메뉴 건너뛰기




Volumn 46, Issue 46, 2007, Pages 13425-13436

Thermodynamic characterization of single mismatches found in naturally occurring RNA

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; DATA STRUCTURES; DATABASE SYSTEMS; FREE ENERGY; PARAMETER ESTIMATION; THERMODYNAMICS;

EID: 36248936612     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi701311c     Document Type: Article
Times cited : (46)

References (48)
  • 1
    • 0037995439 scopus 로고    scopus 로고
    • Mutational analysis of an RNA internal loop as a reactivity epitope for Escherichia coli ribonuclease III substrates
    • Calin-Jageman, I., and Nicholson, A. W. (2003) Mutational analysis of an RNA internal loop as a reactivity epitope for Escherichia coli ribonuclease III substrates, Biochemistry 42, 5025-5034.
    • (2003) Biochemistry , vol.42 , pp. 5025-5034
    • Calin-Jageman, I.1    Nicholson, A.W.2
  • 2
    • 0019821773 scopus 로고
    • Processing of mRNA by ribonuclease III regulates expression of gene 1.2 of bacteriophage T7
    • Saito, H., and Richardson, C. C. (1981) Processing of mRNA by ribonuclease III regulates expression of gene 1.2 of bacteriophage T7, Cell 27, 533-542.
    • (1981) Cell , vol.27 , pp. 533-542
    • Saito, H.1    Richardson, C.C.2
  • 3
    • 28044455435 scopus 로고    scopus 로고
    • MicroPrimer: The biogenesis and function of microRNA
    • Du, T., and Zamore, P. D. (2005) MicroPrimer: The biogenesis and function of microRNA, Development 132, 4645-4652.
    • (2005) Development , vol.132 , pp. 4645-4652
    • Du, T.1    Zamore, P.D.2
  • 4
    • 0035845528 scopus 로고    scopus 로고
    • Structural features of an influenza virus promoter and their implications for viral RNA synthesis
    • Bae, S. H., Cheong, H. K., Lee, J. H., Cheong, C., Kainosho, M., and Choi, B. S. (2001) Structural features of an influenza virus promoter and their implications for viral RNA synthesis, Proc. Natl. Acad. Sci. U.S.A. 98, 10602-10607.
    • (2001) Proc. Natl. Acad. Sci. U.S.A , vol.98 , pp. 10602-10607
    • Bae, S.H.1    Cheong, H.K.2    Lee, J.H.3    Cheong, C.4    Kainosho, M.5    Choi, B.S.6
  • 5
    • 0037143493 scopus 로고    scopus 로고
    • Multiple secondary structure rearrangements during HIV-1 RNA dimerization
    • Huthoff, H., and Berkhout, B. (2002) Multiple secondary structure rearrangements during HIV-1 RNA dimerization, Biochemistry 41, 10439-10445.
    • (2002) Biochemistry , vol.41 , pp. 10439-10445
    • Huthoff, H.1    Berkhout, B.2
  • 7
    • 0039178080 scopus 로고    scopus 로고
    • Selection of viral RNA-derived tRNA-like structures with improved valylation activities
    • Wientges, J., Putz, J., Giege, R., Florentz, C., and Schwienhorst, A. (2000) Selection of viral RNA-derived tRNA-like structures with improved valylation activities, Biochemistry 39, 6207-6218.
    • (2000) Biochemistry , vol.39 , pp. 6207-6218
    • Wientges, J.1    Putz, J.2    Giege, R.3    Florentz, C.4    Schwienhorst, A.5
  • 8
    • 2442705213 scopus 로고    scopus 로고
    • Conserved RNA secondary structures in Flaviviridae genomes
    • Thunder, C., Witwer, C., Hofacker, I. L., and Stadler, P. F. (2004) Conserved RNA secondary structures in Flaviviridae genomes, J. Gen. Virol. 85, 1113-1124.
    • (2004) J. Gen. Virol , vol.85 , pp. 1113-1124
    • Thunder, C.1    Witwer, C.2    Hofacker, I.L.3    Stadler, P.F.4
  • 9
    • 0029994685 scopus 로고    scopus 로고
    • Evidence for the existence of a pseudoknot structure at the 3′ terminus of the Flavivirus genomic RNA
    • Shi, P.-Y., Brinton, M. A., Veal, J. M., Zhong, Y. Y., and Wilson, W. D. (1996) Evidence for the existence of a pseudoknot structure at the 3′ terminus of the Flavivirus genomic RNA, Biochemistry 35, 4222-4230.
    • (1996) Biochemistry , vol.35 , pp. 4222-4230
    • Shi, P.-Y.1    Brinton, M.A.2    Veal, J.M.3    Zhong, Y.Y.4    Wilson, W.D.5
  • 10
    • 8144228406 scopus 로고    scopus 로고
    • Trinucleotide repeats and neurodegenerative disease
    • Everett, C. M., and Wood, N. W. (2004) Trinucleotide repeats and neurodegenerative disease, Brain 127, 2385-2405.
    • (2004) Brain , vol.127 , pp. 2385-2405
    • Everett, C.M.1    Wood, N.W.2
  • 11
    • 2342461060 scopus 로고    scopus 로고
    • Myotonic dystrophy: RNA pathogenesis comes into focus
    • Ranum, L. P. W., and Day, J. W. (2004) Myotonic dystrophy: RNA pathogenesis comes into focus, Am. J. Hum. Gen. 74, 793-804.
    • (2004) Am. J. Hum. Gen , vol.74 , pp. 793-804
    • Ranum, L.P.W.1    Day, J.W.2
  • 13
    • 23844465175 scopus 로고    scopus 로고
    • Thermodynamic stability of RNA structures formed by CNG trinucleotide repeats. Implication for prediction of RNA structure
    • Broda, M., Kierzek, E., Gdaniec, Z., Kulinski, T., and Kierzek, R. (2005) Thermodynamic stability of RNA structures formed by CNG trinucleotide repeats. Implication for prediction of RNA structure, Biochemistry 44, 10873-10882.
    • (2005) Biochemistry , vol.44 , pp. 10873-10882
    • Broda, M.1    Kierzek, E.2    Gdaniec, Z.3    Kulinski, T.4    Kierzek, R.5
  • 14
    • 33750214512 scopus 로고    scopus 로고
    • A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
    • Lu, Z. J., Turner, D. H., and Mathews, D. H. (2006) A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation, Nucleic Acids Res. 34, 4912-4924.
    • (2006) Nucleic Acids Res , vol.34 , pp. 4912-4924
    • Lu, Z.J.1    Turner, D.H.2    Mathews, D.H.3
  • 15
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews, D. H., Sabina, J., Zuker, M., and Turner, D. H. (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
  • 16
    • 2442626706 scopus 로고    scopus 로고
    • Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    • Mathews, D. H., Disney, M. D., Childs, J. C., Schroeder, S. J., Zuker, M., and Turner, D. H. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure, Proc. Natl. Acad. Sci. U.S.A. 101, 7287-7292.
    • (2004) Proc. Natl. Acad. Sci. U.S.A , vol.101 , pp. 7287-7292
    • Mathews, D.H.1    Disney, M.D.2    Childs, J.C.3    Schroeder, S.J.4    Zuker, M.5    Turner, D.H.6
  • 17
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Res. 31, 3406-3415.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 18
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker, I. L. (2003) Vienna RNA secondary structure server, Nucleic Acids Res. 31, 3429-3431.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 19
    • 36249020941 scopus 로고    scopus 로고
    • ISI Web of Knowledge [v3.0], Thomson Corporation, Stamford, CT. http://portal.isiknowledge.com/portal.cgi (accessed July 2007).
    • ISI Web of Knowledge [v3.0], Thomson Corporation, Stamford, CT. http://portal.isiknowledge.com/portal.cgi (accessed July 2007).
  • 20
    • 0024477261 scopus 로고
    • On finding all suboptimal foldings of an RNA molecule
    • Zuker, M. (1989) On finding all suboptimal foldings of an RNA molecule, Science 244, 48-52.
    • (1989) Science , vol.244 , pp. 48-52
    • Zuker, M.1
  • 21
    • 0030815643 scopus 로고    scopus 로고
    • Thermodynamics of nonsymmetric tandem mismatches adjacent to G-C base pairs in RNA
    • Xia, T. B., McDowell, J. A., and Turner, D. H. (1997) Thermodynamics of nonsymmetric tandem mismatches adjacent to G-C base pairs in RNA, Biochemistry 36, 12486-12497.
    • (1997) Biochemistry , vol.36 , pp. 12486-12497
    • Xia, T.B.1    McDowell, J.A.2    Turner, D.H.3
  • 22
    • 0025925206 scopus 로고    scopus 로고
    • SantaLucia, J., Jr., Kierzek, R., and Turner, D. H. (1991) Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U.U and C.C.+ pairs, Biochemistry 30, 8242-8251.
    • SantaLucia, J., Jr., Kierzek, R., and Turner, D. H. (1991) Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U.U and C.C.+ pairs, Biochemistry 30, 8242-8251.
  • 23
    • 0025900996 scopus 로고
    • Thermodynamic study of internal loops in oligoribonucleotides: Symmetric loops are more stable than asymmetric loops
    • Peritz, A. E., Kierzek, R., Sugimoto, N., and Turner, D. H. (1991) Thermodynamic study of internal loops in oligoribonucleotides: Symmetric loops are more stable than asymmetric loops, Biochemistry 30, 6428-6436.
    • (1991) Biochemistry , vol.30 , pp. 6428-6436
    • Peritz, A.E.1    Kierzek, R.2    Sugimoto, N.3    Turner, D.H.4
  • 24
    • 0033607261 scopus 로고    scopus 로고
    • Thermodynamics of single mismatches in RNA duplexes
    • Kierzek, R., Burkard, M. E., and Turner, D. H. (1999) Thermodynamics of single mismatches in RNA duplexes, Biochemistry 38, 14214-14223.
    • (1999) Biochemistry , vol.38 , pp. 14214-14223
    • Kierzek, R.1    Burkard, M.E.2    Turner, D.H.3
  • 25
    • 0032506045 scopus 로고    scopus 로고
    • Thermodynamic analysis of RNA combinatorial library contained in a short hairpin
    • Bevilacqua, J. M., and Bevilacqua, P. C. (1998) Thermodynamic analysis of RNA combinatorial library contained in a short hairpin, Biochemistry 37, 15877-15884.
    • (1998) Biochemistry , vol.37 , pp. 15877-15884
    • Bevilacqua, J.M.1    Bevilacqua, P.C.2
  • 26
    • 0028071557 scopus 로고
    • Collection of small-subunit (16s- and 16s-like) ribosomal-RNA structures-1994
    • Gutell, R. R. (1994) Collection of small-subunit (16s- and 16s-like) ribosomal-RNA structures-1994, Nucleic Acids Res. 22, 3502-3507.
    • (1994) Nucleic Acids Res , vol.22 , pp. 3502-3507
    • Gutell, R.R.1
  • 27
    • 0027225783 scopus 로고
    • A compilation of large subunit (23s-like and 23s-like) ribosomal-RNA structures-1993
    • Gutell, R. R., Gray, M. W., and Schnare, M. N. (1993) A compilation of large subunit (23s-like and 23s-like) ribosomal-RNA structures-1993, Nucleic Acids Res. 21, 3055-3074.
    • (1993) Nucleic Acids Res , vol.21 , pp. 3055-3074
    • Gutell, R.R.1    Gray, M.W.2    Schnare, M.N.3
  • 28
    • 0029877001 scopus 로고    scopus 로고
    • Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA
    • Schnare, M. N., Damberger, S. H., Gray, M. W., and Gutell, R. R. (1996) Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA, J. Mol. Biol. 256, 701-719.
    • (1996) J. Mol. Biol , vol.256 , pp. 701-719
    • Schnare, M.N.1    Damberger, S.H.2    Gray, M.W.3    Gutell, R.R.4
  • 31
    • 0031866668 scopus 로고    scopus 로고
    • The signal recognition particle database (SRPDB)
    • Larsen, N., Samuelsson, T., and Zwieb, C. (1998) The signal recognition particle database (SRPDB), Nucleic Acids Res. 26, 177-178.
    • (1998) Nucleic Acids Res , vol.26 , pp. 177-178
    • Larsen, N.1    Samuelsson, T.2    Zwieb, C.3
  • 32
    • 0031841911 scopus 로고    scopus 로고
    • The ribonuclease P database
    • Brown, J. W. (1998) The ribonuclease P database, Nucleic Acids Res. 26, 351-352.
    • (1998) Nucleic Acids Res , vol.26 , pp. 351-352
    • Brown, J.W.1
  • 33
    • 0028146967 scopus 로고
    • A comparative database of group 1 intron structures
    • Damberger, S. H., and Gutell, R. R. (1994) A comparative database of group 1 intron structures, Nucleic Acids Res. 22, 3508-3510.
    • (1994) Nucleic Acids Res , vol.22 , pp. 3508-3510
    • Damberger, S.H.1    Gutell, R.R.2
  • 34
    • 0021256581 scopus 로고
    • Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing: A review
    • Waring, R. B., and Davies, R. W. (1984) Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing: A review, Gene 28, 277-291.
    • (1984) Gene , vol.28 , pp. 277-291
    • Waring, R.B.1    Davies, R.W.2
  • 35
    • 0024428420 scopus 로고
    • Comparative and functional-anatomy of group-Ii catalytic introns: A review
    • Michel, F., Umesono, K., and Ozeki, H. (1989) Comparative and functional-anatomy of group-Ii catalytic introns: A review, Gene 82, 5-30.
    • (1989) Gene , vol.82 , pp. 5-30
    • Michel, F.1    Umesono, K.2    Ozeki, H.3
  • 36
    • 34247526026 scopus 로고    scopus 로고
    • Nearest neighbor parameters for inosine-uridine pairs in RNA duplexes
    • Wright, D. J., Rice, J. L., Yanker, D. M., and Znosko, B. M. (2007) Nearest neighbor parameters for inosine-uridine pairs in RNA duplexes, Biochemistry 46, 4625-4634.
    • (2007) Biochemistry , vol.46 , pp. 4625-4634
    • Wright, D.J.1    Rice, J.L.2    Yanker, D.M.3    Znosko, B.M.4
  • 37
    • 36248954464 scopus 로고    scopus 로고
    • McDowell, J. A, 1995 RNA Calculations, Version 1.1
    • McDowell, J. A. (1995) RNA Calculations, Version 1.1.
  • 38
    • 0029805937 scopus 로고    scopus 로고
    • 2 by two-dimensional NMR and simulated annealing
    • 2 by two-dimensional NMR and simulated annealing, Biochemistry 35, 14077-14089.
    • (1996) Biochemistry , vol.35 , pp. 14077-14089
    • McDowell, J.A.1    Turner, D.H.2
  • 39
    • 0020674698 scopus 로고
    • Base-stacking and base-pairing contributions to helix stability: Thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp
    • Petersheim, M., and Turner, D. H. (1983) Base-stacking and base-pairing contributions to helix stability: Thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp, Biochemistry 22, 256-263.
    • (1983) Biochemistry , vol.22 , pp. 256-263
    • Petersheim, M.1    Turner, D.H.2
  • 40
    • 0016189342 scopus 로고
    • Stability of ribonucleic-acid double-stranded helices
    • Borer, P. N., Dengler, B., Tinoco, I., and Uhlenbeck, O. (1974) Stability of ribonucleic-acid double-stranded helices, J. Mol. Biol. 86, 843-853.
    • (1974) J. Mol. Biol , vol.86 , pp. 843-853
    • Borer, P.N.1    Dengler, B.2    Tinoco, I.3    Uhlenbeck, O.4
  • 41
    • 0025082690 scopus 로고
    • Effects of GA mismatches on the structure and thermodynamics of RNA internal loops
    • SantaLucia, J., Jr., Kierzek, R., and Turner, D. H. (1990) Effects of GA mismatches on the structure and thermodynamics of RNA internal loops, Biochemistry 29, 8813-8819.
    • (1990) Biochemistry , vol.29 , pp. 8813-8819
    • SantaLucia Jr., J.1    Kierzek, R.2    Turner, D.H.3
  • 42
    • 0023406843 scopus 로고
    • Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves
    • Marky, L. A., and Breslauer, K. J. (1987) Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves, Biopolymers 26, 1601-1620.
    • (1987) Biopolymers , vol.26 , pp. 1601-1620
    • Marky, L.A.1    Breslauer, K.J.2
  • 43
    • 0032552882 scopus 로고    scopus 로고
    • Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
    • Xia, T., SantaLucia, J., Jr., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., Cox, C., and Turner, D. H. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs, Biochemistry 37, 14719-14735.
    • (1998) Biochemistry , vol.37 , pp. 14719-14735
    • Xia, T.1    SantaLucia Jr., J.2    Burkard, M.E.3    Kierzek, R.4    Schroeder, S.J.5    Jiao, X.6    Cox, C.7    Turner, D.H.8
  • 44
    • 0029382234 scopus 로고
    • GU base-pairing motifs in ribosomal-RNA
    • Gautheret, D., Konings, D., and Gutell, R. R. (1995) GU base-pairing motifs in ribosomal-RNA, RNA 1, 807-814.
    • (1995) RNA , vol.1 , pp. 807-814
    • Gautheret, D.1    Konings, D.2    Gutell, R.R.3
  • 45
    • 33846057040 scopus 로고    scopus 로고
    • Folding cooperativity in RNA and DNA is dependent on position in the helix
    • Siegfried, N. A., Metzger, S. L., and Bevilacqua, P. C. (2007) Folding cooperativity in RNA and DNA is dependent on position in the helix, Biochemistry 46, 172-181.
    • (2007) Biochemistry , vol.46 , pp. 172-181
    • Siegfried, N.A.1    Metzger, S.L.2    Bevilacqua, P.C.3
  • 46
    • 0025186882 scopus 로고
    • Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides
    • Longfellow, C. E., Kierzek, R., and Turner, D. H. (1990) Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides, Biochemistry 29, 278-285.
    • (1990) Biochemistry , vol.29 , pp. 278-285
    • Longfellow, C.E.1    Kierzek, R.2    Turner, D.H.3
  • 47
    • 33746320475 scopus 로고    scopus 로고
    • Revolutions in RNA secondary structure prediction
    • Mathews, D. H. (2006) Revolutions in RNA secondary structure prediction, J. Mol. Biol. 359, 526-532.
    • (2006) J. Mol. Biol , vol.359 , pp. 526-532
    • Mathews, D.H.1
  • 48
    • 0030299990 scopus 로고    scopus 로고
    • G·A and U·U mismatches can stabilize RNA internal loops of three nucleotides
    • Schroeder, S., Kim, J., and Turner, D. H. (1996) G·A and U·U mismatches can stabilize RNA internal loops of three nucleotides, Biochemistry 35, 16105-16109.
    • (1996) Biochemistry , vol.35 , pp. 16105-16109
    • Schroeder, S.1    Kim, J.2    Turner, D.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.