-
1
-
-
4243545125
-
Oxidative nucleobase modifications leading to strand scission
-
Burrows, C. J.; Muller, J. G. Oxidative Nucleobase Modifications Leading to Strand Scission. Chem. Rev. 1998, 98 (3), 1109-1152.
-
(1998)
Chem. Rev.
, vol.98
, Issue.3
, pp. 1109-1152
-
-
Burrows, C.J.1
Muller, J.G.2
-
2
-
-
0042342532
-
A mechanistic perspective on the chemistry of DNA repair glycosylases
-
Stivers, J. T.; Jiang, Y. L. A Mechanistic Perspective on the Chemistry of DNA Repair Glycosylases. Chem. Rev. 2003, 103 (7), 2729-2760.
-
(2003)
Chem. Rev.
, vol.103
, Issue.7
, pp. 2729-2760
-
-
Stivers, J.T.1
Jiang, Y.L.2
-
3
-
-
0034708226
-
Structural basis for recognition and repair of endogenous mutagen 8-oxoguanine in DNA
-
Bruner, S. D.; Norman, D. P. G.; Verdine, G. L. Structural basis for recognition and repair of endogenous mutagen 8-oxoguanine in DNA. Nature 2000, 403, 859-866.
-
(2000)
Nature
, vol.403
, pp. 859-866
-
-
Bruner, S.D.1
Norman, D.P.G.2
Verdine, G.L.3
-
4
-
-
0037205477
-
Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA
-
Gilboa, R.; Zharkov, D. O.; Golan, G.; Fernandes, A. S.; Gerchman, S. E.; E. Matz, J. H. K.; Grollman, A. P.; Shoham, G. Structure of Formamidopyrimidine-DNA Glycosylase Covalently Complexed to DNA. J. Biol. Chem. 2002, 277, 19811-19816.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 19811-19816
-
-
Gilboa, R.1
Zharkov, D.O.2
Golan, G.3
Fernandes, A.S.4
Gerchman, S.E.5
Matz, J.H.K.E.6
Grollman, A.P.7
Shoham, G.8
-
5
-
-
0037124320
-
Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA
-
Serre, L. P. d. J. K.; Boiteux, S.; Zelwer, C.; Castaing, B. Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA. EMBO J. 2002, 21 (12), 2854-65.
-
(2002)
EMBO J.
, vol.21
, Issue.12
, pp. 2854-2865
-
-
Serre, L.P.D.J.K.1
Boiteux, S.2
Zelwer, C.3
Castaing, B.4
-
6
-
-
0025802822
-
Site-specific mutagenesis using a gapped duplex vector: A study of translesion synthesis past 8-oxodeoxyguanosine in E. coli
-
Moriya, M. O. C.; Bodepudi, V.; Johnson, F.; Takeshita, M.; Grollman, A. P. Site-specific mutagenesis using a gapped duplex vector: a study of translesion synthesis past 8-oxodeoxyguanosine in E. coli. Mutat Res. 1991, 254, 281-8.
-
(1991)
Mutat Res.
, vol.254
, pp. 281-288
-
-
Moriya, M.O.C.1
Bodepudi, V.2
Johnson, F.3
Takeshita, M.4
Grollman, A.P.5
-
7
-
-
0027160522
-
Translesional synthesis on DNA templates containing 8-oxo-7,8- dihydrodeoxyadenosine
-
Shibutani, S. B. V.; Johnson, F.; Grollman, A. P. Translesional synthesis on DNA templates containing 8-oxo-7,8-dihydrodeoxyadenosine. Biochemistry 1993, 32, 4615-21.
-
(1993)
Biochemistry
, vol.32
, pp. 4615-4621
-
-
Shibutani, S.B.V.1
Johnson, F.2
Grollman, A.P.3
-
8
-
-
0025045198
-
The role of 8-hydroxyguanine in carcinogenesis
-
Floyd, R. The role of 8-hydroxyguanine in carcinogenesis. Carcinogenesis 1990, 11, 1447-1450.
-
(1990)
Carcinogenesis
, vol.11
, pp. 1447-1450
-
-
Floyd, R.1
-
9
-
-
0025373259
-
Oxidative damage I to DNA during aging: 8-hydroxy-2′-deoxyguanosine in rat organ DNA and urine
-
Fraga, C.; Shienaga, M.; Park, J.; Degan, P.; Ames, B. Oxidative damage I to DNA during aging: 8-hydroxy-2′-deoxyguanosine in rat organ DNA and urine. Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 4533-4537.
-
(1990)
Proc. Natl. Acad. Sci. U.S.A.
, vol.87
, pp. 4533-4537
-
-
Fraga, C.1
Shienaga, M.2
Park, J.3
Degan, P.4
Ames, B.5
-
11
-
-
1342304229
-
Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase
-
Fromme, J. C.; Banerjee, A.; Huang, S. J.; Verdine, G. L. Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase. Nature 2004, 427, 652-656.
-
(2004)
Nature
, vol.427
, pp. 652-656
-
-
Fromme, J.C.1
Banerjee, A.2
Huang, S.J.3
Verdine, G.L.4
-
12
-
-
0033579953
-
Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase
-
Stivers, J. T.; Pankiewicz, K. W.; Watanabe, K. A. Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase. Biochemistry 1999, 38, 952-963.
-
(1999)
Biochemistry
, vol.38
, pp. 952-963
-
-
Stivers, J.T.1
Pankiewicz, K.W.2
Watanabe, K.A.3
-
13
-
-
0037036363
-
Flipping duplex DNA inside out: A double base-flipping reaction mechanism by Escherichia coli MutY adenine glycosylase
-
Bernards, A. S.; Miller, J. K.; Bao, K. K.; I., W. Flipping duplex DNA inside out: a double base-flipping reaction mechanism by Escherichia coli MutY adenine glycosylase. J. Biol. Chem. 2002, 277, 20960-20964.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 20960-20964
-
-
Bernards, A.S.1
Miller, J.K.2
Bao, K.K.3
-
14
-
-
0024285807
-
Evidence from base-pair kinetics for two types of adenine tract structures in solution: Their relation to DNA curvature
-
Leroy, J.-L.; Charretier, E.; Kochoyan, M.; Gueron, M. Evidence from base-pair kinetics for two types of adenine tract structures in solution: their relation to DNA curvature. Biochemistry 1988, 27, 8894-8898.
-
(1988)
Biochemistry
, vol.27
, pp. 8894-8898
-
-
Leroy, J.-L.1
Charretier, E.2
Kochoyan, M.3
Gueron, M.4
-
15
-
-
0033548682
-
High base pair opening rates in tracts of GC base pairs
-
Dornberger, U.; Leijon, M.; Fritzsche, H. High base pair opening rates in tracts of GC base pairs. J. Biol. Chem. 1999, 274, 6957-6962.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 6957-6962
-
-
Dornberger, U.1
Leijon, M.2
Fritzsche, H.3
-
16
-
-
0037178070
-
Base flipping in DNA: Pathways and energetics studied with molecular dynamic simulations
-
Varnai, P.; Lavery, R. Base Flipping in DNA: Pathways and Energetics Studied with Molecular Dynamic Simulations J. Am. Chem. Soc. 2002, 124 (25), 7272-7273.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, Issue.25
, pp. 7272-7273
-
-
Varnai, P.1
Lavery, R.2
-
17
-
-
0035915260
-
Energetic and conformational aspects of A:T base-pair opening within the DNA double helix
-
Giudice, E.; Varnai, P.; Lavery, R. Energetic and conformational aspects of A:T base-pair opening within the DNA double helix. ChemPhysChem 2001, 2 (11), 673ff.
-
(2001)
ChemPhysChem
, vol.2
, Issue.11
-
-
Giudice, E.1
Varnai, P.2
Lavery, R.3
-
19
-
-
0037422594
-
Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase
-
Huang, N.; Banavali, N. K.; MacKerell, A. D. Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (1), 68-73.
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, Issue.1
, pp. 68-73
-
-
Huang, N.1
Banavali, N.K.2
MacKerell, A.D.3
-
20
-
-
0031578972
-
Parallel tempering algorithm for conformational studies of biological molecules
-
Hansmann, U. H. E. Parallel tempering algorithm for conformational studies of biological molecules. Chem. Phys. Lett. 1997, 281 (1-3), 140-150.
-
(1997)
Chem. Phys. Lett.
, vol.281
, Issue.1-3
, pp. 140-150
-
-
Hansmann, U.H.E.1
-
21
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 1999, 314 (1-2), 141-151.
-
(1999)
Chem. Phys. Lett.
, vol.314
, Issue.1-2
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
22
-
-
9244260409
-
-
University of California: San Francisco
-
Case, D. A. et al. AMBER 8; University of California: San Francisco, 2004.
-
(2004)
AMBER 8
-
-
Case, D.A.1
-
23
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field For the Simulation Of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 1995, 117 (19), 5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, Issue.19
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
24
-
-
33646940952
-
Numerical-integration of cartesian equations of motion of a system with constraints - Molecular-dynamics of N-alkanes
-
Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes. J. Comput. Phys. 1977, 23 (3), 327-341.
-
(1977)
J. Comput. Phys.
, vol.23
, Issue.3
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
25
-
-
0038626733
-
8-Oxoguanine enhances bending of DNA that favors binding to glycosylases
-
Miller, J. H.; Chiang, C. P.; Straatsma, T. P.; Kennedy, M. A. 8-Oxoguanine Enhances Bending of DNA that Favors Binding to Glycosylases. J. Am. Chem. Soc. 2003, 125, 6331-6336.
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 6331-6336
-
-
Miller, J.H.1
Chiang, C.P.2
Straatsma, T.P.3
Kennedy, M.A.4
-
26
-
-
0037038372
-
Absolute comparison of simulated and experimental protein-folding dynamics
-
Snow, C. D.; Nguyen, N.; Pande, V. S.; Gruebele, M. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 2002, 420 (6911), 102-106.
-
(2002)
Nature
, vol.420
, Issue.6911
, pp. 102-106
-
-
Snow, C.D.1
Nguyen, N.2
Pande, V.S.3
Gruebele, M.4
-
27
-
-
0035312551
-
Macromolecular electrostatics: Continuum models and their growing pains
-
Simonson, T. Macromolecular electrostatics: continuum models and their growing pains. Curr. Opin. Struct. Biol. 2001, 11 (2), 243-252.
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, Issue.2
, pp. 243-252
-
-
Simonson, T.1
-
28
-
-
0019843568
-
Structure of a B-DNA dodecamer. 3. Geometry of hydration
-
Drew, H. R.; Dickerson, R. E. Structure of a B-DNA Dodecamer. 3. Geometry of Hydration. J. Mol. Biol. 1981, 151 (3), 535-556.
-
(1981)
J. Mol. Biol.
, vol.151
, Issue.3
, pp. 535-556
-
-
Drew, H.R.1
Dickerson, R.E.2
-
29
-
-
0024121512
-
Theoretical considerations on the spine of hydration in the minor groove of D(Cgcgaattcgcg)-D(Gcgcttaagcgc) - Monte Carlo computer simulation
-
Subramanian, P. S.; Ravishanker, G.; Beveridge, D. L. Theoretical Considerations on the Spine of Hydration in the Minor Groove of D(Cgcgaattcgcg)-D(Gcgcttaagcgc) - Monte Carlo Computer Simulation. Proc. Natl. Acad. Sci. U.S.A. 1988, 85 (6), 1836-1840.
-
(1988)
Proc. Natl. Acad. Sci. U.S.A.
, vol.85
, Issue.6
, pp. 1836-1840
-
-
Subramanian, P.S.1
Ravishanker, G.2
Beveridge, D.L.3
-
30
-
-
0027058824
-
NMR observation of individual molecules of hydration water bound to DNA duplexes - Direct evidence for a spine of hydration water present in aqueous solution
-
Liepinsh, E.; Otting, G.; Wuthrich, K. NMR Observation of Individual Molecules of Hydration Water Bound to DNA Duplexes - Direct Evidence for a Spine of Hydration Water Present in Aqueous Solution. Nucleic Acids Res. 1992, 20 (24), 6549-6553.
-
(1992)
Nucleic Acids Res.
, vol.20
, Issue.24
, pp. 6549-6553
-
-
Liepinsh, E.1
Otting, G.2
Wuthrich, K.3
-
31
-
-
0034701222
-
Molecular dynamics simulations of nucleic acids with a generalized born solvation model
-
Tsui, V.; Case, D. A. Molecular dynamics simulations of nucleic acids with a generalized born solvation model. J. Am. Chem. Soc. 2000, 122 (11), 2489-2498.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, Issue.11
, pp. 2489-2498
-
-
Tsui, V.1
Case, D.A.2
-
32
-
-
0033064123
-
Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model
-
Williams, D. J.; Hall, K. B. Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model. Biophvs. J. 1999, 76 (6), 3192-3205.
-
(1999)
Biophvs. J.
, vol.76
, Issue.6
, pp. 3192-3205
-
-
Williams, D.J.1
Hall, K.B.2
-
33
-
-
0037120830
-
Conformational heterogeneity observed in simulations of a pyrene-substituted DNA
-
Cui, G. L.; Simmerling, C. Conformational heterogeneity observed in simulations of a pyrene-substituted DNA. J. Am. Chem. Soc. 2002, 124 (41), 12154-12164.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, Issue.41
, pp. 12154-12164
-
-
Cui, G.L.1
Simmerling, C.2
-
34
-
-
0035892161
-
Calculations of the absolute free energies of binding between RNA and metal ions using molecular dynamics simulations and continuum electrostatics
-
Tsui, V.; Case, D. A. Calculations of the absolute free energies of binding between RNA and metal ions using molecular dynamics simulations and continuum electrostatics. J. Phys. Chem. B 2001, 105 (45), 11314-11325.
-
(2001)
J. Phys. Chem. B
, vol.105
, Issue.45
, pp. 11314-11325
-
-
Tsui, V.1
Case, D.A.2
-
36
-
-
84988112508
-
An efficient Newton-like method for molecular mechanics energy minimization of large molecules
-
Ponder, J. W.; Richards, F. M. An Efficient Newton-Like Method for Molecular Mechanics Energy Minimization of Large Molecules. J. Comput. Chem. 1987, 8 (7), 1016-1024.
-
(1987)
J. Comput. Chem.
, vol.8
, Issue.7
, pp. 1016-1024
-
-
Ponder, J.W.1
Richards, F.M.2
-
37
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 1983, 79, 926-935.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
38
-
-
33846823909
-
Particle Mesh Ewald - An N.Log(N) method for ewald sums in large systems
-
Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald - an N.Log(N) Method for Ewald Sums in Large Systems. J. Chem. Phys. 1993, 98 (12), 10089-10092.
-
(1993)
J. Chem. Phys.
, vol.98
, Issue.12
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
39
-
-
0029170114
-
Molecular dynamics simulations on solvated biomolecular systems - The particle Mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins
-
Cheatham, T. E.; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A. Molecular Dynamics Simulations On Solvated Biomolecular Systems - the Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins. J. Am. Chem. Soc. 1995, 117 (14), 4193-4194.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, Issue.14
, pp. 4193-4194
-
-
Cheatham, T.E.1
Miller, J.L.2
Fox, T.3
Darden, T.A.4
Kollman, P.A.5
-
40
-
-
18544381108
-
Modified replica exchange simulation methods for local structure refinement
-
Cheng, X. L.; Cui, G. L.; Hornak, V.; Simmerling, C. Modified Replica Exchange Simulation Methods for Local Structure Refinement. J. Phys. Chem. B 2005, 109 (16), 8220-8230.
-
(2005)
J. Phys. Chem. B
, vol.109
, Issue.16
, pp. 8220-8230
-
-
Cheng, X.L.1
Cui, G.L.2
Hornak, V.3
Simmerling, C.4
-
41
-
-
0037157317
-
On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
-
Fukunishi, H. W. O.; Takada, S. On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction. J. Chem. Phys. 2002, 116 (20), 9058-9067.
-
(2002)
J. Chem. Phys.
, vol.116
, Issue.20
, pp. 9058-9067
-
-
Fukunishi, H.W.O.1
Takada, S.2
-
42
-
-
0037109535
-
On the acceptance probability of replica-exchange Monte Carlo trials
-
i42) Kofke, D. A. On the acceptance probability of replica-exchange Monte Carlo trials. J. Chem. Phys. 2002, 117 (15), 6911-6914.
-
(2002)
J. Chem. Phys.
, vol.117
, Issue.15
, pp. 6911-6914
-
-
Kofke, D.A.1
-
43
-
-
0025600834
-
Enhanced sampling in molecular dynamics - Use of the time-dependent hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
-
Elber, R.; Karplus, M. Enhanced Sampling in Molecular Dynamics - Use of the Time-Dependent Hartree Approximation For a Simulation of Carbon Monoxide Diffusion Through Myoglobin. J. Am. Chem. Soc. 1990, 112 (25), 9161-9175.
-
(1990)
J. Am. Chem. Soc.
, vol.112
, Issue.25
, pp. 9161-9175
-
-
Elber, R.1
Karplus, M.2
-
44
-
-
36449006131
-
Modeling side chains in peptides and proteins - Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations
-
Roitberg, A.; Elber, R. Modeling Side Chains in Peptides and Proteins - Application of the Locally Enhanced Sampling and the Simulated Annealing Methods to Find Minimum Energy Conformations. J. Chem. Phys. 1991, 95 (12), 9277-9287.
-
(1991)
J. Chem. Phys.
, vol.95
, Issue.12
, pp. 9277-9287
-
-
Roitberg, A.1
Elber, R.2
-
45
-
-
0032578192
-
Combined locally enhanced sampling and particle Mesh Ewald as a strategy to locate the experimental structure of a nonhelical nucleic acid
-
Simmerling, C.; Miller, J. L.; Kollman, P. A. Combined Locally Enhanced Sampling and Particle Mesh Ewald as a strategy to locate the experimental structure of a nonhelical nucleic acid. J. Am. Chem. Soc. 1998, 120 (29), 7149-7155.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, Issue.29
, pp. 7149-7155
-
-
Simmerling, C.1
Miller, J.L.2
Kollman, P.A.3
-
46
-
-
1642419747
-
Improved conformational sampling through an efficient combination of mean-field simulation approaches
-
Cheng, X. L.; Hornak, V.; Simmerling, C. Improved conformational sampling through an efficient combination of mean-field simulation approaches. J. Phys. Chem. B 2004, 108 (1), 426-437.
-
(2004)
J. Phys. Chem. B
, vol.108
, Issue.1
, pp. 426-437
-
-
Cheng, X.L.1
Hornak, V.2
Simmerling, C.3
-
47
-
-
3042734385
-
Molecular dynamics simulations of Guanine quadruplex loops: Advances and force field limitations
-
Fadrna, E.; Spackova, N.; Stefl, R.; Koca, J.; Cheatham, T. E., III; Sponer, J. Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations. Biophys. J. 2004, 87 (1), 227-42.
-
(2004)
Biophys. J.
, vol.87
, Issue.1
, pp. 227-242
-
-
Fadrna, E.1
Spackova, N.2
Stefl, R.3
Koca, J.4
Cheatham III, T.E.5
Sponer, J.6
-
48
-
-
0000089213
-
Energy equipartitioning in the classical time-dependent hartree approximation
-
Straub, J. E.; Karplus, M. Energy Equipartitioning in the Classical Time-Dependent Hartree Approximation. J. Chem. Phys. 1991, 94 (10), 6737-6739.
-
(1991)
J. Chem. Phys.
, vol.94
, Issue.10
, pp. 6737-6739
-
-
Straub, J.E.1
Karplus, M.2
-
49
-
-
0001483109
-
The thermal equilibrium aspects of the time dependent hartree and the locally enhanced sampling approximations - Formal properties, a correction, and computational examples for rare gas clusters
-
Ulitsky, A.; Elber, R. The Thermal Equilibrium Aspects of the Time Dependent Hartree and the Locally Enhanced Sampling Approximations - Formal Properties, a Correction, and Computational Examples For Rare Gas Clusters. J. Chem. Phys. 1993, 98 (4), 3380-3388.
-
(1993)
J. Chem. Phys.
, vol.98
, Issue.4
, pp. 3380-3388
-
-
Ulitsky, A.1
Elber, R.2
-
50
-
-
0024539180
-
Defining the structure of irregular nucleic-acids - Conventions and principles
-
Lavery, R.; Sklenar, H. Defining the Structure of Irregular Nucleic-Acids - Conventions and Principles. J. Biomol. Struct. Dyn. 1989, 6 (4), 655-667.
-
(1989)
J. Biomol. Struct. Dyn.
, vol.6
, Issue.4
, pp. 655-667
-
-
Lavery, R.1
Sklenar, H.2
-
51
-
-
0001344298
-
G(syn).A(anti) mismatch formation in DNA dodecamers at acidic pH: PH-dependent conformational transition of G:A mispairs detected by proton NMR
-
Gao, X.; Patel, D. J. G(syn).A(anti) Mismatch Formation in DNA Dodecamers at Acidic pH: pH-Dependent Conformational Transition of G:A Mispairs Detected by Proton NMR. J. Am. Chem. Soc. 1988, 110, 5178-5182.
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 5178-5182
-
-
Gao, X.1
Patel, D.J.2
-
52
-
-
0023628497
-
Helix geometry, hydration, and G:A mismatch in a B-DNA decamer
-
Prive, G.; Heinemann, U.; Chandrasegaran, S.; Kan, L.; Kopka, M.; Dickerson, R. Helix Geometry, Hydration, and G:A Mismatch in a B-DNA Decamer. Science 1987, 238, 498-503.
-
(1987)
Science
, vol.238
, pp. 498-503
-
-
Prive, G.1
Heinemann, U.2
Chandrasegaran, S.3
Kan, L.4
Kopka, M.5
Dickerson, R.6
-
53
-
-
0028783875
-
Influence of the oxidatively damaged adduct 8-oxodeoxyguanosine on the conformation, energetics, and thermodynamic stability of a DNA duplex
-
Plum, G. E.; Grollman, A. P.; Johnson, F.; Breslauer, K. J. Influence of the oxidatively damaged adduct 8-oxodeoxyguanosine on the conformation, energetics, and thermodynamic stability of a DNA duplex. Biochemistry 1995, 34 (49), 16148-60.
-
(1995)
Biochemistry
, vol.34
, Issue.49
, pp. 16148-16160
-
-
Plum, G.E.1
Grollman, A.P.2
Johnson, F.3
Breslauer, K.J.4
-
54
-
-
0024373710
-
Thermodynamic comparison of the base pairs formed by the carcinogenic lesion O6-methylguanine with reference both to Watson-Crick pairs and to mismatched pairs
-
Barbara, L.; Gaffney, R. A. J. Thermodynamic comparison of the base pairs formed by the carcinogenic lesion O6-methylguanine with reference both to Watson-Crick pairs and to mismatched pairs. Biochemistry 1989, 28 (14), 5881-5889.
-
(1989)
Biochemistry
, vol.28
, Issue.14
, pp. 5881-5889
-
-
Barbara, L.1
Gaffney, R.A.J.2
-
55
-
-
0022423486
-
Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A, C, G, T)
-
Aboul-ela, F.; Koh, D.; Tinoco, I.; Martin, F. H. Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A, C, G, T). Nucleic Acids Res. 1985, 13, 4811-4824.
-
(1985)
Nucleic Acids Res.
, vol.13
, pp. 4811-4824
-
-
Aboul-Ela, F.1
Koh, D.2
Tinoco, I.3
Martin, F.H.4
-
56
-
-
0021754242
-
Deoxyguanosine-deoxyadenosine pairing in the d(C-G-A-G-A-A-T-T-C-G-C-G) duplex: Conformation and dynamics at and adjacent to the dG X dA mismatch site
-
Patel, D.; Kozlowski, S.; Ikuta, S.; Itakura, K. Deoxyguanosine- deoxyadenosine pairing in the d(C-G-A-G-A-A-T-T-C-G-C-G) duplex: conformation and dynamics at and adjacent to the dG X dA mismatch site. Biochemistry 1984, 23 (14), 3207-17.
-
(1984)
Biochemistry
, vol.23
, Issue.14
, pp. 3207-3217
-
-
Patel, D.1
Kozlowski, S.2
Ikuta, S.3
Itakura, K.4
-
57
-
-
0023008661
-
Structural features and hydration of d(C-G-C-G-A-A-T-T-A-G-C-G); a double helix containing two G.A mispairs
-
Hunter, W.; Brown, T.; Kennard, O. Structural features and hydration of d(C-G-C-G-A-A-T-T-A-G-C-G); a double helix containing two G.A mispairs. J. Biomol. Struct. Dyn. 1986, 4 (2), 173-91.
-
(1986)
J. Biomol. Struct. Dyn.
, vol.4
, Issue.2
, pp. 173-191
-
-
Hunter, W.1
Brown, T.2
Kennard, O.3
-
58
-
-
0037335588
-
Base pair opening within B-DNA: Free energy pathways for GC and at pairs from umbrella sampling simulations
-
Giudice, E.; Varnai, P.; Lavery, R. Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations. Nucleic Acids Res. 2003, 31 (5), 1434-43.
-
(2003)
Nucleic Acids Res.
, vol.31
, Issue.5
, pp. 1434-1443
-
-
Giudice, E.1
Varnai, P.2
Lavery, R.3
-
59
-
-
0034641947
-
The crystal structure of DNA mismatch repair protein MutS binding to a GT mismatch
-
Lamers, M.; Perrakis, A.; Enzlin, J.; Winterwerp, H.; Wind, N. d.; Sixma, T. The crystal structure of DNA mismatch repair protein MutS binding to a GT mismatch. Nature 2000, 407 (6805), 711-7.
-
(2000)
Nature
, vol.407
, Issue.6805
, pp. 711-717
-
-
Lamers, M.1
Perrakis, A.2
Enzlin, J.3
Winterwerp, H.4
Wind, N.D.5
Sixma, T.6
-
60
-
-
0017772412
-
Carbon-13 magnetic resonance spectra of 8-substituted purine nucleosides. Characteristic shifts for the syn conformation
-
Uesugi, S.; Ikehara, M. Carbon-13 magnetic resonance spectra of 8-substituted purine nucleosides. Characteristic shifts for the syn conformation. J. Am. Chem. Soc. 1977, 99 (10), 3250-3.
-
(1977)
J. Am. Chem. Soc.
, vol.99
, Issue.10
, pp. 3250-3253
-
-
Uesugi, S.1
Ikehara, M.2
-
61
-
-
0034671291
-
DNA structure: What is in charge?
-
McConnell, K. J.; Beveridge, D. L. DNA structure: What is in charge? J. Mol. Biol. 2000, 304 (5), 803-820.
-
(2000)
J. Mol. Biol.
, vol.304
, Issue.5
, pp. 803-820
-
-
McConnell, K.J.1
Beveridge, D.L.2
-
62
-
-
0036245097
-
Molecular dynamics simulation of 7,8-dihydro-8-oxoguanine DNA
-
Ishida, H. Molecular dynamics simulation of 7,8-dihydro-8-oxoguanine DNA. J. Biomol. Struct. Dyn. 2002, 19 (5), 839-51.
-
(2002)
J. Biomol. Struct. Dyn.
, vol.19
, Issue.5
, pp. 839-851
-
-
Ishida, H.1
-
63
-
-
0028864424
-
Studies of base pair kinetics by NMR measurement of proton exchange
-
Gueron, M.; Leroy, J. L. Studies of base pair kinetics by NMR measurement of proton exchange. Methods Enzymol. 1995, 261, 383-413.
-
(1995)
Methods Enzymol.
, vol.261
, pp. 383-413
-
-
Gueron, M.1
Leroy, J.L.2
-
64
-
-
0023256126
-
A single mode of DNA base-pair opening drives imino proton exchange
-
Gueron, M. K. M.; Leroy, J. L. A single mode of DNA base-pair opening drives imino proton exchange Nature 1987, 328, 89.
-
(1987)
Nature
, vol.328
, pp. 89
-
-
Gueron, M.K.M.1
Leroy, J.L.2
-
65
-
-
0000777707
-
Energetic coupling between DNA bending and base pair opening
-
Ramstein, J.; Lavery, R. Energetic Coupling between DNA Bending and Base Pair Opening. Proc. Natl. Acad. Sci. U.S.A. 1988, 85 (19), 7231-7235.
-
(1988)
Proc. Natl. Acad. Sci. U.S.A.
, vol.85
, Issue.19
, pp. 7231-7235
-
-
Ramstein, J.1
Lavery, R.2
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