메뉴 건너뛰기




Volumn 16, Issue 6, 2010, Pages 1108-1117

Evaluation of the information content of RNA structure mapping data for secondary structure prediction

Author keywords

Chemical mapping; DMS; Footprinting; RNA structure; Secondary structure

Indexed keywords

MAGNESIUM CHLORIDE; RIBONUCLEASE T1;

EID: 77952733078     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1988510     Document Type: Article
Times cited : (50)

References (49)
  • 1
    • 33646841501 scopus 로고    scopus 로고
    • Hydroxyl radical footprinting in vivo: Mapping macromolecular structures with synchrotron radiation
    • doi: 10.1093/nar/gkl1291
    • Adilakshmi T, Lease RA, Woodson SA. 2006. Hydroxyl radical footprinting in vivo: Mapping macromolecular structures with synchrotron radiation. Nucleic Acids Res 34: e64. doi: 10.1093/nar/gkl1291.
    • (2006) Nucleic Acids Res , vol.34
    • Adilakshmi, T.1    Lease, R.A.2    Woodson, S.A.3
  • 2
    • 0242500997 scopus 로고    scopus 로고
    • Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA
    • Bartley LE, Zhuang X, Das R, Chu S, Herschlag D. 2003. Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA. J Mol Biol 328: 1011-1026.
    • (2003) J Mol Biol , vol.328 , pp. 1011-1026
    • Bartley, L.E.1    Zhuang, X.2    Das, R.3    Chu, S.4    Herschlag, D.5
  • 4
    • 33644853766 scopus 로고    scopus 로고
    • Local RNA base pairing probabilities in large sequences
    • Bernhart SH, Hofacker IL, Stadler PF. 2006. Local RNA base pairing probabilities in large sequences. Bioinformatics 22: 614-615.
    • (2006) Bioinformatics , vol.22 , pp. 614-615
    • Bernhart, S.H.1    Hofacker, I.L.2    Stadler, P.F.3
  • 5
    • 0033654522 scopus 로고    scopus 로고
    • Probing RNA structure and RNA-ligand complexes with chemical probes
    • Brunel C, Romby P. 2000. Probing RNA structure and RNA-ligand complexes with chemical probes. Methods Enzymol 318: 3-21.
    • (2000) Methods Enzymol , vol.318 , pp. 3-21
    • Brunel, C.1    Romby, P.2
  • 6
    • 2942571539 scopus 로고    scopus 로고
    • The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
    • doi: 10.1186/1471-2105-3-2
    • Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Muller KM, et al. 2002. The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3: 2. doi: 10.1186/1471-2105-3-2.
    • (2002) BMC Bioinformatics , vol.3 , pp. 2
    • Cannone, J.J.1    Subramanian, S.2    Schnare, M.N.3    Collett, J.R.4    D'Souza, L.M.5    Du, Y.6    Feng, B.7    Lin, N.8    Madabusi, L.V.9    Muller, K.M.10
  • 8
    • 0030303844 scopus 로고    scopus 로고
    • An interior trust region approach for nonlinear minimization subject to bounds
    • Coleman TF, Li Y. 1996. An interior, trust region approach for nonlinear minimization subject to bounds. SIAM J Optim 6: 418-445.
    • (1996) SIAM J Optim , vol.6 , pp. 418-445
    • Coleman, T.F.1    Li, Y.2
  • 9
    • 67650727366 scopus 로고    scopus 로고
    • VARNA: Interactive drawing and editing of the RNA secondary structure
    • Darty K, Denise A, Ponty Y. 2009. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 25: 1974-1975.
    • (2009) Bioinformatics , vol.25 , pp. 1974-1975
    • Darty, K.1    Denise, A.2    Ponty, Y.3
  • 10
    • 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 SM, Herschlag D, Altman RB. 2005. SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA 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
  • 12
    • 3242877996 scopus 로고    scopus 로고
    • Sfold web server for statistical folding and rational design of nucleic acids
    • Ding Y, Chan CY, Lawrence CE. 2004. Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res 32: W135-W141.
    • (2004) Nucleic Acids Res , vol.32
    • Ding, Y.1    Chan, C.Y.2    Lawrence, C.E.3
  • 13
    • 23644448438 scopus 로고    scopus 로고
    • RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble
    • Ding Y, Chan CY, Lawrence CE. 2005. RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA 11: 1157-1166.
    • (2005) RNA , vol.11 , pp. 1157-1166
    • Ding, Y.1    Chan, C.Y.2    Lawrence, C.E.3
  • 14
    • 0032712864 scopus 로고    scopus 로고
    • DNA sequencing by capillary electrophoresis (review)
    • Dolnik V. 1999. DNA sequencing by capillary electrophoresis (review). J Biochem Biophys Methods 41: 103-119.
    • (1999) J Biochem Biophys Methods , vol.41 , pp. 103-119
    • Dolnik, V.1
  • 15
  • 17
    • 11444263264 scopus 로고    scopus 로고
    • Crystal structure of a phage Twort group I ribozyme-product complex
    • Golden BL, Kim H, Chase E. 2005. Crystal structure of a phage Twort group I ribozyme-product complex. Nat Struct Mol Biol 12: 82-89.
    • (2005) Nat Struct Mol Biol , vol.12 , pp. 82-89
    • Golden, B.L.1    Kim, H.2    Chase, E.3
  • 18
    • 77952717003 scopus 로고    scopus 로고
    • References to commonly used techniques
    • ed. SL Beaucage et al., Appendix 3A. Wiley, New York
    • Harkins EW. 2001. References to commonly used techniques. In Current protocols in nucleic acid chemistry (ed. SL Beaucage et al.), Appendix 3A. Wiley, New York.
    • (2001) Current Protocols in Nucleic Acid Chemistry
    • Harkins, E.W.1
  • 19
    • 48749083055 scopus 로고    scopus 로고
    • NMR-assisted prediction of RNA secondary structure Identification of a probable pseudoknot in the coding region of an R2 retrotransposon
    • Hart JM, Kennedy SD, Mathews DH, Turner DH. 2008. NMR-assisted prediction of RNA secondary structure: Identification of a probable pseudoknot in the coding region of an R2 retrotransposon. J Am Chem Soc 130: 10233-10239.
    • (2008) J Am Chem Soc , vol.130 , pp. 10233-10239
    • Hart, J.M.1    Kennedy, S.D.2    Mathews, D.H.3    Turner, D.H.4
  • 20
    • 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 RB. 2006. 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 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
  • 21
    • 34249850484 scopus 로고    scopus 로고
    • Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding
    • Laederach A, Shcherbakova I, Jonikas MA, Altman RB, Brenowitz M. 2007. Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding. Proc Natl Acad Sci 104: 7045-7050.
    • (2007) Proc Natl Acad Sci , vol.104 , pp. 7045-7050
    • Laederach, A.1    Shcherbakova, I.2    Jonikas, M.A.3    Altman, R.B.4    Brenowitz, M.5
  • 22
    • 0024359787 scopus 로고
    • Defining the inside and outside of a catalytic RNA molecule
    • Latham JA, Cech TR. 1989. Defining the inside and outside of a catalytic RNA molecule. Science 245: 276-282.
    • (1989) Science , vol.245 , pp. 276-282
    • Latham, J.A.1    Cech, T.R.2
  • 23
    • 0036798116 scopus 로고    scopus 로고
    • RNA canonical and non-canonical base pairing types: A recognition method and complete repertoire
    • Lemieux S, Major F. 2002. RNA canonical and non-canonical base pairing types: A recognition method and complete repertoire. Nucleic Acids Res 30: 4250-4263.
    • (2002) Nucleic Acids Res , vol.30 , pp. 4250-4263
    • Lemieux, S.1    Major, F.2
  • 24
    • 0037102491 scopus 로고    scopus 로고
    • The non-Watson-Crick base pairs and their associated isostericity matrices
    • Leontis NB, Stombaugh J, Westhof E. 2002. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res 30: 3497-3531.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3497-3531
    • Leontis, N.B.1    Stombaugh, J.2    Westhof, E.3
  • 25
    • 0019790241 scopus 로고
    • Mapping tRNA structure in solution using double-strand-specific ribonuclease V1 from cobra venom
    • Lockard RE, Kumar A. 1981. Mapping tRNA structure in solution using double-strand-specific ribonuclease V1 from cobra venom. Nucleic Acids Res 9: 5125-5140.
    • (1981) Nucleic Acids Res , vol.9 , pp. 5125-5140
    • Lockard, R.E.1    Kumar, A.2
  • 26
    • 3342977915 scopus 로고    scopus 로고
    • Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization
    • Mathews DH. 2004. Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. RNA 10: 1178-1190.
    • (2004) RNA , vol.10 , pp. 1178-1190
    • Mathews, D.H.1
  • 27
    • 0031014702 scopus 로고    scopus 로고
    • Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element
    • Mathews DH, Banerjee AR, Luan DD, Eickbush TH, Turner DH. 1997. Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element. RNA 3: 1-16.
    • (1997) RNA , vol.3 , pp. 1-16
    • Mathews, D.H.1    Banerjee, A.R.2    Luan, D.D.3    Eickbush, T.H.4    Turner, D.H.5
  • 28
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews DH, Sabina J, Zuker M, Turner DH. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288: 911-940.
    • (1999) J Mol Biol , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 29
    • 2442626706 scopus 로고    scopus 로고
    • Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    • Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH. 2004. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci 101: 7287-7292.
    • (2004) Proc Natl Acad Sci , vol.101 , pp. 7287-7292
    • Mathews, D.H.1    Disney, M.D.2    Childs, J.L.3    Schroeder, S.J.4    Zuker, M.5    Turner, D.H.6
  • 30
    • 46349099944 scopus 로고    scopus 로고
    • High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis
    • doi: 10.1093/nar/gkn267
    • Mitra S, Shcherbakova IV, Altman RB, Brenowitz M, Laederach A. 2008. High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Res 36: e63. doi: 10.1093/nar/gkn267.
    • (2008) Nucleic Acids Res , vol.36
    • Mitra, S.1    Shcherbakova, I.V.2    Altman, R.B.3    Brenowitz, M.4    Laederach, A.5
  • 31
    • 40749156234 scopus 로고    scopus 로고
    • Into the post-HapMap era
    • Morton NE. 2008. Into the post-HapMap era. Adv Genet 60: 727-742.
    • (2008) Adv Genet , vol.60 , pp. 727742
    • Morton, N.E.1
  • 32
    • 0242417558 scopus 로고    scopus 로고
    • Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme
    • Onoa B, Dumont S, Liphardt J, Smith SB, Tinoco I Jr, Bustamante C. 2003. Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme. Science 299: 1892-1895.
    • (2003) Science , vol.299 , pp. 1892-1895
    • Onoa, B.1    Dumont, S.2    Liphardt, J.3    Smith, S.B.4    Tinoco Jr., I.5    Bustamante, C.6
  • 34
    • 27644457113 scopus 로고    scopus 로고
    • Perturbation of the hierarchical folding of a large RNA by the destabilization of its Scaffold's tertiary structure
    • Shcherbakova I, Brenowitz M. 2005. Perturbation of the hierarchical folding of a large RNA by the destabilization of its Scaffold's tertiary structure. J Mol Biol 354: 483-496.
    • (2005) J Mol Biol , vol.354 , pp. 483-496
    • Shcherbakova, I.1    Brenowitz, M.2
  • 35
    • 39449112406 scopus 로고    scopus 로고
    • Monitoring structural changes in nucleic acids with single residue spatial and millisecond time resolution by quantitative hydroxyl radical footprinting
    • Shcherbakova I, Brenowitz M. 2008. Monitoring structural changes in nucleic acids with single residue spatial and millisecond time resolution by quantitative hydroxyl radical footprinting. Nat Protoc 3: 288-302.
    • (2008) Nat Protoc , vol.3 , pp. 288-302
    • Shcherbakova, I.1    Brenowitz, M.2
  • 36
    • 4444370899 scopus 로고    scopus 로고
    • Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme
    • Shcherbakova I, Gupta S, Chance MR, Brenowitz M. 2004. Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme. J Mol Biol 342: 1431-1442.
    • (2004) J Mol Biol , vol.342 , pp. 1431-1442
    • Shcherbakova, I.1    Gupta, S.2    Chance, M.R.3    Brenowitz, M.4
  • 37
    • 57549096731 scopus 로고    scopus 로고
    • Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs
    • Shcherbakova I, Mitra S, Laederach A, Brenowitz M. 2008. Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs. Curr Opin Chem Biol 12: 655-666.
    • (2008) Curr Opin Chem Biol , vol.12 , pp. 655-666
    • Shcherbakova, I.1    Mitra, S.2    Laederach, A.3    Brenowitz, M.4
  • 38
    • 4344590128 scopus 로고    scopus 로고
    • Semi-automated, single-band peak-fitting analysis of hydroxyl radical nucleic acid footprint autoradiograms for the quantitative analysis of transitions
    • doi: 10.1093/nar/gnh117
    • Takamoto K, Chance MR, Brenowitz M. 2004. Semi-automated, single-band peak-fitting analysis of hydroxyl radical nucleic acid footprint autoradiograms for the quantitative analysis of transitions. Nucleic Acids Res 32: e119. doi: 10.1093/nar/gnh117.
    • (2004) Nucleic Acids Res , vol.32
    • Takamoto, K.1    Chance, M.R.2    Brenowitz, M.3
  • 39
    • 38449119903 scopus 로고    scopus 로고
    • DMS footprinting of structured RNAs and RNA-protein complexes
    • Tijerina P, Mohr S, Russell R. 2007. DMS footprinting of structured RNAs and RNA-protein complexes. Nat Protoc 2: 2608-2623.
    • (2007) Nat Protoc , vol.2 , pp. 2608-2623
    • Tijerina, P.1    Mohr, S.2    Russell, R.3
  • 40
    • 0029258928 scopus 로고
    • Keeping RNA happy
    • Uhlenbeck OC. 1995. Keeping RNA happy. RNA 1: 4-6.
    • (1995) RNA , vol.1 , pp. 4-6
    • Uhlenbeck, O.C.1
  • 41
    • 0021760626 scopus 로고
    • RNA structure analysis using T2 ribonuclease: Detection of pH and metal ion induced conformational changes in yeast tRNAPhe
    • Vary CP, Vournakis JN. 1984. RNA structure analysis using T2 ribonuclease: Detection of pH and metal ion induced conformational changes in yeast tRNAPhe. Nucleic Acids Res 12: 6763-6778.
    • (1984) Nucleic Acids Res , vol.12 , pp. 6763-6778
    • Vary, C.P.1    Vournakis, J.N.2
  • 42
    • 52949152433 scopus 로고    scopus 로고
    • Shape Finder: A software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis
    • Vasa SM, Guex N, Wilkinson KA, Weeks KM, Giddings MC. 2008. Shape Finder: A software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA 14: 1979-1990.
    • (2008) RNA , vol.14 , pp. 1979-1990
    • Vasa, S.M.1    Guex, N.2    Wilkinson, K.A.3    Weeks, K.M.4    Giddings, M.C.5
  • 43
    • 33947725371 scopus 로고    scopus 로고
    • Local RNA structural changes induced by crystallization are revealed by SHAPE
    • Vicens Q, Gooding AR, Laederach A, Cech TR. 2007. Local RNA structural changes induced by crystallization are revealed by SHAPE. RNA 13: 536-548.
    • (2007) RNA , vol.13 , pp. 536-548
    • Vicens, Q.1    Gooding, A.R.2    Laederach, A.3    Cech, T.R.4
  • 44
    • 34248222805 scopus 로고    scopus 로고
    • Computing the partition function and sampling for saturated secondary structures of RNA with respect to the Turner energy model
    • Waldispuhl J, Clote P. 2007. Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model. J Comput Biol 14: 190-215.
    • (2007) J Comput Biol , vol.14 , pp. 190-215
    • Waldispuhl, J.1    Clote, P.2
  • 45
    • 34250359062 scopus 로고    scopus 로고
    • ENCODE: More genomic empowerment
    • Weinstock GM. 2007. ENCODE: More genomic empowerment. Genome Res 17: 667-668.
    • (2007) Genome Res , vol.17 , pp. 667-668
    • Weinstock, G.M.1
  • 46
    • 16344370497 scopus 로고    scopus 로고
    • RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts
    • Wilkinson KA, Merino EJ, Weeks KM. 2005. RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts. J Am Chem Soc 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
  • 47
    • 40849123031 scopus 로고    scopus 로고
    • High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states
    • doi: 10.1371/journal.pbio.0060096
    • Wilkinson KA, Gorelick RJ, Vasa SM, Guex N, Rein A, Mathews DH, Giddings MC, Weeks KM. 2008. High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol 6: e96. doi: 10.1371/journal.pbio.0060096.
    • (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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.