메뉴 건너뛰기




Volumn 2, Issue 1, 2009, Pages 200-214

Exhaustive enumeration of kinetic model topologies for the analysis of time-resolved RNA folding

Author keywords

.OH radical footprinting; Distributed computing; Kinetic modeling; RNA folding; Tetrahymena thermophila group I intron

Indexed keywords


EID: 79960444497     PISSN: None     EISSN: 19994893     Source Type: Journal    
DOI: 10.3390/a2010200     Document Type: Article
Times cited : (7)

References (26)
  • 1
    • 0036864241 scopus 로고    scopus 로고
    • Folding mechanisms of group i ribozymes: role of stability and contact order
    • Woodson, S.A. Folding mechanisms of group i ribozymes: role of stability and contact order. Biochem. Soc. Trans. 2002, 30, 1166-1169.
    • (2002) Biochem. Soc. Trans. , vol.30 , pp. 1166-1169
    • Woodson, S.A.1
  • 2
    • 33947725371 scopus 로고    scopus 로고
    • Local RNA structural changes induced by crystallization are revealed by shape
    • Vicens, Q.; Gooding, A.R.; Laederach, A.; Cech, T.R. Local RNA structural changes induced by crystallization are revealed by shape. RNA 2007, 13, 536-548.
    • (2007) RNA , vol.13 , pp. 536-548
    • Vicens, Q.1    Gooding, A.R.2    Laederach, A.3    Cech, T.R.4
  • 3
    • 16344371778 scopus 로고    scopus 로고
    • RNA and protein folding: common themes and variations
    • Thirumalai, D.; Hyeon, C. RNA and protein folding: common themes and variations. Biochemistry 2005, 44, 4957-4970.
    • (2005) Biochemistry , vol.44 , pp. 4957-4970
    • Thirumalai, D.1    Hyeon, C.2
  • 4
    • 28444479853 scopus 로고    scopus 로고
    • An assembly landscape for the 30s ribosomal subunit
    • Talkington, M.W.; Siuzdak, G.; Williamson, J.R. An assembly landscape for the 30s ribosomal subunit. Nature 2005, 438, 628-632.
    • (2005) Nature , vol.438 , pp. 628-632
    • Talkington, M.W.1    Siuzdak, G.2    Williamson, J.R.3
  • 5
    • 6344242969 scopus 로고    scopus 로고
    • Principles of RNA compaction: insights from the equilibrium folding pathway of the p4-p6 RNA domain in monovalent cations
    • Takamoto, K.; Das, R.; He, Q.; Doniach, S.; Brenowitz, M.; Herschlag, D.; Chance, M.R. Principles of RNA compaction: insights from the equilibrium folding pathway of the p4-p6 RNA domain in monovalent cations. J. Mol. Biol. 2004, 343, 1195-1206.
    • (2004) J. Mol. Biol. , vol.343 , pp. 1195-1206
    • Takamoto, K.1    Das, R.2    He, Q.3    Doniach, S.4    Brenowitz, M.5    Herschlag, D.6    Chance, M.R.7
  • 6
    • 0035906731 scopus 로고    scopus 로고
    • Probing the folding landscape of the tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway
    • Russell, R.; Herschlag, D. Probing the folding landscape of the tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway. J. Mol. Biol. 2001, 308, 839-851.
    • (2001) J. Mol. Biol. , vol.308 , pp. 839-851
    • Russell, R.1    Herschlag, D.2
  • 8
    • 34249850484 scopus 로고    scopus 로고
    • Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding
    • Laederach, A.; Shcherbakova, I.; Jonikas, M.A.; Altman, R. B.; Brenowitz, M. Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding. Proc. Natl. Acad. Sci. USA 2007, 104, 7045-7050.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 7045-7050
    • Laederach, A.1    Shcherbakova, I.2    Jonikas, M.A.3    Altman, R.B.4    Brenowitz, M.5
  • 9
    • 33646089899 scopus 로고    scopus 로고
    • Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule
    • Laederach, A.; Shcherbakova, I.; Liang, M.; Brenowitz, M.; Altman, R.B. Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule. J. Mol. Biol. 2006, 358, 1179-1190.
    • (2006) J. Mol. Biol. , vol.358 , pp. 1179-1190
    • Laederach, A.1    Shcherbakova, I.2    Liang, M.3    Brenowitz, M.4    Altman, R.B.5
  • 10
    • 20444478991 scopus 로고    scopus 로고
    • Riboswitches as versatile gene control elements
    • Tucker, B.J.; Breaker, R.R. Riboswitches as versatile gene control elements. Curr. Opin. Struct. Biol. 2005, 15, 342-348.
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 342-348
    • Tucker, B.J.1    Breaker, R.R.2
  • 11
    • 40849123031 scopus 로고    scopus 로고
    • High-throughput shape analysis reveals structures in hiv-1 genomic RNA strongly conserved across distinct biological states
    • Wilkinson, K.A.; Gorelick, R.J.; Vasa, S.M.; Guex, N.; Rein, A.; Mathews, D.H.; Giddings, M.C.; Weeks, K.M. High-throughput shape analysis reveals structures in hiv-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol. 2008, 6, e96.
    • (2008) PLoS Biol , vol.6
    • Wilkinson, K.A.1    Gorelick, R.J.2    Vasa, S.M.3    Guex, N.4    Rein, A.5    Mathews, D.H.6    Giddings, M.C.7    Weeks, K.M.8
  • 12
    • 16344370497 scopus 로고    scopus 로고
    • RNA shape chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in TRNA(asp) transcripts
    • Wilkinson, K.A.; Merino, E.J.; Weeks, K.M. RNA shape chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in TRNA(asp) transcripts. J. Am. Chem. Soc. 2005, 127, 4659-4667.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 4659-4667
    • Wilkinson, K.A.1    Merino, E.J.2    Weeks, K.M.3
  • 13
    • 46349099944 scopus 로고    scopus 로고
    • High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis
    • Mitra, S.; Shcherbakova, I.V.; Altman, R.B.; Brenowitz, M.; Laederach, A. High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Res. 2008, 36, e63.
    • (2008) Nucleic Acids Res , vol.36
    • Mitra, S.1    Shcherbakova, I.V.2    Altman, R.B.3    Brenowitz, M.4    Laederach, A.5
  • 14
    • 33645819791 scopus 로고    scopus 로고
    • Fast fenton footprinting: a laboratorybased method for the time-resolved analysis of DNA, RNA and proteins
    • Shcherbakova, I.; Mitra, S.; Beer, R.H.; Brenowitz, M. Fast fenton footprinting: a laboratorybased method for the time-resolved analysis of DNA, RNA and proteins. Nucleic Acids Res. 2006, 34, e48.
    • (2006) Nucleic Acids Res , vol.34
    • Shcherbakova, I.1    Mitra, S.2    Beer, R.H.3    Brenowitz, M.4
  • 15
    • 0034043484 scopus 로고    scopus 로고
    • Recent insights on RNA folding mechanisms from catalytic RNA
    • Woodson, S.A. Recent insights on RNA folding mechanisms from catalytic RNA. Cell Mol. Life Sci. 2000, 57, 796-808.
    • (2000) Cell Mol. Life Sci. , vol.57 , pp. 796-808
    • Woodson, S.A.1
  • 16
    • 0031576334 scopus 로고    scopus 로고
    • Folding of RNA involves parallel pathways
    • Pan, J.; Thirumalai, D.; Woodson, S.A. Folding of RNA involves parallel pathways. J. Mol. Biol. 1997, 273, 7-13.
    • (1997) J. Mol. Biol. , vol.273 , pp. 7-13
    • Pan, J.1    Thirumalai, D.2    Woodson, S.A.3
  • 17
    • 0035830964 scopus 로고    scopus 로고
    • Role of counterion condensation in folding of the tetrahymena ribozyme. i. equilibrium stabilization by cations
    • Heilman-Miller, S.L.; Thirumalai, D.; Woodson, S.A. Role of counterion condensation in folding of the tetrahymena ribozyme. i. equilibrium stabilization by cations. J. Mol. Biol. 2001, 306, 1157-1166.
    • (2001) J. Mol. Biol. , vol.306 , pp. 1157-1166
    • Heilman-Miller, S.L.1    Thirumalai, D.2    Woodson, S.A.3
  • 19
    • 0036816641 scopus 로고    scopus 로고
    • Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical " footprinting"
    • Brenowitz, M.; Chance, M. R.; Dhavan, G.; Takamoto, K. Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical " footprinting" . Curr. Opin. Struct. Biol. 2002, 12, 648-653.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 648-653
    • Brenowitz, M.1    Chance, M.R.2    Dhavan, G.3    Takamoto, K.4
  • 20
    • 22544466402 scopus 로고    scopus 로고
    • Protein-independent folding pathway of the 16s RRNA 5' domain
    • Adilakshmi, T.; Ramaswamy, P.; Woodson, S.A. Protein-independent folding pathway of the 16s RRNA 5' domain. J. Mol. Biol. 2005, 351, 508-519.
    • (2005) J. Mol. Biol. , vol.351 , pp. 508-519
    • Adilakshmi, T.1    Ramaswamy, P.2    Woodson, S.A.3
  • 21
    • 55249084867 scopus 로고    scopus 로고
    • Concurrent nucleation of 16s folding and induced fit in 30s ribosome assembly
    • Adilakshmi, T.; Bellur, D.L.; Woodson, S.A. Concurrent nucleation of 16s folding and induced fit in 30s ribosome assembly. Nature 2008, 455, 1268-1272.
    • (2008) Nature , vol.455 , pp. 1268-1272
    • Adilakshmi, T.1    Bellur, D.L.2    Woodson, S.A.3
  • 22
    • 0024359787 scopus 로고
    • Defining the inside and outside of a catalytic RNA molecule
    • Latham, J.A.; Cech, T.R. Defining the inside and outside of a catalytic RNA molecule. Science 1989, 245, 276-282.
    • (1989) Science , vol.245 , pp. 276-282
    • Latham, J.A.1    Cech, T.R.2
  • 23
    • 13944278373 scopus 로고    scopus 로고
    • Safa: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments
    • Das, R.; Laederach, A.; Pearlman, S.M.; Herschlag, D.; Altman, R.B. Safa: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA 2005, 11, 344-354.
    • (2005) RNA , vol.11 , pp. 344-354
    • Das, R.1    Laederach, A.2    Pearlman, S.M.3    Herschlag, D.4    Altman, R.B.5
  • 24
    • 0025367254 scopus 로고
    • Self-splicing of group i introns
    • Cech, T.R. Self-splicing of group i introns. Annu. Rev. Biochem. 1990, 59, 543-568.
    • (1990) Annu. Rev. Biochem. , vol.59 , pp. 543-568
    • Cech, T.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.