-
1
-
-
66549124907
-
The structures of quadruplex nucleic acids and their drug complexes
-
Neidle, S. The structures of quadruplex nucleic acids and their drug complexes Curr. Opin. Struct. Biol. 2009, 19, 239-250
-
(2009)
Curr. Opin. Struct. Biol.
, vol.19
, pp. 239-250
-
-
Neidle, S.1
-
2
-
-
77954710925
-
Metallo-organic G-quadruplex ligands in anticancer drug design
-
Jiang, Y. L.; Liu, Z. P. Metallo-organic G-quadruplex ligands in anticancer drug design Mini-Rev. Med. Chem. 2010, 10, 726-736
-
(2010)
Mini-Rev. Med. Chem.
, vol.10
, pp. 726-736
-
-
Jiang, Y.L.1
Liu, Z.P.2
-
3
-
-
79960840968
-
Binding properties of human telomeric quadruplex multimers: A new route for drug design
-
Cummaro, A.; Fotticchia, I.; Franceschin, M.; Giancola, C.; Petraccone, L. Binding properties of human telomeric quadruplex multimers: A new route for drug design Biochimie 2011, 93, 1392-1400
-
(2011)
Biochimie
, vol.93
, pp. 1392-1400
-
-
Cummaro, A.1
Fotticchia, I.2
Franceschin, M.3
Giancola, C.4
Petraccone, L.5
-
4
-
-
79952749516
-
Quadruplex DNA: A promising drug target for the medicinal inorganic chemist
-
Ralph, S. F. Quadruplex DNA: A promising drug target for the medicinal inorganic chemist Curr. Top. Med. Chem. 2011, 11, 572-590
-
(2011)
Curr. Top. Med. Chem.
, vol.11
, pp. 572-590
-
-
Ralph, S.F.1
-
5
-
-
84865298982
-
DNA aptamer functionalized nanomaterials for intracellular analysis, cancer cell imaging, and drug delivery
-
Xing, H.; Wong, N. Y.; Xiang, Y.; Lu, Y. DNA aptamer functionalized nanomaterials for intracellular analysis, cancer cell imaging, and drug delivery Curr. Opin. Chem. Biol. 2012, 16, 429-435
-
(2012)
Curr. Opin. Chem. Biol.
, vol.16
, pp. 429-435
-
-
Xing, H.1
Wong, N.Y.2
Xiang, Y.3
Lu, Y.4
-
6
-
-
0028318093
-
Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG)
-
Schultze, P.; Macaya, R. F.; Feigon, J. Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG) J. Mol. Biol. 1994, 235, 1532-1547
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1532-1547
-
-
Schultze, P.1
MacAya, R.F.2
Feigon, J.3
-
7
-
-
0034194110
-
Structures of the potassium-saturated, 2:1, and intermediate, 1:1, forms of a quadruplex DNA
-
Marathias, V. M.; Bolton, P. H. Structures of the potassium-saturated, 2:1, and intermediate, 1:1, forms of a quadruplex DNA Nucleic Acids Res. 2000, 28, 1969-1977
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 1969-1977
-
-
Marathias, V.M.1
Bolton, P.H.2
-
8
-
-
0027172294
-
The structure of α-thrombin inhibited by a 15-mer single-stranded DNA aptamer
-
Padmanabhan, K.; Padmanabhan, K. P.; Ferrara, J. D.; Sadler, J. E.; Tulinsky, A. The structure of α-thrombin inhibited by a 15-mer single-stranded DNA aptamer J. Biol. Chem. 1993, 268, 17651-17654
-
(1993)
J. Biol. Chem.
, vol.268
, pp. 17651-17654
-
-
Padmanabhan, K.1
Padmanabhan, K.P.2
Ferrara, J.D.3
Sadler, J.E.4
Tulinsky, A.5
-
9
-
-
79960699716
-
Loop residues of thrombin-binding DNA aptamer impact G-quadruplex stability and thrombin binding
-
Nagatoishi, Satoru; Isono, Noburu; Tsumoto, Kouhei; Sugimoto, N. Loop residues of thrombin-binding DNA aptamer impact G-quadruplex stability and thrombin binding Biochimie 2011, 93, 1231-1238
-
(2011)
Biochimie
, vol.93
, pp. 1231-1238
-
-
Nagatoishi, S.1
Isono, N.2
Tsumoto, K.3
Sugimoto, N.4
-
10
-
-
11144269746
-
NMR study of the folding-unfolding mechanism for the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG)
-
Mao, X. A.; Gmeiner, W. H. NMR study of the folding-unfolding mechanism for the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG) Biophys. Chem. 2005, 113, 155-160
-
(2005)
Biophys. Chem.
, vol.113
, pp. 155-160
-
-
Mao, X.A.1
Gmeiner, W.H.2
-
11
-
-
0035823852
-
2+: Stability, Heat, and Hydration
-
2+: Stability, Heat, and Hydration J. Am. Chem. Soc. 2001, 123, 10799-10804
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 10799-10804
-
-
Kankia, B.I.1
Marky, L.A.2
-
12
-
-
37249066753
-
Geometric formalism for DNA quadruplex folding
-
Silva, M. W. Geometric formalism for DNA quadruplex folding Chem.-Eur. J. 2007, 13, 9738-9745
-
(2007)
Chem.-Eur. J.
, vol.13
, pp. 9738-9745
-
-
Silva, M.W.1
-
13
-
-
0034673130
-
Effect of loop sequence and size on DNA aptamer stability
-
Smirnov, I.; Shafer, R. H. Effect of loop sequence and size on DNA aptamer stability Biochemistry 2000, 39, 1462-1468
-
(2000)
Biochemistry
, vol.39
, pp. 1462-1468
-
-
Smirnov, I.1
Shafer, R.H.2
-
14
-
-
0001505226
-
Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids
-
Hardin, C. C.; Perry, A. G.; White, K. Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids Biopolymers 2001, 56, 147-194
-
(2001)
Biopolymers
, vol.56
, pp. 147-194
-
-
Hardin, C.C.1
Perry, A.G.2
White, K.3
-
15
-
-
33646345847
-
Unfolding of G-quadruplexes: Energetic and ion and water contributions of G-quartet stacking
-
Olsen, C. M.; Gmeiner, W. H.; Marky, L. A. Unfolding of G-quadruplexes: Energetic and ion and water contributions of G-quartet stacking J. Phys. Chem. B 2006, 110, 6962-6969
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 6962-6969
-
-
Olsen, C.M.1
Gmeiner, W.H.2
Marky, L.A.3
-
16
-
-
33745374520
-
Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions
-
Miyoshi, D.; Karimata, H.; Sugimoto, N. Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions J. Am. Chem. Soc. 2006, 128, 7957-7963
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 7957-7963
-
-
Miyoshi, D.1
Karimata, H.2
Sugimoto, N.3
-
17
-
-
36949032125
-
Thermodynamic analysis of quadruplex DNA-drug interaction
-
Pagano, B.; Mattia, C. A.; Virno, A.; Randazzo, A.; Mayol, L.; Giancola, C. Thermodynamic analysis of quadruplex DNA-drug interaction Nucleosides Nucleotides Nucleic Acids 2007, 26, 761-765
-
(2007)
Nucleosides Nucleotides Nucleic Acids
, vol.26
, pp. 761-765
-
-
Pagano, B.1
Mattia, C.A.2
Virno, A.3
Randazzo, A.4
Mayol, L.5
Giancola, C.6
-
18
-
-
63349095582
-
Single-molecule detection of folding and unfolding of the G-quadruplex aptamer in a nanopore nanocavity
-
Shim, J. W.; Tan, Q.; Gu, L. Q. Single-molecule detection of folding and unfolding of the G-quadruplex aptamer in a nanopore nanocavity Nucleic Acids Res. 2009, 37, 972-982
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 972-982
-
-
Shim, J.W.1
Tan, Q.2
Gu, L.Q.3
-
19
-
-
33745184030
-
Protein folding kinetics and thermodynamics from atomistic simulations
-
van der Spoel, D.; Seibert, M. M. Protein folding kinetics and thermodynamics from atomistic simulations Phys. Rev. Lett. 2006, 96, 238102
-
(2006)
Phys. Rev. Lett.
, vol.96
, pp. 238102
-
-
Van Der Spoel, D.1
Seibert, M.M.2
-
20
-
-
73349099062
-
Single Stranded loops of quadruplex DNA as key benchmark for testing nucleic acids force fields
-
Fadrna, E.; Spackova, N.; Sarzynska, J.; Koca, J.; Orozco, M.; Cheatham, T. E.; Kulinski, T.; Sponer, J. Single Stranded loops of quadruplex DNA as key benchmark for testing nucleic acids force fields J. Chem. Theory Comput. 2009, 5, 2514-2530
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 2514-2530
-
-
Fadrna, E.1
Spackova, N.2
Sarzynska, J.3
Koca, J.4
Orozco, M.5
Cheatham, T.E.6
Kulinski, T.7
Sponer, J.8
-
21
-
-
77957958900
-
Structural dynamics of thrombin-binding DNA Aptamer d(GGTTGGTGTGGTTGG) quadruplex DNA studied by large-scale explicit solvent simulations
-
Reshetnikov, R.; Golovin, A.; Spiridonova, V.; Kopylov, A.; Sponer, J. Structural dynamics of thrombin-binding DNA Aptamer d(GGTTGGTGTGGTTGG) quadruplex DNA studied by large-scale explicit solvent simulations J. Chem. Theory Comput. 2010, 6, 3003-3014
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 3003-3014
-
-
Reshetnikov, R.1
Golovin, A.2
Spiridonova, V.3
Kopylov, A.4
Sponer, J.5
-
22
-
-
77958496199
-
Comparison of models of thrombin-binding 15-mer DNA aptamer by molecular dynamics simulation
-
Reshetnikov, R. V.; Golovin, A. V.; Kopylov, A. M. Comparison of models of thrombin-binding 15-mer DNA aptamer by molecular dynamics simulation Biochemistry (Moscow) 2010, 75, 1017-1024
-
(2010)
Biochemistry (Moscow)
, vol.75
, pp. 1017-1024
-
-
Reshetnikov, R.V.1
Golovin, A.V.2
Kopylov, A.M.3
-
23
-
-
83755185482
-
Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process
-
Reshetnikov, R. V.; Sponer, J.; Rassokhina, O. I.; Kopylov, A. M.; Tsvetkov, P. O.; Makarov, A. A.; Golovin, A. V. Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process Nucleic Acids Res. 2011, 39, 9789-9802
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 9789-9802
-
-
Reshetnikov, R.V.1
Sponer, J.2
Rassokhina, O.I.3
Kopylov, A.M.4
Tsvetkov, P.O.5
Makarov, A.A.6
Golovin, A.V.7
-
25
-
-
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
-
26
-
-
34250318638
-
Refinement of the AMBER force field for nucleic acids: Improving the description of α/γ conformers
-
Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T. E., III; Laughton, C. A.; Orozco, M. Refinement of the AMBER force field for nucleic acids: Improving the description of α/γ conformers Biophys. J. 2007, 92, 3817-3829
-
(2007)
Biophys. J.
, vol.92
, pp. 3817-3829
-
-
Perez, A.1
Marchan, I.2
Svozil, D.3
Sponer, J.4
Cheatham Iii, T.E.5
Laughton, C.A.6
Orozco, M.7
-
27
-
-
0028086928
-
Ion-induced stabilization of the G-DNA quadruplex: Free energy perturbation studies
-
Ross, W. S.; Hardin, C. C. Ion-induced stabilization of the G-DNA quadruplex: Free energy perturbation studies J. Am. Chem. Soc. 1994, 116, 6070-6080
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 6070-6080
-
-
Ross, W.S.1
Hardin, C.C.2
-
28
-
-
0001616080
-
Replica-exchange molecular dynamics method for protin folding
-
Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protin folding Chem. Phys. Lett. 1999, 314, 141-151
-
(1999)
Chem. Phys. Lett.
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
30
-
-
38749123962
-
P-LINCS: A parallel linear constraint solver for molecular simulation
-
Hess, B. P-LINCS: A parallel linear constraint solver for molecular simulation J. Chem. Theory Comput. 2008, 4, 116-122
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 116-122
-
-
Hess, B.1
-
31
-
-
33846823909
-
Particle mesh Ewald: An N log(N) method for Ewald sums in large systems
-
Darden, T.; York, D.; Pedersen, L. G. Particle mesh Ewald: An N log(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.G.3
-
32
-
-
33645961739
-
A smooth particle mesh Ewald potential
-
Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A smooth particle mesh Ewald potential J. Chem. Phys. 1995, 103, 8577-5892
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-5892
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
33
-
-
46249092554
-
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 2008, 4, 435-447
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
34
-
-
79961199372
-
Explaining the varied glycosidic conformational, G-tract length, and sequence preferences for anti-parallel G-quadruplexes
-
Cang, X.; Sponer, J.; Cheatham, T. E., III Explaining the varied glycosidic conformational, G-tract length, and sequence preferences for anti-parallel G-quadruplexes Nucleic Acids Res. 2011, 39, 4499-4512
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 4499-4512
-
-
Cang, X.1
Sponer, J.2
Cheatham Iii, T.E.3
-
35
-
-
0033556236
-
Peptide folding: When simulation meets experiment
-
Daura, X.; Gademann, K.; Jaun, B.; Seebach, D.; Gunsteren, W. F. v.; Mark, A. E. Peptide folding: When simulation meets experiment Angew. Chem., Int. Ed. 1999, 38, 236-240
-
(1999)
Angew. Chem., Int. Ed.
, vol.38
, pp. 236-240
-
-
Daura, X.1
Gademann, K.2
Jaun, B.3
Seebach, D.4
Gunsteren, W.F.V.5
Mark, A.E.6
-
36
-
-
49449085241
-
Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations
-
Joung, I. S.; Cheatham, T. E., III Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations J. Phys. Chem. B 2008, 112, 9020-9041
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 9020-9041
-
-
Joung, I.S.1
Cheatham Iii, T.E.2
|