메뉴 건너뛰기




Volumn 19, Issue 12, 2013, Pages 1833-1839

Structural and thermodynamic signatures that define pseudotriloop RNA hairpins

Author keywords

Foamy virus; HBV; NMR; RNA hairpin; UV melting

Indexed keywords

RNA;

EID: 84888412455     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.039636.113     Document Type: Article
Times cited : (6)

References (31)
  • 1
    • 0029852357 scopus 로고    scopus 로고
    • Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge
    • Aboul-Ela F, Karn J, Varani G. 1996. Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge. Nucleic Acids Res 24: 3974-3981.
    • (1996) Nucleic Acids Res , vol.24 , pp. 3974-3981
    • Aboul-Ela, F.1    Karn, J.2    Varani, G.3
  • 2
    • 0030660482 scopus 로고    scopus 로고
    • Structure and dynamics of the iron responsive element RNA: Implications for binding of the RNA by iron regulatory binding proteins
    • Addess KJ, Basilion JP, Klausner RD, Rouault TA, Pardi A. 1997. Structure and dynamics of the iron responsive element RNA: Implications for binding of the RNA by iron regulatory binding proteins. J Mol Biol 274: 72-83.
    • (1997) J Mol Biol , vol.274 , pp. 72-83
    • Addess, K.J.1    Basilion, J.P.2    Klausner, R.D.3    Rouault, T.A.4    Pardi, A.5
  • 3
    • 0026593806 scopus 로고
    • Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops
    • Antao VP, Tinoco I Jr. 1992. Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucleic Acids Res 20: 819-824.
    • (1992) Nucleic Acids Res , vol.20 , pp. 819-824
    • Antao, V.P.1    Tinoco Jr., I.2
  • 4
    • 0025942059 scopus 로고
    • A thermodynamic study of unusually stable RNA and DNA hairpins
    • Antao VP, Lai SY, Tinoco I Jr. 1991. A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res 19: 5901-5905.
    • (1991) Nucleic Acids Res , vol.19 , pp. 5901-5905
    • Antao, V.P.1    Lai, S.Y.2    Tinoco Jr., I.3
  • 5
    • 67650542563 scopus 로고    scopus 로고
    • Contribution of the closing base pair to exceptional stability in RNA tetraloops: Roles for molecular mimicry and electrostatic factors
    • Blose JM, Proctor DJ, Veeraraghavan N, Misra VK, Bevilacqua PC. 2009. Contribution of the closing base pair to exceptional stability in RNA tetraloops: Roles for molecular mimicry and electrostatic factors. J Am Chem Soc 131: 8474-8484.
    • (2009) J Am Chem Soc , vol.131 , pp. 8474-8484
    • Blose, J.M.1    Proctor, D.J.2    Veeraraghavan, N.3    Misra, V.K.4    Bevilacqua, P.C.5
  • 6
    • 0027610610 scopus 로고
    • Modeling and solution structure probing of the HIV-l TAR stem-loop
    • Critchley AD, Haneef I, Cousens DJ, Stockley PG. 1993. Modeling and solution structure probing of the HIV-l TAR stem-loop. J Mol Graph 11: 92-97.
    • (1993) J Mol Graph , vol.11 , pp. 92-97
    • Critchley, A.D.1    Haneef, I.2    Cousens, D.J.3    Stockley, P.G.4
  • 7
    • 56049118219 scopus 로고    scopus 로고
    • Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis
    • Dethoff EA, Hansen AL, Musselman C, Watt ED, Andricioaei I, Al-Hashimi HM. 2008. Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis. Biophys J 95: 3906-3915.
    • (2008) Biophys J , vol.95 , pp. 3906-3915
    • Dethoff, E.A.1    Hansen, A.L.2    Musselman, C.3    Watt, E.D.4    Andricioaei, I.5    Al-Hashimi, H.M.6
  • 9
    • 0036849272 scopus 로고    scopus 로고
    • The apical stem-loop of the hepatitis B virus encapsidation signal folds into a stable tri-loop with two underlying pyrimidine bulges
    • Flodell S, Schleucher J, Cromsigt JAMTC, Ippel H, Kidd-Ljunggren K, Wijmenga SS. 2002. The apical stem-loop of the hepatitis B virus encapsidation signal folds into a stable tri-loop with two underlying pyrimidine bulges. Nucleic Acids Res 30: 4803-4811.
    • (2002) Nucleic Acids Res , vol.30 , pp. 4803-4811
    • Flodell, S.1    Schleucher, J.2    Cromsigt, J.A.M.T.C.3    Ippel, H.4    Kidd-Ljunggren, K.5    Wijmenga, S.S.6
  • 11
    • 0034033255 scopus 로고    scopus 로고
    • A conserved hairpin structure in Alfamovirus and Bromovirus subgenomic promoters is required for efficient RNA synthesis in vitro
    • Haasnoot PCJ, Brederode FT, Olsthoorn RCL, Bol JF. 2000. A conserved hairpin structure in Alfamovirus and Bromovirus subgenomic promoters is required for efficient RNA synthesis in vitro. RNA 6: 708-716.
    • (2000) RNA , vol.6 , pp. 708-716
    • Haasnoot, P.C.J.1    Brederode, F.T.2    Olsthoorn, R.C.L.3    Bol, J.F.4
  • 12
    • 0036203278 scopus 로고    scopus 로고
    • The Brome mosaic virus subgenomic promoter hairpin is structurally similar to the iron-responsive element and functionally equivalent to the minus-strand core promoter stem-loop C
    • Haasnoot PCJ, Olsthoorn RCL, Bol JF. 2002. The Brome mosaic virus subgenomic promoter hairpin is structurally similar to the iron-responsive element and functionally equivalent to the minus-strand core promoter stem-loop C. RNA 8: 110-122.
    • (2002) RNA , vol.8 , pp. 110-122
    • Haasnoot, P.C.J.1    Olsthoorn, R.C.L.2    Bol, J.F.3
  • 13
    • 0242363180 scopus 로고    scopus 로고
    • A plant virus replication system to assay the formation of RNA pseudotriloop motifs in RNA-protein interactions
    • Haasnoot PCJ, Bol JF, Olsthoorn RCL. 2003. A plant virus replication system to assay the formation of RNA pseudotriloop motifs in RNA-protein interactions. Proc Natl Acad Sci 100: 12596-12600.
    • (2003) Proc Natl Acad Sci , vol.100 , pp. 12596-12600
    • Haasnoot, P.C.J.1    Bol, J.F.2    Olsthoorn, R.C.L.3
  • 14
    • 0345731284 scopus 로고    scopus 로고
    • Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations
    • Hall KB, Williams DJ. 2004. Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations. RNA 10: 34-47.
    • (2004) RNA , vol.10 , pp. 34-47
    • Hall, K.B.1    Williams, D.J.2
  • 15
    • 48749149745 scopus 로고
    • Solvent suppression in Fourier transform nuclear magnetic resonance
    • Hore PJ. 1983. Solvent suppression in Fourier transform nuclear magnetic resonance. J Magn Reson 55: 283-300.
    • (1983) J Magn Reson , vol.55 , pp. 283-300
    • Hore, P.J.1
  • 16
    • 0027444622 scopus 로고
    • An NMR study of the HIV-1 TAR element hairpin
    • Jaeger JA, Tinoco I Jr. 1993. An NMR study of the HIV-1 TAR element hairpin. Biochemistry 32: 12522-12530.
    • (1993) Biochemistry , vol.32 , pp. 12522-12530
    • Jaeger, J.A.1    Tinoco Jr., I.2
  • 17
    • 0033744387 scopus 로고    scopus 로고
    • A potential RNA drug target in the hepatitis C virus internal ribosomal entry site
    • Klinck R, Westhof E, Walker S, Afshar M, Collier A, Aboul-ela F. 2000. A potential RNA drug target in the hepatitis C virus internal ribosomal entry site. RNA 6: 1423-1431.
    • (2000) RNA , vol.6 , pp. 1423-1431
    • Klinck, R.1    Westhof, E.2    Walker, S.3    Afshar, M.4    Collier, A.5    Aboul-ela, F.6
  • 19
    • 0037258776 scopus 로고    scopus 로고
    • The lonepair triloop: A new motif in RNA structure
    • Lee JC, Cannone JC, Gutell RR. 2003. The lonepair triloop: A new motif in RNA structure. J Mol Biol 325: 65-83.
    • (2003) J Mol Biol , vol.325 , pp. 65-83
    • Lee, J.C.1    Cannone, J.C.2    Gutell, R.R.3
  • 20
    • 0029861968 scopus 로고    scopus 로고
    • A model of the iron responsive element RNA hairpin loop structure determined from NMR and thermodynamic data
    • Liang LG, Hall KB. 1996. A model of the iron responsive element RNA hairpin loop structure determined from NMR and thermodynamic data. Biochemistry 35: 13586-13596.
    • (1996) Biochemistry , vol.35 , pp. 13586-13596
    • Liang, L.G.1    Hall, K.B.2
  • 21
    • 0033673387 scopus 로고    scopus 로고
    • Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function
    • Lukavsky PJ, Otto GA, Lancaster AM, Sarnow P, Puglisi JD. 2000. Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function. Nat Struct Biol 7: 1105-1110.
    • (2000) Nat Struct Biol , vol.7 , pp. 1105-1110
    • Lukavsky, P.J.1    Otto, G.A.2    Lancaster, A.M.3    Sarnow, P.4    Puglisi, J.D.5
  • 23
    • 33845555707 scopus 로고
    • Exchangeable proton NMR without baseline distorsion, using new strong-pulse sequences
    • Plateau P, Gueron M. 1982. Exchangeable proton NMR without baseline distorsion, using new strong-pulse sequences. J Am Chem Soc 104: 7310-7311.
    • (1982) J Am Chem Soc , vol.104 , pp. 7310-7311
    • Plateau, P.1    Gueron, M.2
  • 24
  • 25
    • 0011275745 scopus 로고
    • WATERGATE: Applications in homonuclear and heteronuclear nD NMR experiments
    • Saudek V, Piotto M, Sklenar V. 1994. WATERGATE: Applications in homonuclear and heteronuclear nD NMR experiments. Bruker Report 140: 6-9.
    • (1994) Bruker Report , vol.140 , pp. 6-9
    • Saudek, V.1    Piotto, M.2    Sklenar, V.3
  • 27
    • 0033576289 scopus 로고    scopus 로고
    • Isolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloop combinatorial library
    • Shu ZY, Bevilacqua PC. 1999. Isolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloop combinatorial library. Biochemistry 38: 15369-15379.
    • (1999) Biochemistry , vol.38 , pp. 15369-15379
    • Shu, Z.Y.1    Bevilacqua, P.C.2
  • 28
    • 0028861734 scopus 로고
    • The importance of a single G in the hairpin loop of the iron responsive element (IRE) in ferritin mRNA for structure: An NMR spectroscopy study
    • Sierzputowska H, McKenzie RA, Theil EC. 1995. The importance of a single G in the hairpin loop of the iron responsive element (IRE) in ferritin mRNA for structure: An NMR spectroscopy study. Nucleic Acids Res 23: 146-153.
    • (1995) Nucleic Acids Res , vol.23 , pp. 146-153
    • Sierzputowska, H.1    McKenzie, R.A.2    Theil, E.C.3
  • 29
    • 84859953908 scopus 로고    scopus 로고
    • The subgenomic promoter of brome mosaic virus folds into a stem-loop structure capped by a pseudo-triloop that is structurally similar to the triloop of the genomic promoter
    • Skov J, Gaudin M, Podbevsek P, Olsthoorn RCL, Petersen M. 2012. The subgenomic promoter of brome mosaic virus folds into a stem-loop structure capped by a pseudo-triloop that is structurally similar to the triloop of the genomic promoter. RNA 18: 992-1000.
    • (2012) RNA , vol.18 , pp. 992-1000
    • Skov, J.1    Gaudin, M.2    Podbevsek, P.3    Olsthoorn, R.C.L.4    Petersen, M.5
  • 30
    • 77958103511 scopus 로고    scopus 로고
    • Thermodynamic characterization of RNA triloops
    • Thulasi P, Pandya LK, Znosko BM. 2010. Thermodynamic characterization of RNA triloops. Biochemistry 49: 9058-9062.
    • (2010) Biochemistry , vol.49 , pp. 9058-9062
    • Thulasi, P.1    Pandya, L.K.2    Znosko, B.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.