메뉴 건너뛰기




Volumn 10, Issue 9, 2004, Pages 1459-1468

Ligand-induced changes in 2-aminopurine fluorescence as a probe for small molecule binding to HIV-1 TAR RNA

Author keywords

2 AP; Conformation; Fluorescence; HIV 1; RNA; TAR

Indexed keywords

2 AMINOPURINE; ANTIVIRUS AGENT; ARGININAMIDE; ARGININE DERIVATIVE; LIGAND; NEOMYCIN; PROTEIN INHIBITOR; TRANSACTIVATOR PROTEIN; UNCLASSIFIED DRUG; VIRUS PROTEIN; VIRUS RNA;

EID: 4344579386     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.7620304     Document Type: Article
Times cited : (70)

References (48)
  • 1
    • 0028864394 scopus 로고
    • The structure of the Human-Immunodeficiency-Virus Type-1 TAR RNA reveals principles of RNA recognition by Tat protein
    • Aboulela, F., Karn, J., and Varani, G. 1995. The structure of the Human-Immunodeficiency-Virus Type-1 TAR RNA reveals principles of RNA recognition by Tat protein. J. Mol. Biol. 253: 313-332.
    • (1995) J. Mol. Biol. , vol.253 , pp. 313-332
    • Aboulela, F.1    Karn, J.2    Varani, G.3
  • 2
    • 0033926729 scopus 로고    scopus 로고
    • Use of the fluorescent nucleoside analogue benzo[g]quinazoline 2′-O-methyl-beta-D-ribofuranoside to monitor the binding of the HIV-1 Tat protein or of antisense oligonucleotides to the TAR RNA stem-loop
    • Arzumanov, A., Godde, F., Moreau, S., Toulme, J.J., Weeds, A., and Gait, M.J. 2000. Use of the fluorescent nucleoside analogue benzo[g]quinazoline 2′-O-methyl-beta-D-ribofuranoside to monitor the binding of the HIV-1 Tat protein or of antisense oligonucleotides to the TAR RNA stem-loop. Helv. Chim. Acta 83: 1424-1436.
    • (2000) Helv. Chim. Acta , vol.83 , pp. 1424-1436
    • Arzumanov, A.1    Godde, F.2    Moreau, S.3    Toulme, J.J.4    Weeds, A.5    Gait, M.J.6
  • 4
    • 0345733992 scopus 로고    scopus 로고
    • Differential modes of recognition in N peptide-boxB complexes
    • Austin, R.J., Xia, T.B., Ren, J.S., Takahashi, T.T., and Roberts, R.W. 2003. Differential modes of recognition in N peptide-boxB complexes. Biochemistry 42: 14957-14967.
    • (2003) Biochemistry , vol.42 , pp. 14957-14967
    • Austin, R.J.1    Xia, T.B.2    Ren, J.S.3    Takahashi, T.T.4    Roberts, R.W.5
  • 5
    • 0242592065 scopus 로고    scopus 로고
    • Achieving specificity in selected and wild-type N peptide-RNA complexes: The importance of discrimination against noncognate RNA targets
    • Barrick, J.E. and Roberts, R.W. 2003. Achieving specificity in selected and wild-type N peptide-RNA complexes: The importance of discrimination against noncognate RNA targets. Biochemistry 42: 12998-13007.
    • (2003) Biochemistry , vol.42 , pp. 12998-13007
    • Barrick, J.E.1    Roberts, R.W.2
  • 6
    • 0141905902 scopus 로고    scopus 로고
    • Using pyrene-labeled HIV-1 TAR to measure RNA-small molecule binding
    • Blount, K.F. and Tor, Y. 2003. Using pyrene-labeled HIV-1 TAR to measure RNA-small molecule binding. Nucleic Acids Res. 31: 5490-5500.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 5490-5500
    • Blount, K.F.1    Tor, Y.2
  • 7
    • 0026035854 scopus 로고
    • Analysis of arginine-rich peptides from the HIV Tat Protein reveals unusual features of RNA protein recognition
    • Calnan, B.J., Biancalana, S., Hudson, D., and Frankel, A.D. 1991a. Analysis of arginine-rich peptides from the HIV Tat Protein reveals unusual features of RNA protein recognition. Genes & Dev. 5: 201-210.
    • (1991) Genes & Dev. , vol.5 , pp. 201-210
    • Calnan, B.J.1    Biancalana, S.2    Hudson, D.3    Frankel, A.D.4
  • 9
    • 0027452957 scopus 로고
    • 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
    • Churcher, M.J., Lamont, C., Hamy, F., Dingwall, C., Green, S.M., Lowe, A.D., Butler, P.J.G., Gait, M.J., and Karn, J. 1993. 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. 230: 90-110.
    • (1993) J. Mol. Biol. , vol.230 , pp. 90-110
    • Churcher, M.J.1    Lamont, C.2    Hamy, F.3    Dingwall, C.4    Green, S.M.5    Lowe, A.D.6    Butler, P.J.G.7    Gait, M.J.8    Karn, J.9
  • 11
    • 0038047131 scopus 로고    scopus 로고
    • Proflavine acts as a Rev inhibitor by targeting the high-affinity Rev binding site of the Rev responsive element of HIV-1
    • Dejong, E.S., Chang, C.-e., Gilson, M.K., and Marino, J.P. 2003. Proflavine acts as a Rev inhibitor by targeting the high-affinity Rev binding site of the Rev responsive element of HIV-1. Biochemistry 42: 8035-8046.
    • (2003) Biochemistry , vol.42 , pp. 8035-8046
    • Dejong, E.S.1    Chang, C.-E.2    Gilson, M.K.3    Marino, J.P.4
  • 12
    • 4344656803 scopus 로고    scopus 로고
    • Inhibitors of the Tat-TAR interactions
    • (eds. M. Demeunynck et al.). Wiley-VCH, Darmstadt, Germany
    • Dinesh, C.U. and Rana, T.M. 2003. Inhibitors of the Tat-TAR interactions. In Small molecule DNA and RNA binders (eds. M. Demeunynck et al.), pp. 58-87. Wiley-VCH, Darmstadt, Germany.
    • (2003) Small Molecule DNA and RNA Binders , pp. 58-87
    • Dinesh, C.U.1    Rana, T.M.2
  • 13
    • 0035986695 scopus 로고    scopus 로고
    • Structure of TAR RNA complexed with a Tat-TAR interaction nanomolar inhibitor that was identified by computational screening
    • Du, Z.H., Lind, K.E., and James, T.L. 2002. Structure of TAR RNA complexed with a Tat-TAR interaction nanomolar inhibitor that was identified by computational screening. Chem. Biol. 9: 707-712.
    • (2002) Chem. Biol. , vol.9 , pp. 707-712
    • Du, Z.H.1    Lind, K.E.2    James, T.L.3
  • 14
    • 0034617166 scopus 로고    scopus 로고
    • Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B
    • Faber, C., Sticht, H., Schweimer, K., and Rosch, P. 2000. Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B. J. Biol. Chem. 275: 20660-20666.
    • (2000) J. Biol. Chem. , vol.275 , pp. 20660-20666
    • Faber, C.1    Sticht, H.2    Schweimer, K.3    Rosch, P.4
  • 15
    • 0032973905 scopus 로고    scopus 로고
    • Molecular basis of HIV-1 TAR RNA specific recognition by an acridine tat-antagonist
    • Gelus, N., Hamy, F., and Bailly, C. 1999. Molecular basis of HIV-1 TAR RNA specific recognition by an acridine tat-antagonist. Bioorg. Med. Chem. 7: 1075-1079.
    • (1999) Bioorg. Med. Chem. , vol.7 , pp. 1075-1079
    • Gelus, N.1    Hamy, F.2    Bailly, C.3
  • 18
    • 0029893132 scopus 로고    scopus 로고
    • A critical role for the TAR element in promoting efficient human immunodeficiency virus type 1 reverse transcription
    • Harrich, D., Ulich, C., and Gaynor, R.B. 1996. A critical role for the TAR element in promoting efficient human immunodeficiency virus type 1 reverse transcription. J. Virol. 70: 4017-4027.
    • (1996) J. Virol. , vol.70 , pp. 4017-4027
    • Harrich, D.1    Ulich, C.2    Gaynor, R.B.3
  • 19
    • 0030957531 scopus 로고    scopus 로고
    • Tat is required for efficient HIV-1 reverse transcription
    • Harrich, D., Ulich, C., GarciaMartinez, L.F., and Gaynor, R.B. 1997. Tat is required for efficient HIV-1 reverse transcription. EMBO J. 16: 1224-1235.
    • (1997) EMBO J. , vol.16 , pp. 1224-1235
    • Harrich, D.1    Ulich, C.2    GarciaMartinez, L.F.3    Gaynor, R.B.4
  • 20
    • 0037044320 scopus 로고    scopus 로고
    • Local conformational changes in the catalytic core of the trans-acting hepatitis delta virus ribozyme accompany catalysis
    • Harris, D.A., Rueda, D., and Walter, N.G. 2002. Local conformational changes in the catalytic core of the trans-acting hepatitis delta virus ribozyme accompany catalysis. Biochemistry 41: 12051-12061.
    • (2002) Biochemistry , vol.41 , pp. 12051-12061
    • Harris, D.A.1    Rueda, D.2    Walter, N.G.3
  • 21
    • 0141866666 scopus 로고    scopus 로고
    • Discovery of a small molecule Tat-trans-activation-responsive RNA antagonist that potently inhibits human immunodeficiency virus-1 replication
    • Hwang, S., Tamilarasu, N., Kibler, K., Cao, H., Ali, A., Ping, Y.H., Jeang, K.T., and Rana, T.M. 2003. Discovery of a small molecule Tat-trans-activation-responsive RNA antagonist that potently inhibits human immunodeficiency virus-1 replication. J. Biol. Chem. 278: 39092-39103.
    • (2003) J. Biol. Chem. , vol.278 , pp. 39092-39103
    • Hwang, S.1    Tamilarasu, N.2    Kibler, K.3    Cao, H.4    Ali, A.5    Ping, Y.H.6    Jeang, K.T.7    Rana, T.M.8
  • 22
    • 0038001437 scopus 로고    scopus 로고
    • Trans-acting hepatitis delta virus ribozyme: Catalytic core and global structure are dependent on the 5′ substrate sequence
    • Jeong, S., Sefcikova, J., Tinsley, R.A., Rueda, D., and Walter, N.G. 2003. Trans-acting hepatitis delta virus ribozyme: Catalytic core and global structure are dependent on the 5′ substrate sequence. Biochemistry 42: 7727-7740.
    • (2003) Biochemistry , vol.42 , pp. 7727-7740
    • Jeong, S.1    Sefcikova, J.2    Tinsley, R.A.3    Rueda, D.4    Walter, N.G.5
  • 23
    • 1642347123 scopus 로고    scopus 로고
    • Fluorescence-based approach for detecting and characterizing antibiotic-induced conformational changes in ribosomal RNA: Comparing aminoglycoside binding to prokaryotic and eukaryotic ribosomal RNA sequences
    • Kaul, M., Barbieri, C.M., and Pilch, D.S. 2004. Fluorescence-based approach for detecting and characterizing antibiotic-induced conformational changes in ribosomal RNA: Comparing aminoglycoside binding to prokaryotic and eukaryotic ribosomal RNA sequences. J. Am. Chem. Soc. 126: 3447-3453.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 3447-3453
    • Kaul, M.1    Barbieri, C.M.2    Pilch, D.S.3
  • 24
    • 0034847595 scopus 로고    scopus 로고
    • 2-Aminopurine as a real-time probe of enzymatic cleavage and inhibition of hammer-head ribozymes
    • Kirk, S.R., Luedtke, N.W., and Tor, Y. 2001. 2-aminopurine as a real-time probe of enzymatic cleavage and inhibition of hammer-head ribozymes. Bioorg. Med. Chem. 9: 2295-2301.
    • (2001) Bioorg. Med. Chem. , vol.9 , pp. 2295-2301
    • Kirk, S.R.1    Luedtke, N.W.2    Tor, Y.3
  • 25
    • 0034674040 scopus 로고    scopus 로고
    • Mechanism of Neomycin and Rev peptide binding to the Rev responsive element of HIV-1 as determined by fluorescence and NMR spectroscopy
    • Lacourciere, K.A., Stivers, J.T., and Marino, J.P. 2000. Mechanism of Neomycin and Rev peptide binding to the Rev responsive element of HIV-1 as determined by fluorescence and NMR spectroscopy. Biochemistry 39: 5630-5641.
    • (2000) Biochemistry , vol.39 , pp. 5630-5641
    • Lacourciere, K.A.1    Stivers, J.T.2    Marino, J.P.3
  • 26
    • 0036008846 scopus 로고    scopus 로고
    • Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA
    • Lind, K.E., Du, Z.H., Fujinaga, K., Peterlin, B.M., and James, T.L. 2002. Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA. Chem. Biol. 9: 185-193.
    • (2002) Chem. Biol. , vol.9 , pp. 185-193
    • Lind, K.E.1    Du, Z.H.2    Fujinaga, K.3    Peterlin, B.M.4    James, T.L.5
  • 27
    • 0035951091 scopus 로고    scopus 로고
    • Neomycin B-arginine conjugate, a novel HIV-1 Tat antagonist: Synthesis and anti-HIV activities
    • Litovchick, A., Lapidot, A., Eisenstein, M., Kalinkovich, A., and Borkow, G. 2001. Neomycin B-arginine conjugate, a novel HIV-1 Tat antagonist: Synthesis and anti-HIV activities. Biochemistry 40: 15612-15623.
    • (2001) Biochemistry , vol.40 , pp. 15612-15623
    • Litovchick, A.1    Lapidot, A.2    Eisenstein, M.3    Kalinkovich, A.4    Borkow, G.5
  • 28
    • 0033520106 scopus 로고    scopus 로고
    • Characterization of the solution conformations of unbound and Tat peptide-bound forms of HIV-1 TAR RNA
    • Long, K.S. and Crothers, D.M. 1999. Characterization of the solution conformations of unbound and Tat peptide-bound forms of HIV-1 TAR RNA. Biochemistry 38: 10059-10069.
    • (1999) Biochemistry , vol.38 , pp. 10059-10069
    • Long, K.S.1    Crothers, D.M.2
  • 29
    • 0034718520 scopus 로고    scopus 로고
    • Inhibition of Tat-mediated transactivation of HIV-1 LTR transcription by polyamide nucleic acid targeted to TAR hairpin element
    • Mayhood, T., Kaushik, N., Pandey, P.K., Kashanchi, F., Deng, L.W., and Pandey, V.N. 2000. Inhibition of Tat-mediated transactivation of HIV-1 LTR transcription by polyamide nucleic acid targeted to TAR hairpin element. Biochemistry 39: 11532-11539.
    • (2000) Biochemistry , vol.39 , pp. 11532-11539
    • Mayhood, T.1    Kaushik, N.2    Pandey, P.K.3    Kashanchi, F.4    Deng, L.W.5    Pandey, V.N.6
  • 32
    • 0032491152 scopus 로고    scopus 로고
    • Inhibitors of protein-RNA complexation that target the RNA: Specific recognition of human immunodeficiency virus type 1 TAR RNA by small organic molecules
    • Mei, H.Y., Cui, M., Heldsinger, A., Lemrow, S.M., Loo, J.A., Sannes-Lowery, K.A., Sharmeen, L., and Czarnik, A.W. 1998. Inhibitors of protein-RNA complexation that target the RNA: Specific recognition of human immunodeficiency virus type 1 TAR RNA by small organic molecules. Biochemistry 37: 14204-14212.
    • (1998) Biochemistry , vol.37 , pp. 14204-14212
    • Mei, H.Y.1    Cui, M.2    Heldsinger, A.3    Lemrow, S.M.4    Loo, J.A.5    Sannes-Lowery, K.A.6    Sharmeen, L.7    Czarnik, A.W.8
  • 33
    • 0033553127 scopus 로고    scopus 로고
    • Oligonucleotide inhibition of the interaction of HIV-1 Tat protein with the trans-activation responsive region (TAR) of HIV RNA
    • Mestre, B., Arzumanov, A., Singh, M., Boulme, F., Litvak, S., and Gait, M.J. 1999. Oligonucleotide inhibition of the interaction of HIV-1 Tat protein with the trans-activation responsive region (TAR) of HIV RNA. Biochim. Biophys. Acta 1445: 86-98.
    • (1999) Biochim. Biophys. Acta , vol.1445 , pp. 86-98
    • Mestre, B.1    Arzumanov, A.2    Singh, M.3    Boulme, F.4    Litvak, S.5    Gait, M.J.6
  • 35
    • 0036051817 scopus 로고    scopus 로고
    • HIV-1 regulatory proteins: Targets for novel drug development
    • Ptak, R.G. 2002. HIV-1 regulatory proteins: Targets for novel drug development. Expert Opin. Investigat. Drugs 11: 1099-1115.
    • (2002) Expert Opin. Investigat. Drugs , vol.11 , pp. 1099-1115
    • Ptak, R.G.1
  • 36
    • 0026651395 scopus 로고
    • Conformation of the TAR RNA-arginine complex by NMR spectroscopy
    • Puglisi, J.D., Tan, R., Calnan, B.J., Frankel, A.D., and Williamson, J.R. 1992. Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science 257: 76-80.
    • (1992) Science , vol.257 , pp. 76-80
    • Puglisi, J.D.1    Tan, R.2    Calnan, B.J.3    Frankel, A.D.4    Williamson, J.R.5
  • 37
    • 0036308302 scopus 로고    scopus 로고
    • Fluorescent nucleotide base analogs as probes of nucleic acid structure, dynamics and interactions
    • Rist, M. and Marino, J.P. 2001. Fluorescent nucleotide base analogs as probes of nucleic acid structure, dynamics and interactions. Curr. Org. Chem. 6: 775-793.
    • (2001) Curr. Org. Chem. , vol.6 , pp. 775-793
    • Rist, M.1    Marino, J.P.2
  • 38
    • 0037126724 scopus 로고    scopus 로고
    • Mechanism of nucleocapsid protein catalyzed structural isomerization of the dimerization initiation site of HIV-1
    • -. 2002. Mechanism of nucleocapsid protein catalyzed structural isomerization of the dimerization initiation site of HIV-1. Biochemistry 41: 14762-14770.
    • (2002) Biochemistry , vol.41 , pp. 14762-14770
  • 39
    • 0033590014 scopus 로고    scopus 로고
    • Studying aminoglycoside antibiotic binding to HIV-1 TAR RNA by electrospray ionization mass spectrometry
    • Sannes-Lowery, K.A., Mei, H.Y., and Loo, J.A. 1999. Studying aminoglycoside antibiotic binding to HIV-1 TAR RNA by electrospray ionization mass spectrometry. Int. J. Mass Spect. 193: 115-122.
    • (1999) Int. J. Mass Spect. , vol.193 , pp. 115-122
    • Sannes-Lowery, K.A.1    Mei, H.Y.2    Loo, J.A.3
  • 40
    • 0016160429 scopus 로고
    • Measurement of protein by spectrophotometry at 205 nm
    • Scopes, R.K. 1974. Measurement of protein by spectrophotometry at 205 nm. Anal. Biochem. 59: 277-282.
    • (1974) Anal. Biochem. , vol.59 , pp. 277-282
    • Scopes, R.K.1
  • 41
  • 42
    • 0034192495 scopus 로고    scopus 로고
    • Design, synthesis, and biological activity of a cyclic peptide: An inhibitor of HIV-1 Tat-TAR interactions in human cells
    • Tamilarasu, N., Huq, I., and Rana, T.M. 2000. Design, synthesis, and biological activity of a cyclic peptide: An inhibitor of HIV-1 Tat-TAR interactions in human cells. Bioorg. Med. Chem. Letts. 10: 971-974.
    • (2000) Bioorg. Med. Chem. Letts , vol.10 , pp. 971-974
    • Tamilarasu, N.1    Huq, I.2    Rana, T.M.3
  • 43
    • 0026589545 scopus 로고
    • Specific binding of arginine to TAR RNA
    • Tao, J.S. and Frankel, A.D. 1992. Specific binding of arginine to TAR RNA. Proc. Natl. Acad. Sci. 89: 2723-2726.
    • (1992) Proc. Natl. Acad. Sci. , vol.89 , pp. 2723-2726
    • Tao, J.S.1    Frankel, A.D.2
  • 44
    • 0142011647 scopus 로고    scopus 로고
    • Targeting RNA with small molecules
    • Tor, Y. 2003. Targeting RNA with small molecules. Chembiochem 4: 998-1007.
    • (2003) Chembiochem , vol.4 , pp. 998-1007
    • Tor, Y.1
  • 45
    • 0032554635 scopus 로고    scopus 로고
    • Binding of neomycin to the TAR element of HIV-1 RNA induces dissociation of Tat protein by an allosteric mechanism
    • Wang, S., Huber, P.W., Cui, M., Czarnik, A.W., and Mei, H.Y. 1998. Binding of neomycin to the TAR element of HIV-1 RNA induces dissociation of Tat protein by an allosteric mechanism. Biochemistry 37: 5549-5557.
    • (1998) Biochemistry , vol.37 , pp. 5549-5557
    • Wang, S.1    Huber, P.W.2    Cui, M.3    Czarnik, A.W.4    Mei, H.Y.5
  • 46
    • 0025996720 scopus 로고
    • RNA recognition by Tat-derived peptides: Interaction in the major groove?
    • Weeks, K.M. and Crothers, D.M. 1991. RNA recognition by Tat-derived peptides: Interaction in the major groove? Cell 66: 577-588.
    • (1991) Cell , vol.66 , pp. 577-588
    • Weeks, K.M.1    Crothers, D.M.2
  • 47
    • 0026497842 scopus 로고
    • RNA binding assays for Tat-derived peptides: Implications for specificity
    • -. 1992. RNA binding assays for Tat-derived peptides: Implications for specificity. Biochemistry 31: 10281-10287.
    • (1992) Biochemistry , vol.31 , pp. 10281-10287
  • 48
    • 0025168740 scopus 로고
    • Fragments of the HIV-1 Tat protein specifically bind TAR RNA
    • Weeks, K.M., Ampe, C., Schultz, S.C., Steitz, T.A., and Crothers, D.M. 1990. Fragments of the HIV-1 Tat protein specifically bind TAR RNA. Science 249: 1281-1285.
    • (1990) Science , vol.249 , pp. 1281-1285
    • Weeks, K.M.1    Ampe, C.2    Schultz, S.C.3    Steitz, T.A.4    Crothers, D.M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.