-
1
-
-
0026761859
-
Hairpin and parallel quartet structures for telomeric sequences
-
Balagurumoorthy, P., S. K. Brahmachari, D. Mohanty, M. Bansal, and V. Sasisekharan. 1992. Hairpin and parallel quartet structures for telomeric sequences. Nucleic Acids Res. 20:4061-4067.
-
(1992)
Nucleic Acids Res.
, vol.20
, pp. 4061-4067
-
-
Balagurumoorthy, P.1
Brahmachari, S.K.2
Mohanty, D.3
Bansal, M.4
Sasisekharan, V.5
-
2
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C., J. P. M. Postma, W. F. van Gusteren, A. Di Nola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gusteren, W.F.3
Di Nola, A.4
Haak, J.R.5
-
3
-
-
0026575221
-
Selection of single-stranded DNA molecules that bind and inhibit human thrombin
-
Bock, L. C., L. C. Griffin, J. A. Latham, E. H. Vermaas, and J. J. Toole. 1992. Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature. 355:564-566.
-
(1992)
Nature
, vol.355
, pp. 564-566
-
-
Bock, L.C.1
Griffin, L.C.2
Latham, J.A.3
Vermaas, E.H.4
Toole, J.J.5
-
4
-
-
11244279679
-
Relaxation matrix analysis of 2D-NMR data
-
Borgias, B. A., M. Gochin, D. J. Kerwood, and T. L. James. 1990. Relaxation matrix analysis of 2D-NMR data. Prog. Nucl. Magn. Res. Spectrosc. 22:83-100.
-
(1990)
Prog. Nucl. Magn. Res. Spectrosc.
, vol.22
, pp. 83-100
-
-
Borgias, B.A.1
Gochin, M.2
Kerwood, D.J.3
James, T.L.4
-
5
-
-
0000425457
-
MARDIGRAS - A procedure for matrix analysis of relaxation for discerning geometry of an aqueous structure
-
Borgias, B. A., and T. L. James. 1990. MARDIGRAS - a procedure for matrix analysis of relaxation for discerning geometry of an aqueous structure. J. Magn. Res. 87:475-487.
-
(1990)
J. Magn. Res.
, vol.87
, pp. 475-487
-
-
Borgias, B.A.1
James, T.L.2
-
6
-
-
0026601995
-
Investigations on the dynamic structures of adenine- and thymine-containing DNA
-
Brahms, S., V. Fritsch, J. G. Brahms, and E. Westhof. 1992. Investigations on the dynamic structures of adenine- and thymine-containing DNA. J. Mol. Biol. 223:455-476.
-
(1992)
J. Mol. Biol.
, vol.223
, pp. 455-476
-
-
Brahms, S.1
Fritsch, V.2
Brahms, J.G.3
Westhof, E.4
-
7
-
-
0030953141
-
Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes
-
Cheatham, T. E., and P. A. Kollman. 1997. Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes. J. Am. Chem. Soc. 119:4805-4825.
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 4805-4825
-
-
Cheatham, T.E.1
Kollman, P.A.2
-
8
-
-
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., J. L. Miller, T. Fox, T. A. Darden, and P. A. Kollman. 1995. 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. 117:4193-4194.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 4193-4194
-
-
Cheatham, T.E.1
Miller, J.L.2
Fox, T.3
Darden, T.A.4
Kollman, P.A.5
-
9
-
-
0030832691
-
Mode of interaction of G-quartets with the integrase of human immunodeficiency virus type 1
-
Cherepanov, P., J. A. Este, R. F. Rando, J. O. Ojwang, G. Reekmans, R. Steinfeld, G. David, E. De Clercq, and Z. Debyser. 1997. Mode of interaction of G-quartets with the integrase of human immunodeficiency virus type 1. Mol. Pharmacol. 52:771-780.
-
(1997)
Mol. Pharmacol.
, vol.52
, pp. 771-780
-
-
Cherepanov, P.1
Este, J.A.2
Rando, R.F.3
Ojwang, J.O.4
Reekmans, G.5
Steinfeld, R.6
David, G.7
De Clercq, E.8
Debyser, Z.9
-
10
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W. D., P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117: 5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, 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
-
11
-
-
33845378943
-
1H NMR spectra via two-dimensional homonuclear Hartmann-Hahn spectroscopy
-
1H NMR spectra via two-dimensional homonuclear Hartmann-Hahn spectroscopy. J. Am. Chem. Soc. 107:2820-2821.
-
(1985)
J. Am. Chem. Soc.
, vol.107
, pp. 2820-2821
-
-
Davis, D.1
Bax, A.2
-
12
-
-
0029979192
-
Kinetics of sodium ion binding to DNA quadruplexes
-
Deng, H., and W. H. Braunlin. 1996. Kinetics of sodium ion binding to DNA quadruplexes. J. Mol. Biol. 255:476-483.
-
(1996)
J. Mol. Biol.
, vol.255
, pp. 476-483
-
-
Deng, H.1
Braunlin, W.H.2
-
13
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann, U., L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen. 1995. A smooth particle mesh Ewald method. J. Chem. Phys. 103:8577-8593.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
14
-
-
0000009663
-
Investigations of crystals by means of Roentgen rays
-
Ewald, P. 1921. Investigations of crystals by means of Roentgen rays. Ann. Phys. (Leipzig). 64:253-264.
-
(1921)
Ann. Phys. (Leipzig)
, vol.64
, pp. 253-264
-
-
Ewald, P.1
-
16
-
-
49149148488
-
Radiofrequency pulse sequences which compensate their own imperfections
-
Freeman, R., S. P. Kempsell, and M. H. Levitt. 1980. Radiofrequency pulse sequences which compensate their own imperfections. J. Magn. Res. 38:453.
-
(1980)
J. Magn. Res.
, vol.38
, pp. 453
-
-
Freeman, R.1
Kempsell, S.P.2
Levitt, M.H.3
-
17
-
-
0025649498
-
4-Stranded nucleic acid structures 25 years later - From guanosine gels to telomere DNA
-
Guschlbauer, W., J. F. Chantot, and D. Thiele. 1990. 4-Stranded nucleic acid structures 25 years later - from guanosine gels to telomere DNA. J. Biomol. Struct. Dyn. 8:491-511.
-
(1990)
J. Biomol. Struct. Dyn.
, vol.8
, pp. 491-511
-
-
Guschlbauer, W.1
Chantot, J.F.2
Thiele, D.3
-
19
-
-
0022691667
-
On loop folding in nucleic acid hairpin-type structures
-
Haasnoot, C. A., C. W. Hilbers, G. A. van der Marel, J. H. van Boom, U. C. Singh, N. Pattabiraman, and P. A. Kollman. 1986. On loop folding in nucleic acid hairpin-type structures. J. Biomol. Struct. Dyn. 3:843-857.
-
(1986)
J. Biomol. Struct. Dyn.
, vol.3
, pp. 843-857
-
-
Haasnoot, C.A.1
Hilbers, C.W.2
Van Der Marel, G.A.3
Van Boom, J.H.4
Singh, U.C.5
Pattabiraman, N.6
Kollman, P.A.7
-
20
-
-
0030687511
-
Allosteric interactions between DNA strands and monovalent cations in DNA quadruplex assembly: Thermodynamic evidence for three linked association pathways
-
Hardin, C. C., M. J. Corregan, D. V. Lieberman, and B. A. Brown. 1997. Allosteric interactions between DNA strands and monovalent cations in DNA quadruplex assembly: thermodynamic evidence for three linked association pathways. Biochemistry. 36:15428-15450.
-
(1997)
Biochemistry
, vol.36
, pp. 15428-15450
-
-
Hardin, C.C.1
Corregan, M.J.2
Lieberman, D.V.3
Brown, B.A.4
-
21
-
-
0025896273
-
Monovalent cation induced structural transitions in telomeric DNAs: G-DNA folding intermediates
-
Hardin, C. C., E. Henderson, T. Watson, and J. K. Prosser. 1991. Monovalent cation induced structural transitions in telomeric DNAs: G-DNA folding intermediates. Biochemistry. 30:4460-4472.
-
(1991)
Biochemistry
, vol.30
, pp. 4460-4472
-
-
Hardin, C.C.1
Henderson, E.2
Watson, T.3
Prosser, J.K.4
-
23
-
-
0001430231
-
The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition
-
Harvey, S. C., R. K.-Z. Tan, and T. E. Cheatham. 1998. The flying ice cube: velocity rescaling in molecular dynamics leads to violation of energy equipartition. J. Comp. Chem. 19:726-740.
-
(1998)
J. Comp. Chem.
, vol.19
, pp. 726-740
-
-
Harvey, S.C.1
Tan, R.K.-Z.2
Cheatham, T.E.3
-
24
-
-
48749149745
-
Solvent suppression in Fourier transform nuclear magnetic resonance
-
Hore, P. J. 1983. Solvent suppression in Fourier transform nuclear magnetic resonance. J. Magn. Res. 55:283-300.
-
(1983)
J. Magn. Res.
, vol.55
, pp. 283-300
-
-
Hore, P.J.1
-
26
-
-
0026591751
-
Crystal structure of four-stranded Oxytricha telomeric DNA
-
Kang, C., X. Zhang, R. Ratliff, R. Moyzis, and A. Rich. 1992. Crystal structure of four-stranded Oxytricha telomeric DNA. Nature. 356: 126-131.
-
(1992)
Nature
, vol.356
, pp. 126-131
-
-
Kang, C.1
Zhang, X.2
Ratliff, R.3
Moyzis, R.4
Rich, A.5
-
27
-
-
0030712117
-
The contribution of thymine-thymine interactions to the stability of folded dimeric quadruplexes
-
Keniry, M. A., E. A. Owen, and R. H. Shafer. 1997. The contribution of thymine-thymine interactions to the stability of folded dimeric quadruplexes. Nucleic Acids Res. 25:4389-4392.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 4389-4392
-
-
Keniry, M.A.1
Owen, E.A.2
Shafer, R.H.3
-
31
-
-
0028024737
-
The high-resolution crystal structure of a parallel-stranded guanine tetraplex
-
Laughlan, G., A. I. Murchie, D. G. Norman, M. H. Moore, P. C. Moody, D. M. Lilley, and B. Luisi. 1994. The high-resolution crystal structure of a parallel-stranded guanine tetraplex. Science. 265:520-524.
-
(1994)
Science
, vol.265
, pp. 520-524
-
-
Laughlan, G.1
Murchie, A.I.2
Norman, D.G.3
Moore, M.H.4
Moody, P.C.5
Lilley, D.M.6
Luisi, B.7
-
32
-
-
0001087903
-
Averaging of cross-relaxation rates and distances for methyl, methylene, and aromatic ring protons due to motion or overlap - Extraction of accurate distances iteratively via relaxation matrix analysis of 2D-NOE spectra
-
Liu, H., P. D. Thomas, and T. L. James. 1992. Averaging of cross-relaxation rates and distances for methyl, methylene, and aromatic ring protons due to motion or overlap - extraction of accurate distances iteratively via relaxation matrix analysis of 2D-NOE spectra. J. Magn. Reson. 98:163-175.
-
(1992)
J. Magn. Reson.
, vol.98
, pp. 163-175
-
-
Liu, H.1
Thomas, P.D.2
James, T.L.3
-
34
-
-
0029964978
-
Inhibition of the human immunodeficiency virus type 1 integrase by guanosine quartet structures
-
Mazumder, A., N. Neamati, J. O. Ojwang, S. Sunder, R. F. Rando, and Y. Pommier. 1996. Inhibition of the human immunodeficiency virus type 1 integrase by guanosine quartet structures. Biochemistry. 35: 13762-13771.
-
(1996)
Biochemistry
, vol.35
, pp. 13762-13771
-
-
Mazumder, A.1
Neamati, N.2
Ojwang, J.O.3
Sunder, S.4
Rando, R.F.5
Pommier, Y.6
-
35
-
-
0027172294
-
The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer
-
Padmanabhan, K., K. P. Padmanabhan, J. D. Ferrara, J. E. Sadler, and A. Tulinsky. 1993. The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer. J. Biol. Chem. 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
-
36
-
-
0030064793
-
An ambiguous structure of a DNA 15-mer thrombin complex
-
Padmanabhan, K., and A. Tulinsky. 1996. An ambiguous structure of a DNA 15-mer thrombin complex. Acta Crystallogr. D. 52:272-282.
-
(1996)
Acta Crystallogr. D.
, vol.52
, pp. 272-282
-
-
Padmanabhan, K.1
Tulinsky, A.2
-
37
-
-
0004279414
-
-
University of California, San Francisco
-
Pearlman, D., D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham, D. M. Ferguson, G. L. Seibel, U. C. Singh, P. K. Weiner, and P. A. Kollman. 1995. AMBER 4.1. University of California, San Francisco.
-
(1995)
AMBER 4.1
-
-
Pearlman, D.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.5
Ferguson, D.M.6
Seibel, G.L.7
Singh, U.C.8
Weiner, P.K.9
Kollman, P.A.10
-
38
-
-
0031576353
-
The crystal structure of a parallel-stranded guanine tetraplex at 0.95 angstrom resolution
-
Phillips, K., Z. Dauter, A. I. H. Murchie, D. M. J. Lilley, and B. Luisi. 1997. The crystal structure of a parallel-stranded guanine tetraplex at 0.95 angstrom resolution. J. Mol. Biol. 273:171-182.
-
(1997)
J. Mol. Biol.
, vol.273
, pp. 171-182
-
-
Phillips, K.1
Dauter, Z.2
Murchie, A.I.H.3
Lilley, D.M.J.4
Luisi, B.5
-
39
-
-
0028086928
-
Ion-induced stabilization of the G-DNA quadruplex - Free energy perturbation studies
-
Ross, W. S., and C. C. Hardin. 1994. Ion-induced stabilization of the G-DNA quadruplex - free energy perturbation studies. J. Am. Chem. Soc. 116:6070-6080.
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 6070-6080
-
-
Ross, W.S.1
Hardin, C.C.2
-
40
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J. P., G. Cicotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23: 327-341.
-
(1977)
J. Comp. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Cicotti, G.2
Berendsen, H.J.C.3
-
42
-
-
0028892069
-
How to generate accurate solution structures of double-helical nucleic acid fragments using nuclear magnetic resonance and restrained molecular dynamics
-
Schmitz, U., and T. L. James. 1995. How to generate accurate solution structures of double-helical nucleic acid fragments using nuclear magnetic resonance and restrained molecular dynamics. Methods Enzymol. 261:3-44.
-
(1995)
Methods Enzymol.
, vol.261
, pp. 3-44
-
-
Schmitz, U.1
James, T.L.2
-
43
-
-
0028773155
-
Refined solution structure of the dimeric quadruplex formed from the Oxytricha telomeric oligonucleotide d(GGGGTTTTGGGG)
-
Schultze, P., F. W. Smith, and J. Feigon. 1994. Refined solution structure of the dimeric quadruplex formed from the Oxytricha telomeric oligonucleotide d(GGGGTTTTGGGG). Structure. 2:221-233.
-
(1994)
Structure
, vol.2
, pp. 221-233
-
-
Schultze, P.1
Smith, F.W.2
Feigon, J.3
-
44
-
-
0028173090
-
3) forms an asymmetric diagonally looped dimeric quadruplex with guanosine 5′-syn-syn-anti and 5′-syn-anti-anti N-glycosidic conformations
-
3) forms an asymmetric diagonally looped dimeric quadruplex with guanosine 5′-syn-syn-anti and 5′-syn-anti-anti N-glycosidic conformations. Proc. Natl. Acad. Sci. USA. 91:10546-10550.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 10546-10550
-
-
Smith, F.W.1
Lau, F.W.2
Feigon, J.3
-
45
-
-
2642628181
-
A two-dimentional nuclear Overhauser experiment with pure absorption phase in four quadrants
-
States, D. J., R. A. Haberkorn, and D. J. Ruben. 1982. A two-dimentional nuclear Overhauser experiment with pure absorption phase in four quadrants. J. Magn. Reson. 48:286-292.
-
(1982)
J. Magn. Reson.
, vol.48
, pp. 286-292
-
-
States, D.J.1
Haberkorn, R.A.2
Ruben, D.J.3
-
47
-
-
0024843757
-
Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops
-
Sundquist, W. I., and A. Klug. 1989. Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops. Nature. 342: 825-829.
-
(1989)
Nature
, vol.342
, pp. 825-829
-
-
Sundquist, W.I.1
Klug, A.2
-
48
-
-
0028815252
-
Probability assessment of conformational ensembles: Sugar repuckering in a DNA duplex in solution
-
Ulyanov, N. B., U. Schmitz, A. Kumar, and T. L. James. 1995. Probability assessment of conformational ensembles: sugar repuckering in a DNA duplex in solution. Biophys. J. 68:13-24.
-
(1995)
Biophys. J.
, vol.68
, pp. 13-24
-
-
Ulyanov, N.B.1
Schmitz, U.2
Kumar, A.3
James, T.L.4
|