메뉴 건너뛰기




Volumn 43, Issue 16, 2015, Pages 7675-7687

Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization

Author keywords

[No Author keywords available]

Indexed keywords

2 THIOURIDINE; SINGLE STRANDED RNA; THIOURIDINE; UNCLASSIFIED DRUG; 2-THIOURIDINE; DOUBLE STRANDED RNA; NUCLEOSIDE; RNA;

EID: 84942279269     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv761     Document Type: Article
Times cited : (43)

References (55)
  • 1
    • 67349123194 scopus 로고    scopus 로고
    • Comparative enzymology and structural biology of RNA self-cleavage
    • Fedor, M. J. (2009) Comparative enzymology and structural biology of RNA self-cleavage. Annu. Rev. Biophys., 38, 271-299.
    • (2009) Annu. Rev. Biophys. , vol.38 , pp. 271-299
    • Fedor, M.J.1
  • 2
    • 20444441572 scopus 로고    scopus 로고
    • Ribozyme catalysis: Not different, just worse
    • Doudna, J. A. And Lorsch, J. R. (2005) Ribozyme catalysis: not different, just worse. Nat. Struct. Mol. Biol., 12, 395-402.
    • (2005) Nat. Struct. Mol. Biol. , vol.12 , pp. 395-402
    • Doudna, J.A.1    Lorsch, J.R.2
  • 3
    • 58049217240 scopus 로고    scopus 로고
    • Riboswitch RNAs: Using RNA to sense cellular metabolism
    • Henkin, T. M. (2008) Riboswitch RNAs: using RNA to sense cellular metabolism. Genes Dev., 22, 3383-3390.
    • (2008) Genes Dev. , vol.22 , pp. 3383-3390
    • Henkin, T.M.1
  • 4
    • 67650713931 scopus 로고    scopus 로고
    • The structural and functional diversity of metabolite-binding riboswitches
    • Roth, A. And Breaker, R. R. (2009) The structural and functional diversity of metabolite-binding riboswitches. Annu. Rev. Biochem., 78, 305-334.
    • (2009) Annu. Rev. Biochem. , vol.78 , pp. 305-334
    • Roth, A.1    Breaker, R.R.2
  • 5
    • 0037102491 scopus 로고    scopus 로고
    • The non-Watson-Crick base pairs and their associated isostericity matrices
    • Leontis, N. B., Stombaugh, J. And 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
  • 6
    • 84864875884 scopus 로고    scopus 로고
    • The eightfold path to non-enzymatic RNA replication
    • Szostak, J. W. (2012) The eightfold path to non-enzymatic RNA replication. J. Syst. Chem., 3:2, 1-14.
    • (2012) J. Syst. Chem., 3 , vol.2 , pp. 1-14
    • Szostak, J.W.1
  • 7
    • 84890400820 scopus 로고    scopus 로고
    • Structural insights of non-canonical U.U pair and Hoogsteen interaction probed with Se atom
    • Sheng, J., Gan, J., Soares, A. S., Salon, J. And Huang, Z. (2013) Structural insights of non-canonical U.U pair and Hoogsteen interaction probed with Se atom. Nucleic Acids Res., 41, 10476-10487.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 10476-10487
    • Sheng, J.1    Gan, J.2    Soares, A.S.3    Salon, J.4    Huang, Z.5
  • 9
    • 36849148382 scopus 로고
    • Origin of life: The RNA world
    • Gilbert, W. (1986) Origin of life: The RNA world. Nature, 319, 618.
    • (1986) Nature , vol.319 , pp. 618
    • Gilbert, W.1
  • 10
    • 1242309517 scopus 로고    scopus 로고
    • Decoding the genome: A modified view
    • Agris, P. F. (2004) Decoding the genome: A modified view. Nucleic Acids Res., 32, 223-238.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 223-238
    • Agris, P.F.1
  • 13
    • 0015133749 scopus 로고
    • Selforganization of matter and evolution of biological macromolecules
    • Eigen, M. (1971) Selforganization of matter and evolution of biological macromolecules. Naturwissenschaften, 58, 465-523.
    • (1971) Naturwissenschaften , vol.58 , pp. 465-523
    • Eigen, M.1
  • 14
    • 84890042199 scopus 로고    scopus 로고
    • In-ice evolution of RNA polymerase ribozyme activity
    • Attwater, J., Wochner, A. And Holliger, P. (2013) In-ice evolution of RNA polymerase ribozyme activity. Nat. Chem, 5, 1011-1018.
    • (2013) Nat. Chem , vol.5 , pp. 1011-1018
    • Attwater, J.1    Wochner, A.2    Holliger, P.3
  • 16
    • 77952562924 scopus 로고    scopus 로고
    • Effect of stalling after mismatches on the error catastrophe in nonenzymatic nucleic acid replication
    • Rajamani, S., Ichida, J. K., Antal, T., Treco, D. A., Leu, K., Nowak, M. A., Szostak, J. W. And Chen, I. A. (2010) Effect of stalling after mismatches on the error catastrophe in nonenzymatic nucleic acid replication. J. Am. Chem. Soc., 132, 5880-5885.
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 5880-5885
    • Rajamani, S.1    Ichida, J.K.2    Antal, T.3    Treco, D.A.4    Leu, K.5    Nowak, M.A.6    Szostak, J.W.7    Chen, I.A.8
  • 17
    • 0030839446 scopus 로고    scopus 로고
    • Synthesis and studies on the effect of 2-thiouridine and 4-thiouridine on sugar conformation and RNA duplex stability
    • Kumar, R. K. And Davis, D. R. (1997) Synthesis and studies on the effect of 2-thiouridine and 4-thiouridine on sugar conformation and RNA duplex stability. Nucleic Acids Res., 25, 1272-1280.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 1272-1280
    • Kumar, R.K.1    Davis, D.R.2
  • 18
    • 0028955347 scopus 로고
    • Minor groove recognition of the conserved G-U pair at the Tetrahymena ribozyme reaction site
    • Strobel, S. A. And Cech, T. R. (1995) Minor groove recognition of the conserved G-U pair at the Tetrahymena ribozyme reaction site. Science, 267, 675-679.
    • (1995) Science , vol.267 , pp. 675-679
    • Strobel, S.A.1    Cech, T.R.2
  • 19
    • 0034698866 scopus 로고    scopus 로고
    • Synthesis and properties of 2-O-Methyl-2-thiouridine and oligoribonucleotides containing 2-O-Methyl-2-thiouridine
    • Shohda, K.-I., Okamoto, I., Wada, T., Seio, K. And Sekine, M. (2000) Synthesis and properties of 2-O-Methyl-2-thiouridine and oligoribonucleotides containing 2-O-Methyl-2-thiouridine. Bioorg. Med. Chem. Lett., 10, 1795-1798.
    • (2000) Bioorg. Med. Chem. Lett. , vol.10 , pp. 1795-1798
    • Shohda, K.-I.1    Okamoto, I.2    Wada, T.3    Seio, K.4    Sekine, M.5
  • 20
    • 84923612842 scopus 로고    scopus 로고
    • Replacing uridine with 2-thiouridine enhances the rate and fidelity of nonenzymatic RNA primer extension
    • Heuberger, B. D., Pal, A., Del Frate, F., Topkar, V. V. And Szostak, J. W. (2015) Replacing uridine with 2-thiouridine enhances the rate and fidelity of nonenzymatic RNA primer extension. J. Am. Chem. Soc., 137, 2769-2775.
    • (2015) J. Am. Chem. Soc. , vol.137 , pp. 2769-2775
    • Heuberger, B.D.1    Pal, A.2    Del Frate, F.3    Topkar, V.V.4    Szostak, J.W.5
  • 21
    • 0033554848 scopus 로고    scopus 로고
    • Thermodynamics of RNARNA duplexes with 2-or 4-thiouridines: Implications for antisense design and targeting a group i intron
    • Testa, S. M., Disney, M. D., Turner, D. H. And Kierzek, R. (1999) Thermodynamics of RNARNA duplexes with 2-or 4-thiouridines: implications for antisense design and targeting a group I intron. Biochemistry, 38, 16655-16662.
    • (1999) Biochemistry , vol.38 , pp. 16655-16662
    • Testa, S.M.1    Disney, M.D.2    Turner, D.H.3    Kierzek, R.4
  • 22
    • 0016158388 scopus 로고
    • Molecular structure of poly-2-thiouridylic acid, a double helix with non-equivalent polynucleotide chains
    • Mazumdar, S. K., Saenger, W. And Scheit, K. H. (1974) Molecular structure of poly-2-thiouridylic acid, a double helix with non-equivalent polynucleotide chains. Mol. Biol., 85, 213-219.
    • (1974) Mol. Biol. , vol.85 , pp. 213-219
    • Mazumdar, S.K.1    Saenger, W.2    Scheit, K.H.3
  • 23
    • 33947290420 scopus 로고
    • Synthesis of 2-thiouridine and 2-thioisouridine by Mercuri procedure
    • Pal, B. C. (1971) Synthesis of 2-thiouridine and 2-thioisouridine by Mercuri procedure. J. Org. Chem., 36, 3026-3028.
    • (1971) J. Org. Chem. , vol.36 , pp. 3026-3028
    • Pal, B.C.1
  • 24
    • 0000635454 scopus 로고
    • Thiolation of uridine carbon-2 restricts the motional dynamics of the transfer RNA wobble position nucleoside
    • Agris, P. F., Sierzputowska-Gracz, H., Smith, W., Malkiewicz, A., Sochacka, E. And Nawrot, B. (1992) Thiolation of uridine carbon-2 restricts the motional dynamics of the transfer RNA wobble position nucleoside. J. Am. Chem. Soc., 114, 2652-2656.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 2652-2656
    • Agris, P.F.1    Sierzputowska-Gracz, H.2    Smith, W.3    Malkiewicz, A.4    Sochacka, E.5    Nawrot, B.6
  • 25
    • 77951032586 scopus 로고    scopus 로고
    • Role of unsatisfied hydrogen bond acceptors in RNA energetics and specificity
    • Siegfried, N. A., Kierzek, R. And Bevilacqua, P. C. (2010) Role of unsatisfied hydrogen bond acceptors in RNA energetics and specificity. J. Am. Chem. Soc., 132, 5342-5344.
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 5342-5344
    • Siegfried, N.A.1    Kierzek, R.2    Bevilacqua, P.C.3
  • 26
    • 84985545870 scopus 로고
    • Preorganization-from solvents to spherands
    • Cram, D. J. (1986) Preorganization-from solvents to spherands. Angew. Chem. Int. Ed., 25, 1039-1057.
    • (1986) Angew. Chem. Int. Ed. , vol.25 , pp. 1039-1057
    • Cram, D.J.1
  • 27
    • 84907546437 scopus 로고    scopus 로고
    • Crystal structure studies of RNA duplexes containing s2U:A and s2U:U base pairs
    • Sheng, J., Larsen, A., Heuberger, B. D., Blain, J. C. And Szostak, J. W. (2014) Crystal structure studies of RNA duplexes containing s2U:A and s2U:U base pairs. J. Am. Chem. Soc., 136, 13916-13924.
    • (2014) J. Am. Chem. Soc. , vol.136 , pp. 13916-13924
    • Sheng, J.1    Larsen, A.2    Heuberger, B.D.3    Blain, J.C.4    Szostak, J.W.5
  • 28
    • 0034650726 scopus 로고    scopus 로고
    • Exact analysis of competition ligand binding by displacement isothermal titration calorimetry
    • Sigurskjold, B. W. (2000) Exact analysis of competition ligand binding by displacement isothermal titration calorimetry. Anal. Biochem., 277, 260-266.
    • (2000) Anal. Biochem. , vol.277 , pp. 260-266
    • Sigurskjold, B.W.1
  • 29
    • 30744467696 scopus 로고    scopus 로고
    • Heat capacity changes associated with DNA duplex formation: Salt-and sequence-dependent effects
    • Mikulecky, P. J. And Feig, A. L. (2006) Heat capacity changes associated with DNA duplex formation: Salt-and sequence-dependent effects. Biochemistry, 45, 604-616.
    • (2006) Biochemistry , vol.45 , pp. 604-616
    • Mikulecky, P.J.1    Feig, A.L.2
  • 30
    • 0026726087 scopus 로고
    • Furanose sugar conformations in DNA from NMR coupling-constants
    • van Wijk, J., Huckriede, B. D., Ippel, J. H. And Altona, C. (1992) Furanose sugar conformations in DNA from NMR coupling-constants. Methods Enzymol., 211, 286-306.
    • (1992) Methods Enzymol. , vol.211 , pp. 286-306
    • Van Wijk, J.1    Huckriede, B.D.2    Ippel, J.H.3    Altona, C.4
  • 31
    • 60749116042 scopus 로고    scopus 로고
    • A user-friendly Matlab program and GUI for the pseudorotation analysis of saturated five-membered ring systems based on scalar coupling constants
    • Hendrickx, P. M. S. And Martins, J. C. (2008) A user-friendly Matlab program and GUI for the pseudorotation analysis of saturated five-membered ring systems based on scalar coupling constants. Chem. Cent. J., 2, 20.
    • (2008) Chem. Cent. J. , vol.2 , pp. 20
    • Hendrickx, P.M.S.1    Martins, J.C.2
  • 33
    • 33846592515 scopus 로고    scopus 로고
    • Parametrization of 2-thiouracil and 4-thiouracil in CHARMM all-atom empirical force field
    • Sarzýnska, J. And Kuli ński, T. (2005) Parametrization of 2-thiouracil and 4-thiouracil in CHARMM all-atom empirical force field. Comput. Methods Sci. Technol., 11, 49-55.
    • (2005) Comput. Methods Sci. Technol. , vol.11 , pp. 49-55
    • Sarzýnska, J.1    Kuli Nski, T.2
  • 34
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics simulation: The Langevin piston method
    • Feller, S. E., Zhang, Y., Pastor, R. W. And Brooks, B. R. (1995) Constant pressure molecular dynamics simulation: The Langevin piston method. J. Chem. Phys., 103, 4613-4621.
    • (1995) J. Chem. Phys. , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.2    Pastor, R.W.3    Brooks, B.R.4
  • 35
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems
    • Darden, T., York, D. And Pedersen, L. (1993) Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems. J. Chem. Phys., 98, 10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 36
    • 1842692143 scopus 로고
    • General definition of ring puckering coordinates
    • Cremer, D. And Pople, J. A. (1975) General definition of ring puckering coordinates. J. Am. Chem. Soc., 97, 1354-1358.
    • (1975) J. Am. Chem. Soc. , vol.97 , pp. 1354-1358
    • Cremer, D.1    Pople, J.A.2
  • 38
    • 84942048668 scopus 로고
    • Octanol-water partition-coefficients of simple organic-compounds
    • Sangster, J. (1989) Octanol-water partition-coefficients of simple organic-compounds. J. Phys. Chem. Ref. Data, 18, 1111-1229.
    • (1989) J. Phys. Chem. Ref. Data , vol.18 , pp. 1111-1229
    • Sangster, J.1
  • 40
    • 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
  • 41
    • 84900333264 scopus 로고    scopus 로고
    • Surprising base pairing and structural properties of 2-trifluoromethylthio-modified ribonucleic acids
    • Kosutíc, M., Jud, L., Da Veiga, C., Frener, M., Fauster, K., Kreutz, C., Ennifar, E. And Micura, R. (2014) Surprising base pairing and structural properties of 2-trifluoromethylthio-modified ribonucleic acids. J. Am. Chem. Soc., 136, 6656-6663.
    • (2014) J. Am. Chem. Soc. , vol.136 , pp. 6656-6663
    • Kosutíc, M.1    Jud, L.2    Da Veiga, C.3    Frener, M.4    Fauster, K.5    Kreutz, C.6    Ennifar, E.7    Micura, R.8
  • 43
    • 0031432659 scopus 로고    scopus 로고
    • The question of long-range allosteric transitions in DNA
    • Schurr, J. M., Delrow, J. J., Fujimoto, B. S. And Benight, A. S. (1997) The question of long-range allosteric transitions in DNA. Biopolymers, 44, 283-308.
    • (1997) Biopolymers , vol.44 , pp. 283-308
    • Schurr, J.M.1    Delrow, J.J.2    Fujimoto, B.S.3    Benight, A.S.4
  • 44
    • 77954360115 scopus 로고    scopus 로고
    • Direct observation of the temperature-induced melting process of the Salmonella fourU RNA thermometer at base-pair resolution
    • Rinnenthal, J., Klinkert, B., Narberhaus, F. And Schwalbe, H. (2010) Direct observation of the temperature-induced melting process of the Salmonella fourU RNA thermometer at base-pair resolution. Nucleic Acids Res., 38, 3834-3847.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 3834-3847
    • Rinnenthal, J.1    Klinkert, B.2    Narberhaus, F.3    Schwalbe, H.4
  • 45
    • 84894454265 scopus 로고    scopus 로고
    • The free energy landscape of pseudorotation in 3-5- and 2-5- linked nucleic acids
    • Li, L. And Szostak, J. W. (2014) The free energy landscape of pseudorotation in 3-5- and 2-5- linked nucleic acids. J. Am. Chem. Soc., 136, 2858-2865.
    • (2014) J. Am. Chem. Soc. , vol.136 , pp. 2858-2865
    • Li, L.1    Szostak, J.W.2
  • 46
    • 84863257824 scopus 로고    scopus 로고
    • Activated ribonucleotides undergo a sugar pucker switch upon binding to a single-stranded RNA template
    • Zhang, N., Zhang, S. And Szostak, J. W. (2012) Activated ribonucleotides undergo a sugar pucker switch upon binding to a single-stranded RNA template. J. Am. Chem. Soc., 134, 3691-3694.
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 3691-3694
    • Zhang, N.1    Zhang, S.2    Szostak, J.W.3
  • 47
    • 4243224015 scopus 로고
    • Relationships between torsional angles and ring-puckering coordinates
    • Déz, E., Esteban, A. L., Guilleme, J. And Bermejo, F. L. (1981) Relationships between torsional angles and ring-puckering coordinates. J. Mol. Struct., 70, 61-64.
    • (1981) J. Mol. Struct. , vol.70 , pp. 61-64
    • Déz, E.1    Esteban, A.L.2    Guilleme, J.3    Bermejo, F.L.4
  • 50
    • 0001509942 scopus 로고    scopus 로고
    • Prediction of physicochemical parameters by atomic contributions
    • Wildman, S. A. And Crippen, G. M. (1999) Prediction of physicochemical parameters by atomic contributions. J. Chem. Inf. Comput. Sci., 39, 868-873.
    • (1999) J. Chem. Inf. Comput. Sci. , vol.39 , pp. 868-873
    • Wildman, S.A.1    Crippen, G.M.2
  • 51
    • 0008442317 scopus 로고
    • The Born equation and ionic solvation
    • Atkins, P. W. And MacDermott, A. J. (1982) The Born equation and ionic solvation. J. Chem. Educ., 59, 359-360.
    • (1982) J. Chem. Educ. , vol.59 , pp. 359-360
    • Atkins, P.W.1    MacDermott, A.J.2
  • 52
    • 0001120760 scopus 로고    scopus 로고
    • Preorganization of DNA: Design principles for improving nucleic acid recognition by synthetic oligonucleotides
    • Kool, E. T. (1997) Preorganization of DNA: Design principles for improving nucleic acid recognition by synthetic oligonucleotides. Chem. Rev., 97, 1473-1487.
    • (1997) Chem. Rev. , vol.97 , pp. 1473-1487
    • Kool, E.T.1
  • 53
    • 0037016023 scopus 로고    scopus 로고
    • Energetics of hydrogen bond networks in RNA: Hydrogen bonds surrounding G+1 and U42 are the major determinants for the tertiary structure stability of the hairpin ribozyme
    • Klostermeier, D. And Millar, D. P. (2002) Energetics of hydrogen bond networks in RNA: hydrogen bonds surrounding G+1 and U42 are the major determinants for the tertiary structure stability of the hairpin ribozyme. Biochemistry, 41, 14095-14102.
    • (2002) Biochemistry , vol.41 , pp. 14095-14102
    • Klostermeier, D.1    Millar, D.P.2
  • 54
    • 0345531141 scopus 로고    scopus 로고
    • Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-ending codons
    • Takai, K. And Yokoyama, S. (2003) Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-ending codons. Nucleic Acids Res., 31, 6383-6391.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 6383-6391
    • Takai, K.1    Yokoyama, S.2
  • 55
    • 66249145702 scopus 로고    scopus 로고
    • Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins
    • Zhou, P., Tian, F., Lv, F. And Shang, Z. (2009) Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins. Proteins, 76, 151-163.
    • (2009) Proteins , vol.76 , pp. 151-163
    • Zhou, P.1    Tian, F.2    Lv, F.3    Shang, Z.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.