-
1
-
-
33846887629
-
Alternative roles for metal ions in enzyme catalysis and the implications for ribozyme chemistry
-
Sigel, R. K., and Pyle, A. M. (2007) Alternative roles for metal ions in enzyme catalysis and the implications for ribozyme chemistry. Chem. Rev. 107, 97-113.
-
(2007)
Chem. Rev.
, vol.107
, pp. 97-113
-
-
Sigel, R.K.1
Pyle, A.M.2
-
2
-
-
33644877702
-
MeRNA: A database of metal ion binding sites in RNA structures
-
Stefan, L. R., Zhang, R., Levitan, A. G., Hendrix, D. K., Brenner, S. E., and Holbrook, S. R. (2006) MeRNA: A database of metal ion binding sites in RNA structures. Nucleic Acids Res. 34, D131-D134.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Stefan, L.R.1
Zhang, R.2
Levitan, A.G.3
Hendrix, D.K.4
Brenner, S.E.5
Holbrook, S.R.6
-
3
-
-
20444502087
-
Structure, folding and mechanisms of ribozymes
-
Lilley, D. M. (2005) Structure, folding and mechanisms of ribozymes. Curr. Opin. Struct. Biol. 15, 313-323.
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 313-323
-
-
Lilley, D.M.1
-
4
-
-
0002198148
-
-
In The RNA World (Cech, T. R., Gesteland, R. F., and Atkins, J. F., Eds.) Cold Spring Harbor Laboratory Press, Plainview, NY.
-
Feig, A. L., and Uhlenbeck, O. C. (1999) The Role of Metal Ions in RNA Biochemistry. In The RNA World (Cech, T. R., Gesteland, R. F., and Atkins, J. F., Eds.) pp 287- 320, Cold Spring Harbor Laboratory Press, Plainview, NY.
-
(1999)
The Role of Metal Ions in RNA Biochemistry
, pp. 287-320
-
-
Feig, A.L.1
Uhlenbeck, O.C.2
-
5
-
-
0038713248
-
A thermodynamic framework for the magnesium-dependent folding of RNA
-
Misra, V. K., Shiman, R., and Draper, D. E. (2003)Athermodynamic framework for the magnesium-dependent folding of RNA. Biopolymers 69, 118-136. (Pubitemid 36547061)
-
(2003)
Biopolymers
, vol.69
, pp. 118-136
-
-
Misra, V.K.1
Shiman, R.2
Draper, D.E.3
-
6
-
-
0036295964
-
The linkage between magnesium binding and RNA folding
-
Misra, V. K., and Draper, D. E. (2002) The linkage between magnesium binding and RNA folding. J. Mol. Biol. 317, 507-521.
-
(2002)
J. Mol. Biol.
, vol.317
, pp. 507-521
-
-
Misra, V.K.1
Draper, D.E.2
-
8
-
-
0034625314
-
2- binding to tRNA revisited: The nonlinear Poisson-Boltzmann model
-
2- binding to tRNA revisited: The nonlinear Poisson-Boltzmann model. J. Mol. Biol. 299, 813-825.
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 813-825
-
-
Misra, V.K.1
Draper, D.E.2
-
9
-
-
0032419499
-
On the role of magnesium ions in RNA stability
-
Misra,V.K., and Draper, D.E. (1998) On the role of magnesium ions in RNA stability. Biopolymers 48, 113-135.(Pubitemid 128584747)
-
(1998)
Biopolymers
, vol.48
, pp. 113-135
-
-
Misra, V.K.1
Draper, D.E.2
-
12
-
-
48249121539
-
Detection of innersphere interactions between magnesium hydrate and the phosphate backbone of the HDV ribozyme using Raman crystallography
-
Gong, B., Chen, Y., Christian, E. L., Chen, J. H., Chase, E., Chadalavada, D. M., Yajima, R., Golden, B. L., Bevilacqua, P. C., and Carey, P. R. (2008) Detection of innersphere interactions between magnesium hydrate and the phosphate backbone of the HDV ribozyme using Raman crystallography. J. Am. Chem. Soc. 130, 9670-9672.
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 9670-9672
-
-
Gong, B.1
Chen, Y.2
Christian, E.L.3
Chen, J.H.4
Chase, E.5
Chadalavada, D.M.6
Yajima, R.7
Golden, B.L.8
Bevilacqua, P.C.9
Carey, P.R.10
-
13
-
-
0027365639
-
Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd
-
Duguid, J., Bloomfield, V. A., Benevides, J., and Thomas, G. J., Jr. (1993) Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd. Biophys. J. 65, 1916-1928.
-
(1993)
Biophys. J.
, Issue.65
, pp. 1916-1928
-
-
Duguid, J.1
Bloomfield, V.A.2
Benevides, J.3
Thomas Jr., G.J.4
-
14
-
-
0000765465
-
Vibrational spectroscopic study of the interaction of metal ions with diethyl phosphate, a model for biological systems
-
Stangret, J., and Savoie, R. (1992) Vibrational spectroscopic study of the interaction of metal ions with diethyl phosphate, a model for biological systems. Can. J. Chem. 70, 2875-2883.
-
(1992)
Can. J. Chem.
, vol.70
, pp. 2875-2883
-
-
Stangret, J.1
Savoie, R.2
-
16
-
-
17644374548
-
Computational study of dimethyl phosphate anion and its complexes with water, magnesium, and calcium
-
Petrov, A. S., Funseth-Smotzer, J., and Paqcl, G. R. (2007) Computational study of dimethyl phosphate anion and its complexes with water, magnesium, and calcium. Int. J. Quantum Chem. 1-2, 645-655.
-
(2007)
Int. J. Quantum Chem.
, vol.1-2
, pp. 645-655
-
-
Petrov, A.S.1
Funseth-Smotzer, J.2
Paqcl, G.R.3
-
17
-
-
0032497521
-
Crystal structure of a hepatitis delta virus ribozyme
-
Ferre-D'Amare, A. R., Zhou, K., and Doudna, J. A. (1998) Crystal structure of a hepatitis delta virus ribozyme. Nature 395, 567-574. (Pubitemid 28475703)
-
(1998)
Nature
, vol.395
, pp. 567-574
-
-
Ferre-D'Amare, A.R.1
Zhou, K.2
Doudna, J.A.3
-
18
-
-
0035085466
-
Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions
-
Juneau, K., Podell, E., Harrington, D. J., and Cech, T. R. (2001) Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions. Structure 9, 221-231. (Pubitemid 32245873)
-
(2001)
Structure
, vol.9
, pp. 221-231
-
-
Juneau, K.1
Podell, E.2
Harrington, D.J.3
Cech, T.R.4
-
19
-
-
0035833978
-
Mechanistic characterization of the HDV genomic ribozyme: Assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism
-
Nakano, S., Proctor, D. J., and Bevilacqua, P. C. (2001) Mechanistic characterization of the HDV genomic ribozyme: Assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism. Biochemistry 40, 12022-12038. (Pubitemid 32946544)
-
(2001)
Biochemistry
, vol.40
, pp. 12022-12038
-
-
Nakano, S.1
Proctor, D.J.2
Bevilacqua, P.C.3
-
20
-
-
0033835305
-
Solution structure and metalion binding of the P4 element from bacterial RNase P RNA
-
Schmitz, M., and Tinoco, I., Jr. (2000) Solution structure and metalion binding of the P4 element from bacterial RNase P RNA. RNA 6, 1212-1225.
-
(2000)
RNA
, vol.6
, pp. 1212-1225
-
-
Schmitz, M.1
Tinoco Jr., I.2
-
22
-
-
0021769550
-
2+ complexes of adenine nucleotides and thionucleotides and rate constants for formation and dissociation of MgATP and MgADP
-
2+ complexes of adenine nucleotides and thionucleotides and rate constants for formation and dissociation of MgATP and MgADP. Biochemistry 23, 5262-5271.
-
(1984)
Biochemistry
, vol.23
, pp. 5262-5271
-
-
Pecoraro, V.L.1
Hermes, J.D.2
Cleland, W.W.3
-
23
-
-
0018627368
-
Diastereomers of the nucleoside phosphorothioates as probes of the structure of the metal nucleotide substrates and of the nucleotide binding site of yeast hexokinase
-
Jaffe, E. K., and Cohn, M. (1979) Diastereomers of the nucleoside phosphorothioates as probes of the structure of the metal nucleotide substrates and of the nucleotide binding site of yeast hexokinase. J. Biol. Chem. 254, 10839-10845.
-
(1979)
J. Biol. Chem.
, vol.254
, pp. 10839-10845
-
-
Jaffe, E.K.1
Cohn, M.2
-
24
-
-
0008907571
-
The apparent stability constants of ionic complexes of various adenosine phosphates with divalent cations
-
Smith, R., and Alberty, R. A. (1956) The Apparent Stability Constants of Ionic Complexes of Various Adenosine Phosphates with Divalent Cations. J. Am. Chem. Soc. 78, 2376-2380.
-
(1956)
J. Am. Chem. Soc.
, vol.78
, pp. 2376-2380
-
-
Smith, R.1
Alberty, R.A.2
-
25
-
-
0034602926
-
Solution structure of cobalt-(III)hexammine complexed to the GAAA tetraloop, and metal-ion binding to G3A mismatches
-
Rudisser, S., and Tinoco, I., Jr. (2000) Solution structure of cobalt-(III)hexammine complexed to the GAAA tetraloop, and metal-ion binding to G3A mismatches. J. Mol. Biol. 295, 1211-1223.
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 1211-1223
-
-
Rudisser, S.1
Tinoco Jr., I.2
-
26
-
-
0021891882
-
Nucleoside phosphorothioates
-
Eckstein, F. (1985) Nucleoside phosphorothioates. Annu. Rev. Biochem. 54, 367-402.
-
(1985)
Annu. Rev. Biochem.
, vol.54
, pp. 367-402
-
-
Eckstein, F.1
-
27
-
-
0030948291
-
2(POS)]
-
2(POS)]. J. Biomol. Struct. Dyn. 14, 509-516.
-
(1997)
J. Biomol. Struct. Dyn.
, vol.14
, pp. 509-516
-
-
Steinke, C.A.1
Reeves, K.K.2
Powell, J.W.3
Lee, S.A.4
Chen, Y.Z.5
Wyrzykiewicz, T.6
Griffey, R.H.7
Mohan, V.8
-
29
-
-
0018786911
-
A Raman spectroscopic study of the interaction of divalent metal ions with adenine moiety of adenosine 5′-triphosphate
-
Lanir, A., and Yu, N. T. (1979) A Raman spectroscopic study of the interaction of divalent metal ions with adenine moiety of adenosine 5′-triphosphate. J. Biol. Chem. 254, 5882-5887.
-
(1979)
J. Biol. Chem.
, vol.254
, pp. 5882-5887
-
-
Lanir, A.1
Yu, N.T.2
-
30
-
-
0000685751
-
Macrochelate formation in monomeric metal ion complexes of nucleoside 5′-triphosphates and the promotion of stacking by metal ions. Comparison of the self-association of purine and pyrimidine 5′-triphosphates using proton nuclear magnetic resonance
-
Scheller, K. H., Hofstetter, F., Mitchell, P. R., Prijs, B., and Sigel, H. (1981) Macrochelate formation in monomeric metal ion complexes of nucleoside 5′-triphosphates and the promotion of stacking by metal ions. Comparison of the self-association of purine and pyrimidine 5′-triphosphates using proton nuclear magnetic resonance. J. Am. Chem. Soc. 103, 247-260.
-
(1981)
J. Am. Chem. Soc.
, vol.103
, pp. 247-260
-
-
Scheller, K.H.1
Hofstetter, F.2
Mitchell, P.R.3
Prijs, B.4
Sigel, H.5
-
31
-
-
0023874937
-
Macrochelate complexes of purine 50-nucleotide triphosphates and monophosphates: Definitive multinuclear NMR evidence supported by molecular mechanics calculations
-
Reily, M. D., Hambley, T. W., and Marzilli, L. G. (1988) Macrochelate complexes of purine 50-nucleotide triphosphates and monophosphates: Definitive multinuclear NMR evidence supported by molecular mechanics calculations. J. Am. Chem. Soc. 110, 2999-3007.
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 2999-3007
-
-
Reily, M.D.1
Hambley, T.W.2
Marzilli, L.G.3
-
34
-
-
33845279880
-
Absolute electronegativity and hardness: Application to inorganic chemistry
-
Pearson, R. G. (1988) Absolute Electronegativity and Hardness: Application to Inorganic Chemistry. Inorg. Chem. 27, 734-740.
-
(1988)
Inorg. Chem.
, vol.27
, pp. 734-740
-
-
Pearson, R.G.1
-
35
-
-
0035957280
-
Altering the intermediate in the equilibrium folding of unmodified yeast tRNAPhe with monovalent and divalent cations
-
Shelton, V. M., Sosnick, T. R., and Pan, T. (2001) Altering the intermediate in the equilibrium folding of unmodified yeast tRNAPhe with monovalent and divalent cations. Biochemistry 40, 3629-3638.
-
(2001)
Biochemistry
, vol.40
, pp. 3629-3638
-
-
Shelton, V.M.1
Sosnick, T.R.2
Pan, T.3
-
36
-
-
0033592945
-
Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding
-
Shelton, V. M., Sosnick, T. R., and Pan, T. (1999) Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding. Biochemistry 38, 16831-16839. (Pubitemid 30013688)
-
(1999)
Biochemistry
, vol.38
, pp. 16831-16839
-
-
Shelton, V.M.1
Sosnick, T.R.2
Pan, T.3
-
37
-
-
0033862354
-
The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: A classic structure revisited
-
Shi, H., and Moore, P. B. (2000) The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: A classic structure revisited. RNA 6, 1091-1105. (Pubitemid 30620393)
-
(2000)
RNA
, vol.6
, pp. 1091-1105
-
-
Shi, H.1
Moore, P.B.2
-
38
-
-
61749093844
-
A catalytic metal ion interacts with the cleavage site G3U wobble in the HDV ribozyme
-
Chen, J. H., Gong, B., Bevilacqua, P. C., Carey, P. R., and Golden, B. L. (2009) A catalytic metal ion interacts with the cleavage site G3U wobble in the HDV ribozyme. Biochemistry 48, 1498-1507.
-
(2009)
Biochemistry
, vol.48
, pp. 1498-1507
-
-
Chen, J.H.1
Gong, B.2
Bevilacqua, P.C.3
Carey, P.R.4
Golden, B.L.5
-
40
-
-
36848999901
-
Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids
-
Bai, Y., Greenfeld, M., Travers, K. J., Chu,V. B., Lipfert, J., Doniach, S., and Herschlag, D. (2007) Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids. J. Am. Chem. Soc. 129, 14981-14988.
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 14981-14988
-
-
Bai, Y.1
Greenfeld, M.2
Travers, K.J.3
Chu, V.B.4
Lipfert, J.5
Doniach, S.6
Herschlag, D.7
-
42
-
-
33749032381
-
2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures
-
2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures. Proc. Natl. Acad. Sci. U.S.A. 103, 14003-14008.
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 14003-14008
-
-
Grilley, D.1
Soto, A.M.2
Draper, D.E.3
|