domain of Tat is critical for trans-activation and complex formation with TAR RNA. Proc Natl Acad Sci U S A. 1991 Jul 15;88(14):6234–6238. doi: 10.1073/pnas.88.14.6234. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Denny W. A., Wakelin L. P. Kinetic and equilibrium studies of the interaction of amsacrine and anilino ring-substituted analogues with DNA. Cancer Res. 1986 Apr;46(4 Pt 1):1717–1721. [PubMed] [Google Scholar]
  12. Dingwall C., Ernberg I., Gait M. J., Green S. M., Heaphy S., Karn J., Lowe A. D., Singh M., Skinner M. A. HIV-1 tat protein stimulates transcription by binding to a U-rich bulge in the stem of the TAR RNA structure. EMBO J. 1990 Dec;9(12):4145–4153. doi: 10.1002/j.1460-2075.1990.tb07637.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gait M. J., Karn J. RNA recognition by the human immunodeficiency virus Tat and Rev proteins. Trends Biochem Sci. 1993 Jul;18(7):255–259. doi: 10.1016/0968-0004(93)90176-n. [DOI] [PubMed] [Google Scholar]
  14. Gatti C., Houssier C., Fredericq E. Binding of ethidium bromide to ribosomal RNA. Absorption, fluorescence, circular and electric dichroism study. Biochim Biophys Acta. 1975 Oct 15;407(3):308–319. [PubMed] [Google Scholar]
  15. Hamy F., Asseline U., Grasby J., Iwai S., Pritchard C., Slim G., Butler P. J., Karn J., Gait M. J. Hydrogen-bonding contacts in the major groove are required for human immunodeficiency virus type-1 tat protein recognition of TAR RNA. J Mol Biol. 1993 Mar 5;230(1):111–123. doi: 10.1006/jmbi.1993.1129. [DOI] [PubMed] [Google Scholar]
  16. Hecht S. M. RNA degradation by bleomycin, a naturally occurring bioconjugate. Bioconjug Chem. 1994 Nov-Dec;5(6):513–526. doi: 10.1021/bc00030a006. [DOI] [PubMed] [Google Scholar]
  17. Holmes C. E., Carter B. J., Hecht S. M. Characterization of iron (II).bleomycin-mediated RNA strand scission. Biochemistry. 1993 Apr 27;32(16):4293–4307. doi: 10.1021/bi00067a019. [DOI] [PubMed] [Google Scholar]
  18. Kappen L. S., Goldberg I. H. Bulge-specific cleavage in transactivation response region RNA and its DNA analogue by neocarzinostatin chromophore. Biochemistry. 1995 May 2;34(17):5997–6002. doi: 10.1021/bi00017a029. [DOI] [PubMed] [Google Scholar]
  19. McConnaughie A. W., Spychala J., Zhao M., Boykin D., Wilson W. D. Design and synthesis of RNA-specific groove-binding cations: implications for antiviral drug design. J Med Chem. 1994 Apr 15;37(8):1063–1069. doi: 10.1021/jm00034a004. [DOI] [PubMed] [Google Scholar]
  20. Nickol J., Rau D. C. Zinc induces a bend within the transcription factor IIIA-binding region of the 5 S RNA gene. J Mol Biol. 1992 Dec 20;228(4):1115–1123. doi: 10.1016/0022-2836(92)90319-f. [DOI] [PubMed] [Google Scholar]
  21. Norden B., Kubista M., Kurucsev T. Linear dichroism spectroscopy of nucleic acids. Q Rev Biophys. 1992 Feb;25(1):51–170. doi: 10.1017/s0033583500004728. [DOI] [PubMed] [Google Scholar]
  22. Nordén B., Kurucsev T. Analysing DNA complexes by circular and linear dichroism. J Mol Recognit. 1994 Jun;7(2):141–155. doi: 10.1002/jmr.300070211. [DOI] [PubMed] [Google Scholar]
  23. Pilch D. S., Kirolos M. A., Liu X., Plum G. E., Breslauer K. J. Berenil [1,3-bis(4'-amidinophenyl)triazene] binding to DNA duplexes and to a RNA duplex: evidence for both intercalative and minor groove binding properties. Biochemistry. 1995 Aug 8;34(31):9962–9976. doi: 10.1021/bi00031a019. [DOI] [PubMed] [Google Scholar]
  24. Ratmeyer L. S., Vinayak R., Zon G., Wilson W. D. An ethidium analogue that binds with high specificity to a base-bulged duplex from the TAR RNA region of the HIV-I genome. J Med Chem. 1992 Mar 6;35(5):966–968. doi: 10.1021/jm00083a024. [DOI] [PubMed] [Google Scholar]
  25. Seeman N. C., Rosenberg J. M., Rich A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc Natl Acad Sci U S A. 1976 Mar;73(3):804–808. doi: 10.1073/pnas.73.3.804. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Tanious F. A., Veal J. M., Buczak H., Ratmeyer L. S., Wilson W. D. DAPI (4',6-diamidino-2-phenylindole) binds differently to DNA and RNA: minor-groove binding at AT sites and intercalation at AU sites. Biochemistry. 1992 Mar 31;31(12):3103–3112. doi: 10.1021/bi00127a010. [DOI] [PubMed] [Google Scholar]
  27. Vieira J., Messing J. Production of single-stranded plasmid DNA. Methods Enzymol. 1987;153:3–11. doi: 10.1016/0076-6879(87)53044-0. [DOI] [PubMed] [Google Scholar]
  28. Wada A., Kawata I., Miura K. Flow-dichroic spectra of double-stranded RNA. Biopolymers. 1971;10(7):1153–1157. doi: 10.1002/bip.360100706. [DOI] [PubMed] [Google Scholar]
  29. Wakelin L. P., Chetcuti P., Denny W. A. Kinetic and equilibrium binding studies of amsacrine-4-carboxamides: a class of asymmetrical DNA-intercalating agents which bind by threading through the DNA helix. J Med Chem. 1990 Jul;33(7):2039–2044. doi: 10.1021/jm00169a039. [DOI] [PubMed] [Google Scholar]
  30. Weeks K. M., Crothers D. M. RNA recognition by Tat-derived peptides: interaction in the major groove? Cell. 1991 Aug 9;66(3):577–588. doi: 10.1016/0092-8674(81)90020-9. [DOI] [PubMed] [Google Scholar]
  31. Wilson W. D., Ratmeyer L., Zhao M., Strekowski L., Boykin D. The search for structure-specific nucleic acid-interactive drugs: effects of compound structure on RNA versus DNA interaction strength. Biochemistry. 1993 Apr 20;32(15):4098–4104. doi: 10.1021/bi00066a035. [DOI] [PubMed] [Google Scholar]
  32. Wilson W. D., Tanious F. A., Barton H. J., Jones R. L., Fox K., Wydra R. L., Strekowski L. DNA sequence dependent binding modes of 4',6-diamidino-2-phenylindole (DAPI). Biochemistry. 1990 Sep 11;29(36):8452–8461. doi: 10.1021/bi00488a036. [DOI] [PubMed] [Google Scholar]
  33. Yao S., Wilson W. D. A molecular mechanics investigation of RNA complexes. I. Ethidium intercalation in an HIV-1 TAR RNA sequence with an unpaired adenosine. J Biomol Struct Dyn. 1992 Oct;10(2):367–387. doi: 10.1080/07391102.1992.10508653. [DOI] [PubMed] [Google Scholar]
  34. Zacharias M., Hagerman P. J. Bulge-induced bends in RNA: quantification by transient electric birefringence. J Mol Biol. 1995 Mar 31;247(3):486–500. doi: 10.1006/jmbi.1995.0155. [DOI] [PubMed] [Google Scholar]
  35. Zacharias M., Hagerman P. J. The bend in RNA created by the trans-activation response element bulge of human immunodeficiency virus is straightened by arginine and by Tat-derived peptide. Proc Natl Acad Sci U S A. 1995 Jun 20;92(13):6052–6056. doi: 10.1073/pnas.92.13.6052. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Zapp M. L., Stern S., Green M. R. Small molecules that selectively block RNA binding of HIV-1 Rev protein inhibit Rev function and viral production. Cell. 1993 Sep 24;74(6):969–978. doi: 10.1016/0092-8674(93)90720-b. [DOI] [PubMed] [Google Scholar]
  37. Zhao M., Janda L., Nguyen J., Strekowski L., Wilson W. D. The interaction of substituted 2-phenylquinoline intercalators with poly(A).poly(U): classical and threading intercalation modes with RNA. Biopolymers. 1994 Jan;34(1):61–73. doi: 10.1002/bip.360340108. [DOI] [PubMed] [Google Scholar]
  38. Zhao M., Ratmeyer L., Peloquin R. G., Yao S., Kumar A., Spychala J., Boykin D. W., Wilson W. D. Small changes in cationic substituents of diphenylfuran derivatives have major effects on the binding affinity and the binding mode with RNA helical duplexes. Bioorg Med Chem. 1995 Jun;3(6):785–794. doi: 10.1016/0968-0896(95)00057-n. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES