메뉴 건너뛰기




Volumn 43, Issue 1, 2015, Pages 51-62

Identification of a pKa-regulating motif stabilizing imidazole-modified double-stranded DNA

Author keywords

[No Author keywords available]

Indexed keywords

DNA; IMIDAZOLE; IMIDAZOLE DERIVATIVE; THYMINE;

EID: 84941091701     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1306     Document Type: Article
Times cited : (10)

References (60)
  • 1
    • 0014201592 scopus 로고
    • 3-dimensional structure of Tosyl-Alpha-Chymotrypsin
    • Matthews,B.W., Sigler,P.B., Henderso,R. and Blow,D.M. (1967) 3-dimensional structure of Tosyl-Alpha-Chymotrypsin. Nature, 214, 652-656.
    • (1967) Nature , vol.214 , pp. 652-656
    • Matthews, B.W.1    Sigler, P.B.2    Henderso, R.3    Blow, D.M.4
  • 2
    • 33847799412 scopus 로고
    • Structure and mechanism of Chymotrypsin
    • Blow,D.M. (1976) Structure and mechanism of Chymotrypsin. Accounts Chem. Res., 9, 145-152.
    • (1976) Accounts Chem. Res. , vol.9 , pp. 145-152
    • Blow, D.M.1
  • 3
    • 0036882394 scopus 로고    scopus 로고
    • Serine protease mechanism and specificity
    • Hedstrom,L. (2002) Serine protease mechanism and specificity. Chem. Rev., 102, 4501-4523.
    • (2002) Chem. Rev. , vol.102 , pp. 4501-4523
    • Hedstrom, L.1
  • 4
    • 0001005285 scopus 로고    scopus 로고
    • Ribonuclease A
    • Raines,R.T. (1998) Ribonuclease A. Chem. Rev., 98, 1045-1065.
    • (1998) Chem. Rev. , vol.98 , pp. 1045-1065
    • Raines, R.T.1
  • 7
    • 0035961485 scopus 로고    scopus 로고
    • Bridging the gap between proteins and nucleic acids: A metal-independent RNAseA mimic with two protein-like functionalities
    • Perrin,D.M., Garestier,T. and Helene,C. (2001) Bridging the gap between proteins and nucleic acids: A metal-independent RNAseA mimic with two protein-like functionalities. J. Am. Chem. Soc., 123, 1556-1563.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 1556-1563
    • Perrin, D.M.1    Garestier, T.2    Helene, C.3
  • 8
    • 36749073859 scopus 로고    scopus 로고
    • Catalysis of the cleavage of uridine 3'-2,2,2-trichloroethylphosphate by a designed Helix-Loop-Helix motif peptide
    • Razkin,J., Nilsson,H. and Baltzer,L. (2007) Catalysis of the cleavage of uridine 3'-2,2,2-trichloroethylphosphate by a designed Helix-Loop-Helix motif peptide. J. Am. Chem. Soc., 129, 14752-14758.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 14752-14758
    • Razkin, J.1    Nilsson, H.2    Baltzer, L.3
  • 9
    • 54349095412 scopus 로고    scopus 로고
    • Enhanced complexity and catalytic efficiency in the hydrolysis of phosphate diesters by rationally designed helix-loop-helix motifs
    • Razkin,J., Lindgren,J., Nilsson,H. and Baltzer,L. (2008) Enhanced complexity and catalytic efficiency in the hydrolysis of phosphate diesters by rationally designed helix-loop-helix motifs. Chembiochem, 9, 1975-1984.
    • (2008) Chembiochem , vol.9 , pp. 1975-1984
    • Razkin, J.1    Lindgren, J.2    Nilsson, H.3    Baltzer, L.4
  • 10
    • 67849104696 scopus 로고    scopus 로고
    • Investigation of the catalytic mechanism of a synthetic DNAzyme with protein-like functionality: An RNaseA mimic
    • Thomas,J.M., Yoon,J.K. and Perrin,D.M. (2009) Investigation of the catalytic mechanism of a synthetic DNAzyme with protein-like functionality: an RNaseA mimic? J. Am. Chem. Soc., 131, 5648-5658.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 5648-5658
    • Thomas, J.M.1    Yoon, J.K.2    Perrin, D.M.3
  • 12
    • 0025074907 scopus 로고
    • Invitro selection of RNA molecules that bind specific ligands
    • Ellington,A.D. and Szostak,J.W. (1990) Invitro selection of RNA molecules that bind specific ligands. Nature, 346, 818-822.
    • (1990) Nature , vol.346 , pp. 818-822
    • Ellington, A.D.1    Szostak, J.W.2
  • 13
    • 0028191743 scopus 로고
    • All you wanted to know about SELEX
    • Klug,S.J. and Famulok,M. (1994) All you wanted to know about SELEX. Mol. Biol. Rep., 20, 97-107.
    • (1994) Mol. Biol. Rep. , vol.20 , pp. 97-107
    • Klug, S.J.1    Famulok, M.2
  • 14
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponantial enrichment-RNA ligand to bacteriophage-T4 DNA-polymerase
    • Tuerk,C. and Gold,L. (1990) Systematic evolution of ligands by exponantial enrichment-RNA ligand to bacteriophage-T4 DNA-polymerase. Science, 249, 505-510.
    • (1990) Science , vol.249 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 15
    • 3042732096 scopus 로고    scopus 로고
    • Directed evolution of nucleic acid enzymes
    • Joyce,G.F. (2004) Directed evolution of nucleic acid enzymes. Annu. Rev. Biochem., 73, 791-836.
    • (2004) Annu. Rev. Biochem. , vol.73 , pp. 791-836
    • Joyce, G.F.1
  • 16
    • 0028011717 scopus 로고
    • Molecular recognition of amino-acids by RNA-aptamers-an L-Citrulline binding RNA motif and its evolution into an L-Arginine binder
    • Famulok,M. (1994) Molecular recognition of amino-acids by RNA-aptamers-an L-Citrulline binding RNA motif and its evolution into an L-Arginine binder. J. Am. Chem. Soc., 116, 1698-1706.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 1698-1706
    • Famulok, M.1
  • 17
    • 0029062420 scopus 로고
    • In-vitro selection of RNA ligands to Substance-P
    • Nieuwlandt,D.,Wecker,M. and Gold,L. (1995) In-vitro selection of RNA ligands to Substance-P. Biochemistry, 34, 5651-5659.
    • (1995) Biochemistry , vol.34 , pp. 5651-5659
    • Nieuwlandt, D.1    Wecker, M.2    Gold, L.3
  • 18
    • 80052946478 scopus 로고    scopus 로고
    • A ribonucleopeptide module for effective conversion of an RNA aptamer to a fluorescent sensor
    • Liew,F.F., Hayashi,H., Nakano,S., Nakata,E. and Morii,T. (2011) A ribonucleopeptide module for effective conversion of an RNA aptamer to a fluorescent sensor. Bioorg. Med. Chem., 19, 5771-5775.
    • (2011) Bioorg. Med. Chem. , vol.19 , pp. 5771-5775
    • Liew, F.F.1    Hayashi, H.2    Nakano, S.3    Nakata, E.4    Morii, T.5
  • 19
    • 84867935571 scopus 로고    scopus 로고
    • Artificial specific binders directly recovered from chemically modified nucleic acid libraries
    • Kasahara,Y. and Kuwahara,M. (2012) Artificial specific binders directly recovered from chemically modified nucleic acid libraries. J. Nucleic Acids, 2012, 156482.
    • (2012) J. Nucleic Acids , vol.2012 , pp. 156482
    • Kasahara, Y.1    Kuwahara, M.2
  • 20
    • 1842618467 scopus 로고    scopus 로고
    • Sequence-specific cleavage of RNA in the absence of divalent metal ions by a DNAzyme incorporating imidazolyl and amino functionalities
    • Sidorov,A.V., Grasby,J.A. and Williams,D.M. (2004) Sequence-specific cleavage of RNA in the absence of divalent metal ions by a DNAzyme incorporating imidazolyl and amino functionalities. Nucleic Acids Res., 32, 1591-1601.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1591-1601
    • Sidorov, A.V.1    Grasby, J.A.2    Williams, D.M.3
  • 22
    • 33750993500 scopus 로고    scopus 로고
    • Systematic characterization of 2 '-deoxynucleoside-5 '-triphosphate analogs as substrates for DNA polymerases by polymerase chain reaction and kinetic studies on enzymatic production of modified DNA
    • Kuwahara,M., Nagashima,J., Hasegawa,M., Tamura,T., Kitagata,R., Hanawa,K., Hososhima,S., Kasamatsu,T., Ozaki,H. and Sawai,H. (2006) Systematic characterization of 2 '-deoxynucleoside-5 '-triphosphate analogs as substrates for DNA polymerases by polymerase chain reaction and kinetic studies on enzymatic production of modified DNA. Nucleic Acids Res., 34, 5383-5394.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 5383-5394
    • Kuwahara, M.1    Nagashima, J.2    Hasegawa, M.3    Tamura, T.4    Kitagata, R.5    Hanawa, K.6    Hososhima, S.7    Kasamatsu, T.8    Ozaki, H.9    Sawai, H.10
  • 25
    • 17344372249 scopus 로고    scopus 로고
    • Modified oligonucleotides: Synthesis and strategy for users
    • Verma,S. and Eckstein,F. (1998) Modified oligonucleotides: synthesis and strategy for users. Annu. Rev. Biochem., 67, 99-134.
    • (1998) Annu. Rev. Biochem. , vol.67 , pp. 99-134
    • Verma, S.1    Eckstein, F.2
  • 26
    • 84884860458 scopus 로고    scopus 로고
    • DNA modification under mild conditions by Suzuki-Miyaura cross-coupling for the generation of functional probes
    • Lercher,L., McGouran,J.F., Kessler,B.M., Schofield,C.J. and Davis,B.G. (2013) DNA modification under mild conditions by Suzuki-Miyaura cross-coupling for the generation of functional probes. Angewandte Chemie-Int. Edition, 52, 10553-10558.
    • (2013) Angewandte Chemie-Int. Edition , vol.52 , pp. 10553-10558
    • Lercher, L.1    McGouran, J.F.2    Kessler, B.M.3    Schofield, C.J.4    Davis, B.G.5
  • 27
    • 30044446290 scopus 로고    scopus 로고
    • Syntheses and oligonucleotide incorporation of nucleoside analogues containing pendant imidazolyl or amino functionalities -The search for sequence-specific artificial ribonucleases
    • Holmes,S.C. and Gait,M.J. (2005) Syntheses and oligonucleotide incorporation of nucleoside analogues containing pendant imidazolyl or amino functionalities-the search for sequence-specific artificial ribonucleases. Eur. J. Org. Chem., 2005, 5171-5183.
    • (2005) Eur. J. Org. Chem. , vol.2005 , pp. 5171-5183
    • Holmes, S.C.1    Gait, M.J.2
  • 28
    • 49149135789 scopus 로고
    • Deoxynucleoside phosphoramidites -A new class of key intermediates for deoxypolynocleotide synthesis
    • Beaucage,S.L. and Caruthers,M.H. (1981) Deoxynucleoside phosphoramidites-a new class of key intermediates for deoxypolynocleotide synthesis. Tetrahedron Lett., 22, 1859-1862.
    • (1981) Tetrahedron Lett. , vol.22 , pp. 1859-1862
    • Beaucage, S.L.1    Caruthers, M.H.2
  • 29
    • 0036700531 scopus 로고    scopus 로고
    • Differentiation between unlabeled and very-low-level fully N-15,C-13-labeled nucleotides for resonance assignments in nucleic acids
    • Phan,A.T. and Patel,D.J. (2002) Differentiation between unlabeled and very-low-level fully N-15,C-13-labeled nucleotides for resonance assignments in nucleic acids. J. Biomol. NMR, 23, 257-262.
    • (2002) J. Biomol. NMR , vol.23 , pp. 257-262
    • Phan, A.T.1    Patel, D.J.2
  • 30
    • 0037138634 scopus 로고    scopus 로고
    • A site-specific low-enrichment N-15,C-13 isotope-labeling approach to unambiguous NMR spectral assignments in nucleic acids
    • Phan,A.T. and Patel,D.J. (2002) A site-specific low-enrichment N-15,C-13 isotope-labeling approach to unambiguous NMR spectral assignments in nucleic acids. J. Am. Chem. Soc., 124, 1160-1161.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 1160-1161
    • Phan, A.T.1    Patel, D.J.2
  • 32
    • 0000445956 scopus 로고
    • Excitation sculpting in high-resolution nuclear-magnetic-resonance spectroscopy-application to selective NOE experiments
    • Stott,K., Stonehouse,J., Keeler,J., Hwang,T.L. and Shaka,A.J. (1995) Excitation sculpting in high-resolution nuclear-magnetic-resonance spectroscopy-application to selective NOE experiments. J. Am. Chem. Soc., 117, 4199-4200.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 4199-4200
    • Stott, K.1    Stonehouse, J.2    Keeler, J.3    Hwang, T.L.4    Shaka, A.J.5
  • 33
    • 0026951903 scopus 로고
    • Gradient-tailored excitation for single-quantum NMR-spectroscopy of aqueous solutions
    • Piotto,M., Saudek,V. and Sklenar,V. (1992) Gradient-tailored excitation for single-quantum NMR-spectroscopy of aqueous solutions. J. Biomol. NMR, 2, 661-665.
    • (1992) J. Biomol. NMR , vol.2 , pp. 661-665
    • Piotto, M.1    Saudek, V.2    Sklenar, V.3
  • 35
    • 0017284903 scopus 로고
    • Charge-relay system of serine proteinases-proton magnetic-resonance titration studies of 4 Histidines of Porcine trypsin
    • Markley,J.L. and Porubcan,M.A. (1976) Charge-relay system of serine proteinases-proton magnetic-resonance titration studies of 4 Histidines of Porcine trypsin. J. Mol. Biol., 102, 487-509.
    • (1976) J. Mol. Biol. , vol.102 , pp. 487-509
    • Markley, J.L.1    Porubcan, M.A.2
  • 37
    • 0000327631 scopus 로고
    • Standard errors and confidence intervals in nonlinear-regression-comparison of Monte-Carlo and parametric statistics
    • Alper,J.S. and Gelb,R.I. (1990) Standard errors and confidence intervals in nonlinear-regression-comparison of Monte-Carlo and parametric statistics. J. Phys. Chem., 94, 4747-4751.
    • (1990) J. Phys. Chem. , vol.94 , pp. 4747-4751
    • Alper, J.S.1    Gelb, R.I.2
  • 39
  • 40
    • 84884192184 scopus 로고    scopus 로고
    • Routine microsecond molecular dynamics simulations with AMBER on GPUs 2. Explicit solvent particleMesh Ewald
    • Salomon-Ferrer,R., Götz,A.W., Poole,D., Le Grand,S. and Walker,R.C. (2013) Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particleMesh Ewald. J. Chem. Theory Comput., 9, 3878-3888.
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 3878-3888
    • Salomon-Ferrer, R.1    Götz, A.W.2    Poole, D.3    Le Grand, S.4    Walker, R.C.5
  • 41
    • 33846823909 scopus 로고
    • Particle Mesh Ewald-an n log(n) method for Ewald sums in large systems
    • Darden,T., York,D. and Pedersen,L. (1993) Particle Mesh Ewald-an n.log(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
  • 42
    • 33646940952 scopus 로고
    • Numerical-integrations of Cartesian equations of motion of a system with constraints-molecular dynamics of n-alkanes
    • Ryckaert,J.P., Ciccotti,G. and Berendsen,H.J.C. (1977) Numerical-integrations of Cartesian equations of motion of a system with constraints-molecular dynamics of n-alkanes. J. Comput. Phys., 23, 327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 43
    • 2342504649 scopus 로고    scopus 로고
    • Synchronization of trajectories in canonical molecular-dynamics simulations: Observation, explanation, and exploitation
    • Uberuaga,B.P., Anghel,M. and Voter,A.F. (2004) Synchronization of trajectories in canonical molecular-dynamics simulations: observation, explanation, and exploitation. J. Chem. Phys., 120, 6363-6374.
    • (2004) J. Chem. Phys. , vol.120 , pp. 6363-6374
    • Uberuaga, B.P.1    Anghel, M.2    Voter, A.F.3
  • 45
    • 50349085962 scopus 로고    scopus 로고
    • 3DNA: A versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures
    • Lu,X.J. and Olson,W.K. (2008) 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nat. Protoc., 3, 1213-1227.
    • (2008) Nat. Protoc. , vol.3 , pp. 1213-1227
    • Lu, X.J.1    Olson, W.K.2
  • 46
    • 80053894476 scopus 로고    scopus 로고
    • HBonanza: A computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis
    • Durrant,J.D. and McCammon,J.A. (2011) HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis. J. Mol. Graph., 31, 5-9.
    • (2011) J. Mol. Graph. , vol.31 , pp. 5-9
    • Durrant, J.D.1    McCammon, J.A.2
  • 49
    • 1242314385 scopus 로고    scopus 로고
    • DNA fine structure and dynamics in crystals and in solution: The impact of BI/BII backbone conformations
    • Djuranovic,D. and Hartmann,B. (2004) DNA fine structure and dynamics in crystals and in solution: the impact of BI/BII backbone conformations. Biopolymers, 73, 356-368.
    • (2004) Biopolymers , vol.73 , pp. 356-368
    • Djuranovic, D.1    Hartmann, B.2
  • 50
    • 77949918051 scopus 로고    scopus 로고
    • Surprising duplex stabilisation upon mismatch introduction within triply modified duplexes
    • Catry,M.A., Gheerardijn,V. and Madder,A. (2010) Surprising duplex stabilisation upon mismatch introduction within triply modified duplexes. Bioorgan. Chem., 38, 92-97.
    • (2010) Bioorgan. Chem. , vol.38 , pp. 92-97
    • Catry, M.A.1    Gheerardijn, V.2    Madder, A.3
  • 51
    • 0022423486 scopus 로고
    • Base-base mismatches-thermodynamics of double helix formation for DCA3XA3G + DCT3YT3G (X, y = A,C,G,T)
    • Aboulela,F., Koh,D., Tinoco,I. and Martin,F.H. (1985) Base-base mismatches-thermodynamics of double helix formation for DCA3XA3G + DCT3YT3G (X, Y = A,C,G,T). Nucleic Acids Res., 13, 4811-4824.
    • (1985) Nucleic Acids Res. , vol.13 , pp. 4811-4824
    • Aboulela, F.1    Koh, D.2    Tinoco, I.3    Martin, F.H.4
  • 52
    • 0036827022 scopus 로고    scopus 로고
    • H-1 NMR determination of base-pair lifetimes in oligonucleotides containing single base mismatches
    • Bhattacharya,P.K., Cha,J. and Barton,J.K. (2002) H-1 NMR determination of base-pair lifetimes in oligonucleotides containing single base mismatches. Nucleic Acids Res., 30, 4740-4750.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 4740-4750
    • Bhattacharya, P.K.1    Cha, J.2    Barton, J.K.3
  • 53
    • 0029789894 scopus 로고    scopus 로고
    • The mechanism of self-catalyzed site-selective functionalization of a designed helix-loop-helix motif
    • Broo,K., Brive,L., Lundh,A.C., Ahlberg,P. and Baltzer,L. (1996) The mechanism of self-catalyzed site-selective functionalization of a designed helix-loop-helix motif. J. Am. Chem. Soc., 118, 8172-8173.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 8172-8173
    • Broo, K.1    Brive, L.2    Lundh, A.C.3    Ahlberg, P.4    Baltzer, L.5
  • 54
    • 33947463803 scopus 로고
    • Imidazole catalysis 2. The reaction of substituted imidazoles with phenyl acetates in aqueous solution
    • Bruice,T.C. and Schmir,G.L. (1958) Imidazole catalysis.2. The reaction of substituted imidazoles with phenyl acetates in aqueous solution. J. Am. Chem. Soc., 80, 148-156.
    • (1958) J. Am. Chem. Soc. , vol.80 , pp. 148-156
    • Bruice, T.C.1    Schmir, G.L.2
  • 56
    • 0000146208 scopus 로고
    • Sequential assignment of imino-proton and amino-proton resonances in H-1-NMR spectra of oligonucleotides by two-dimensional NMR-spectroscopy-application to a Lac operator fragment
    • Boelens,R., Scheek,R.M., Dijkstra,K. and Kaptein,R. (1985) Sequential assignment of imino-proton and amino-proton resonances in H-1-NMR spectra of oligonucleotides by two-dimensional NMR-spectroscopy-application to a Lac operator fragment. J. Magn. Reson., 62, 378-386.
    • (1985) J. Magn. Reson. , vol.62 , pp. 378-386
    • Boelens, R.1    Scheek, R.M.2    Dijkstra, K.3    Kaptein, R.4
  • 57
  • 58
    • 64649101249 scopus 로고    scopus 로고
    • Long-timescale molecular dynamics simulations of protein structure and function
    • Klepeis,J.L., Lindorff-Larsen,K., Dror,R.O. and Shaw,D.E. (2009) Long-timescale molecular dynamics simulations of protein structure and function. Curr. Opin. Struct. Biol., 19, 120-127.
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 120-127
    • Klepeis, J.L.1    Lindorff-Larsen, K.2    Dror, R.O.3    Shaw, D.E.4
  • 60
    • 50849107000 scopus 로고    scopus 로고
    • Molecular dynamics of a kappa B DNA element: Base flipping via cross-strand intercalative stacking in a microsecond-scale simulation
    • Mura,C. and McCammon,J.A. (2008) Molecular dynamics of a kappa B DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation. Nucleic Acids Res., 36, 4941-4955.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 4941-4955
    • Mura, C.1    McCammon, J.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.