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Volumn 46, Issue 15, 2007, Pages 4625-4634

Nearest neighbor parameters for inosine·uridine pairs in RNA duplexes

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; ENZYMES; LEAST SQUARES APPROXIMATIONS; MELTING; OPTICAL PROPERTIES; THERMODYNAMIC PROPERTIES;

EID: 34247526026     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0616910     Document Type: Article
Times cited : (50)

References (31)
  • 1
    • 0035997389 scopus 로고    scopus 로고
    • RNA editing by adenosine deaminases that act on RNA
    • Bass, B. L. (2002) RNA editing by adenosine deaminases that act on RNA, Annu. Rev. Biochem. 71, 817-846.
    • (2002) Annu. Rev. Biochem , vol.71 , pp. 817-846
    • Bass, B.L.1
  • 2
    • 0023638382 scopus 로고
    • Antisense RNA injections in fertilized frog eggs reveal an RNA duplex unwinding activity
    • Rebagliati, M. R., and Melton, D. A. (1987) Antisense RNA injections in fertilized frog eggs reveal an RNA duplex unwinding activity, Cell 48, 599-605.
    • (1987) Cell , vol.48 , pp. 599-605
    • Rebagliati, M.R.1    Melton, D.A.2
  • 3
    • 0027972952 scopus 로고
    • Molecular-cloning of cDNA for double-stranded-RNA adenosine-deaminase, a candidate enzyme for nuclear-RNA editing
    • Kim, U., Wang, Y., Sanford, T., Zeng, Y., and Nishikura, K. (1994) Molecular-cloning of cDNA for double-stranded-RNA adenosine-deaminase, a candidate enzyme for nuclear-RNA editing, Proc. Natl. Acad. Sci. U.S.A. 91, 11457-11461.
    • (1994) Proc. Natl. Acad. Sci. U.S.A , vol.91 , pp. 11457-11461
    • Kim, U.1    Wang, Y.2    Sanford, T.3    Zeng, Y.4    Nishikura, K.5
  • 4
    • 0029116348 scopus 로고
    • Chicken double-stranded-RNA adenosine-deaminase has apparent specificity for Z-DNA
    • Herbert, A., Lowenhaupt, K., Spitzner, J., and Rich, A. (1995) Chicken double-stranded-RNA adenosine-deaminase has apparent specificity for Z-DNA, Proc. Natl. Acad. Sci. U.S.A. 92, 7550-7554.
    • (1995) Proc. Natl. Acad. Sci. U.S.A , vol.92 , pp. 7550-7554
    • Herbert, A.1    Lowenhaupt, K.2    Spitzner, J.3    Rich, A.4
  • 5
    • 0030904143 scopus 로고    scopus 로고
    • Analysis of Xenopus dsRNA adenosine deaminase cDNAs reveals similarities to DNA methyltransferases
    • Hough, R. F., and Bass, B. L. (1997) Analysis of Xenopus dsRNA adenosine deaminase cDNAs reveals similarities to DNA methyltransferases, RNA 3, 356-370.
    • (1997) RNA , vol.3 , pp. 356-370
    • Hough, R.F.1    Bass, B.L.2
  • 6
    • 0343963739 scopus 로고    scopus 로고
    • Comparative analysis of the DRADA A-to-I RNA editing gene from mammals, pufferfish and zebrafish
    • Slavov, D., Crnogorac-Jurcevic, T., Clark, M., and Gardiner, K. (2000) Comparative analysis of the DRADA A-to-I RNA editing gene from mammals, pufferfish and zebrafish, Gene 250, 53-60.
    • (2000) Gene , vol.250 , pp. 53-60
    • Slavov, D.1    Crnogorac-Jurcevic, T.2    Clark, M.3    Gardiner, K.4
  • 7
    • 0033943052 scopus 로고    scopus 로고
    • dADAR, a Drosophila double-stranded RNA-specific adenosine deaminase is highly developmentally regulated and is itself a target for RNA editing
    • Palladino, M. J., Keegan, L. P., O'Connell, M. A., and Reenan, R. A. (2000) dADAR, a Drosophila double-stranded RNA-specific adenosine deaminase is highly developmentally regulated and is itself a target for RNA editing, RNA 6, 1004-1018.
    • (2000) RNA , vol.6 , pp. 1004-1018
    • Palladino, M.J.1    Keegan, L.P.2    O'Connell, M.A.3    Reenan, R.A.4
  • 8
    • 0037112823 scopus 로고    scopus 로고
    • RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans
    • Tonkin, L. A., Saccomanno, L., Morse, D. P., Brodigan, T., Krause, M., and Bass, B. L. (2002) RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans, EMBO J. 21, 6025-6035.
    • (2002) EMBO J , vol.21 , pp. 6025-6035
    • Tonkin, L.A.1    Saccomanno, L.2    Morse, D.P.3    Brodigan, T.4    Krause, M.5    Bass, B.L.6
  • 9
    • 0032481315 scopus 로고    scopus 로고
    • Inosine exists in mRNA at tissue-specific levels and is most abundant in brain mRNA
    • Paul, M. S., and Bass, B. L. (1998) Inosine exists in mRNA at tissue-specific levels and is most abundant in brain mRNA, EMBO J. 17, 1120-1127.
    • (1998) EMBO J , vol.17 , pp. 1120-1127
    • Paul, M.S.1    Bass, B.L.2
  • 10
    • 0036810232 scopus 로고    scopus 로고
    • The role of RNA editing by ADARs in RNAi
    • Knight, S. W., and Bass, B. L. (2002) The role of RNA editing by ADARs in RNAi, Mol. Cell 10, 809-817.
    • (2002) Mol. Cell , vol.10 , pp. 809-817
    • Knight, S.W.1    Bass, B.L.2
  • 11
    • 0022429804 scopus 로고
    • Base-pairing involving deoxyinosine-Implications for probe design
    • Martin, F. H., Castro, M. M., Aboulela, F., & Tinoco, I. (1985) Base-pairing involving deoxyinosine-Implications for probe design, Nucleic Acids Res. 13, 8927-8938.
    • (1985) Nucleic Acids Res , vol.13 , pp. 8927-8938
    • Martin, F.H.1    Castro, M.M.2    Aboulela, F.3    Tinoco, I.4
  • 12
    • 28544447850 scopus 로고    scopus 로고
    • Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes
    • Watkins, N. E., and SantaLucia, J. Jr. (2005) Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes, Nucleic Acids Res. 33, 6258-6267.
    • (2005) Nucleic Acids Res , vol.33 , pp. 6258-6267
    • Watkins, N.E.1    SantaLucia Jr., J.2
  • 13
    • 12044257509 scopus 로고
    • Functional-group substitutions as probes of hydrogen-bonding between GA mismatches in RNA internal loops
    • SantaLucia, J., Kierzek, R., and Turner, D. H. (1991) Functional-group substitutions as probes of hydrogen-bonding between GA mismatches in RNA internal loops, J. Am. Chem. Soc. 113, 4313-4322.
    • (1991) J. Am. Chem. Soc , vol.113 , pp. 4313-4322
    • SantaLucia, J.1    Kierzek, R.2    Turner, D.H.3
  • 14
    • 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
  • 15
    • 0000789168 scopus 로고
    • Free energy increments for hydrogen bonds in nucleic acid base pairs
    • Turner, D. H., Sugimoto, N., Kierzek, R., and Dreiker, S. D. (1987) Free energy increments for hydrogen bonds in nucleic acid base pairs, J. Am. Chem. Soc. 109, 3783-3785.
    • (1987) J. Am. Chem. Soc , vol.109 , pp. 3783-3785
    • Turner, D.H.1    Sugimoto, N.2    Kierzek, R.3    Dreiker, S.D.4
  • 16
    • 3042693157 scopus 로고    scopus 로고
    • Pronounced instability of tandem IU base pairs in RNA
    • Serra, M. J., Smolter, P. E., and Westhof, E. (2004) Pronounced instability of tandem IU base pairs in RNA, Nucleic Acids Res. 32, 1824-1828.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1824-1828
    • Serra, M.J.1    Smolter, P.E.2    Westhof, E.3
  • 17
    • 0028003846 scopus 로고
    • The 2,6-diaminopurine riboside-5-methylisocytidine wobble base pair: An isoenergetic substitution for the study of GU pairs in RNA
    • Strobel, S. A., Cech, T. R., Usman, N., and Beigelman, L. (1994) The 2,6-diaminopurine riboside-5-methylisocytidine wobble base pair: An isoenergetic substitution for the study of GU pairs in RNA, Biochemistry 33, 13824-13835.
    • (1994) Biochemistry , vol.33 , pp. 13824-13835
    • Strobel, S.A.1    Cech, T.R.2    Usman, N.3    Beigelman, L.4
  • 18
    • 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
  • 19
    • 0023518718 scopus 로고
    • Automated chemical synthesis of long oligoribonucleotides using 2′-O-silylated ribonucleoside 3′-O-phosphoramidites on a controlled-pore glass support-Synthesis of a 43-nucleotide sequence similar to the 3′-half molecule of an Escherichia-coli formylmethionine transfer-RNA
    • Usman, N., Ogilvie, K. K., Jiang, M. Y., and Cedergren, R. J. (1987) Automated chemical synthesis of long oligoribonucleotides using 2′-O-silylated ribonucleoside 3′-O-phosphoramidites on a controlled-pore glass support-Synthesis of a 43-nucleotide sequence similar to the 3′-half molecule of an Escherichia-coli formylmethionine transfer-RNA, J. Am. Chem. Soc. 109, 7845-7854.
    • (1987) J. Am. Chem. Soc , vol.109 , pp. 7845-7854
    • Usman, N.1    Ogilvie, K.K.2    Jiang, M.Y.3    Cedergren, R.J.4
  • 21
    • 0000019472 scopus 로고
    • Evaluation of the use of the tert-butyldimethylsilyl group for 2′-protection in RNA-synthesis via the H-phosphonate approach
    • Stawinski, J., Stromberg, R., Thelin, M., and Westman, E. (1988) Evaluation of the use of the tert-butyldimethylsilyl group for 2′-protection in RNA-synthesis via the H-phosphonate approach, Nucleosides Nucleotides 7, 779-782.
    • (1988) Nucleosides Nucleotides , vol.7 , pp. 779-782
    • Stawinski, J.1    Stromberg, R.2    Thelin, M.3    Westman, E.4
  • 22
    • 0024593905 scopus 로고
    • Solid-phase synthesis and high-resolution NMR-studies of two synthetic double-helical RNA dodecamers-r(CGCGAAUUCGCG) and r(CGCGUAUACGCG)
    • Chou, S. H., Flynn, P., and Reid, B. (1989) Solid-phase synthesis and high-resolution NMR-studies of two synthetic double-helical RNA dodecamers-r(CGCGAAUUCGCG) and r(CGCGUAUACGCG), Biochemistry 28, 2422-2435.
    • (1989) Biochemistry , vol.28 , pp. 2422-2435
    • Chou, S.H.1    Flynn, P.2    Reid, B.3
  • 23
    • 34247471702 scopus 로고    scopus 로고
    • accessed Oct 6
    • Devor, E. J., and Behlke, M. A. (2005). Integrated DNA Technologies, http://www.idtdna.com/support/technical/TechnicalBulletinPDF/ Oligonucleotide_Yield_Resuspension_and_Storage.pdf (accessed Oct 6, 2004).
    • (2004) Integrated DNA Technologies
    • Devor, E.J.1    Behlke, M.A.2
  • 24
    • 34247482821 scopus 로고    scopus 로고
    • Sigma-Proligo, http://www.proligo.com/pro_primprobes/PP_08-8. UVAbsorbance.html (accessed Oct 4, 2004).
    • Sigma-Proligo, http://www.proligo.com/pro_primprobes/PP_08-8.
  • 25
    • 34247503267 scopus 로고    scopus 로고
    • 3.5: Melt Curve Processing Program
    • McDowell, J. A. (1996) MeltWin v. 3.5: Melt Curve Processing Program.
    • (1996) MeltWin v
    • McDowell, J.A.1
  • 26
    • 0020674698 scopus 로고
    • Base-stacking and base-pairing contributions to helix stability: Thermodynamics of double-helix formation with CCGG, CCGGp, mCCGGAp, 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, mCCGGAp, ACCGGp, CCGGUp, and ACCGGUp, Biochemistry 22, 256-263.
    • (1983) Biochemistry , vol.22 , pp. 256-263
    • Petersheim, M.1    Turner, D.H.2
  • 27
    • 0029805937 scopus 로고    scopus 로고
    • Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: Solution structure of (rGAGGUCUC)2 by two-dimensional NMR and simulated annealing
    • McDowell, J. A., and Turner, D. H. (1996) Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: solution structure of (rGAGGUCUC)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
  • 28
    • 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
  • 29
    • 0024233053 scopus 로고
    • An unwinding activity that covalently modifies its double-stranded-RNA substrate
    • Bass, B. L., and Weintraub, H. (1988) An unwinding activity that covalently modifies its double-stranded-RNA substrate, Cell 55, 1089-1098.
    • (1988) Cell , vol.55 , pp. 1089-1098
    • Bass, B.L.1    Weintraub, H.2
  • 30
    • 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
  • 31
    • 0002409464 scopus 로고    scopus 로고
    • Grosjean, H, and Benne, R, Eds, pp, ASM Press, Washington, D.C
    • Rueter, S. M., and Emeson, R. B. (1998) in Modification and editing of RNA (Grosjean, H., and Benne, R., Eds.) pp 343-361, ASM Press, Washington, D.C.
    • (1998) Modification and editing of RNA , pp. 343-361
    • Rueter, S.M.1    Emeson, R.B.2


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