-
1
-
-
77950519937
-
Origins of specificity in protein-DNA recognition
-
Rohs,R., Jin,X., West,S. M., Joshi,R., Honig,B. and Mann,R. S. (2010) Origins of specificity in protein-DNA recognition. Ann. Rev. Biochem., 79, 233-269.
-
(2010)
Ann. Rev. Biochem.
, vol.79
, pp. 233-269
-
-
Rohs, R.1
Jin, X.2
West, S.M.3
Joshi, R.4
Honig, B.5
Mann, R.S.6
-
2
-
-
77955570043
-
The many twists and turns of DNA: Template, telomere, tool, and target
-
Egli,M. and Pallan,P. S. (2010) The many twists and turns of DNA: template, telomere, tool, and target. Curr. Opin. Struct. Biol., 20, 262-275.
-
(2010)
Curr. Opin. Struct. Biol.
, vol.20
, pp. 262-275
-
-
Egli, M.1
Pallan, P.S.2
-
3
-
-
84860477162
-
Frontiers in molecular dynamics simulations of DNA
-
Perez,A., Luque,F. J. and Orozco,M. (2012) Frontiers in molecular dynamics simulations of DNA. Account. Chem. Res., 45, 196-205.
-
(2012)
Account. Chem. Res.
, vol.45
, pp. 196-205
-
-
Perez, A.1
Luque, F.J.2
Orozco, M.3
-
4
-
-
84883590358
-
DNAshape: A method for the high-throughput prediction of DNA structural features on a genomic scale
-
Zhou,T., Yang,L., Lu,Y., Dror,I., Dantas Machado,A. C., Ghane,T., Di Felice,R. and Rohs,R. (2013) DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale. Nucleic Acids Res., 41, W56-W62.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. W56-W62
-
-
Zhou, T.1
Yang, L.2
Lu, Y.3
Dror, I.4
Dantas Machado, A.C.5
Ghane, T.6
Di Felice, R.7
Rohs, R.8
-
5
-
-
0032530555
-
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
-
Olson,W. K., Gorin,A. A., Lu,X. J., Hock,L. M. and Zhurkin,V. B. (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl. Acad. Sci. U. S. A., 95, 11163-11168.
-
(1998)
Proc. Natl. Acad. Sci. U. S. A
, vol.95
, pp. 11163-11168
-
-
Olson, W.K.1
Gorin, A.A.2
Lu, X.J.3
Hock, L.M.4
Zhurkin, V.B.5
-
6
-
-
65249089637
-
Local DNA topography correlates with functional noncoding regions of the human genome
-
Parker,S. C., Hansen,L., Abaan,H. O., Tullius,T. D. and Margulies,E. H. (2009) Local DNA topography correlates with functional noncoding regions of the human genome. Science (N. Y.), 324, 389-392.
-
(2009)
Science (N. Y.)
, vol.324
, pp. 389-392
-
-
Parker, S.C.1
Hansen, L.2
Abaan, H.O.3
Tullius, T.D.4
Margulies, E.H.5
-
7
-
-
0028108981
-
Investigation of structure and dynamics in membrane proteins using site-directed spin labeling
-
Hubbell,W. L. and Altenbach,C. (1994) Investigation of structure and dynamics in membrane proteins using site-directed spin labeling. Curr. Opin. Struct. Biol., 4, 566-573.
-
(1994)
Curr. Opin. Struct. Biol.
, vol.4
, pp. 566-573
-
-
Hubbell, W.L.1
Altenbach, C.2
-
8
-
-
33749041288
-
Recent advances and applications of site-directed spin labeling
-
Fanucci,G. E. and Cafiso,D. S. (2006) Recent advances and applications of site-directed spin labeling. Curr. Opin. Struct. Biol., 16, 644-653.
-
(2006)
Curr. Opin. Struct. Biol.
, vol.16
, pp. 644-653
-
-
Fanucci, G.E.1
Cafiso, D.S.2
-
9
-
-
84885863331
-
Technological advances in site-directed spin labeling of proteins
-
Hubbell,W. L., López,C. J., Altenbach,C. and Yang,Z. (2013) Technological advances in site-directed spin labeling of proteins. Curr. Opin. Struct. Biol., 23, 725-733.
-
(2013)
Curr. Opin. Struct. Biol.
, vol.23
, pp. 725-733
-
-
Hubbell, W.L.1
López, C.J.2
Altenbach, C.3
Yang, Z.4
-
10
-
-
53049087579
-
Site-directed spin labeling studies on nucleic acid structure and dynamics
-
Sowa,G. Z. and Qin,P. Z. (2008) Site-directed spin labeling studies on nucleic acid structure and dynamics. Prog. Nucleic Acids Res. Mol. Biol., 82, 147-197.
-
(2008)
Prog. Nucleic Acids Res. Mol. Biol.
, vol.82
, pp. 147-197
-
-
Sowa, G.Z.1
Qin, P.Z.2
-
11
-
-
77149142936
-
Studying RNA using site-directed spin-labeling and continuous-wave electron paramagnetic resonance spectroscopy
-
Zhang,X., Cekan,P., Sigurdsson,S. T. and Qin,P. Z. (2009) Studying RNA using site-directed spin-labeling and continuous-wave electron paramagnetic resonance spectroscopy. Methods Enzymol., 469, 303-328.
-
(2009)
Methods Enzymol.
, vol.469
, pp. 303-328
-
-
Zhang, X.1
Cekan, P.2
Sigurdsson, S.T.3
Qin, P.Z.4
-
12
-
-
79551492492
-
Studying biomolecular complexes with pulsed electron-electron double resonance spectroscopy
-
Reginsson,G. W. and Schiemann,O. (2011) Studying biomolecular complexes with pulsed electron-electron double resonance spectroscopy. Biochem. Soc. Trans., 39, 128-139.
-
(2011)
Biochem. Soc. Trans.
, vol.39
, pp. 128-139
-
-
Reginsson, G.W.1
Schiemann, O.2
-
13
-
-
84859757968
-
Structure and dynamics of nucleic acids
-
Krstic,I., Endeward,B., Margraf,D.,Marko,A. and Prisner,T. F. (2012) Structure and dynamics of nucleic acids. Topics Curr. Chem., 321, 159-198.
-
(2012)
Topics Curr. Chem.
, vol.321
, pp. 159-198
-
-
Krstic, I.1
Endeward, B.2
Margraf, D.3
Marko, A.4
Prisner, T.F.5
-
14
-
-
84859586717
-
Site-directed spin labelling of nucleic acids
-
Shelke,S. A. and Sigurdsson,S. T. (2012) Site-directed spin labelling of nucleic acids. Eur. J. Org. Chem., 2012, 2291-2301.
-
(2012)
Eur. J. Org. Chem.
, vol.2012
, pp. 2291-2301
-
-
Shelke, S.A.1
Sigurdsson, S.T.2
-
15
-
-
84922354070
-
Pulsed electron double resonance in structural studies of spin-labeled nucleic acids
-
Fedorova,O. S. and Tsvetkov,Y. D. (2013) Pulsed electron double resonance in structural studies of spin-labeled nucleic acids. Acta Naturae, 5, 9-32.
-
(2013)
Acta Naturae
, vol.5
, pp. 9-32
-
-
Fedorova, O.S.1
Tsvetkov, Y.D.2
-
16
-
-
0035925208
-
Site-specific incorporation of nitroxide spin-labels into internal sites of the TAR RNA; Structure-dependent dynamics of RNA by EPR spectroscopy
-
Edwards,T. E., Okonogi,T. M., Robinson,B. H. and Sigurdsson,S. T. (2001) Site-specific incorporation of nitroxide spin-labels into internal sites of the TAR RNA; structure-dependent dynamics of RNA by EPR spectroscopy. J. Am. Chem. Soc., 123, 1527-1528.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 1527-1528
-
-
Edwards, T.E.1
Okonogi, T.M.2
Robinson, B.H.3
Sigurdsson, S.T.4
-
17
-
-
0035986696
-
Investigation of RNA-protein and RNA-metal ion interactions by electron paramagnetic resonance spectroscopy
-
Edwards,T. E., Okonogi,T. M. and Sigurdsson,S. T. (2002) Investigation of RNA-protein and RNA-metal ion interactions by electron paramagnetic resonance spectroscopy. The HIV TAR-Tat motif. Chem. Biol., 9, 699-706.
-
(2002)
The HIV TAR-Tat Motif. Chem. Biol.
, vol.9
, pp. 699-706
-
-
Edwards, T.E.1
Okonogi, T.M.2
Sigurdsson, S.T.3
-
18
-
-
0037984764
-
Monitoring RNA base structure and dynamics using site-directed spin labeling
-
Qin,P. Z., Hideg,K., Feigon,J. and Hubbell,W. L. (2003) Monitoring RNA base structure and dynamics using site-directed spin labeling. Biochemistry, 42, 6772-6783.
-
(2003)
Biochemistry
, vol.42
, pp. 6772-6783
-
-
Qin, P.Z.1
Hideg, K.2
Feigon, J.3
Hubbell, W.L.4
-
19
-
-
15744376752
-
Identification of amino acids that promote specific and rigid TAR RNA-tat protein complex formation
-
Edwards,T. E., Robinson,B. H. and Sigurdsson,S. T. (2005) Identification of amino acids that promote specific and rigid TAR RNA-tat protein complex formation. Chem. Biol., 12, 329-337.
-
(2005)
Chem. Biol.
, vol.12
, pp. 329-337
-
-
Edwards, T.E.1
Robinson, B.H.2
Sigurdsson, S.T.3
-
20
-
-
26844503355
-
Separate metal requirements for loop interactions and catalysis in the extended hammerhead ribozyme
-
Kim,N. K., Murali,A. and DeRose,V. J. (2005) Separate metal requirements for loop interactions and catalysis in the extended hammerhead ribozyme. J. Am. Chem. Soc., 127, 14134-14135.
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 14134-14135
-
-
Kim, N.K.1
Murali, A.2
DeRose, V.J.3
-
21
-
-
70149120741
-
Site-specific DNA structural and dynamic features revealed by nucleotide-independent nitroxide probes
-
Popova,A. M., Kalai,T., Hideg,K. and Qin,P. Z. (2009) Site-specific DNA structural and dynamic features revealed by nucleotide-independent nitroxide probes. Biochemistry, 48, 8540-8550.
-
(2009)
Biochemistry
, vol.48
, pp. 8540-8550
-
-
Popova, A.M.1
Kalai, T.2
Hideg, K.3
Qin, P.Z.4
-
22
-
-
67651183860
-
Folding of the cocaine aptamer studied by EPR and fluorescence spectroscopies using the bifunctional spectroscopic probe C
-
Cekan,P., Jonsson,E. O. and Sigurdsson,S. T. (2009) Folding of the cocaine aptamer studied by EPR and fluorescence spectroscopies using the bifunctional spectroscopic probe C. Nucleic Acids Res., 37, 3990-3995.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 3990-3995
-
-
Cekan, P.1
Jonsson, E.O.2
Sigurdsson, S.T.3
-
23
-
-
0035849534
-
Quantitative analysis of the GAAA tetraloop/receptor interaction in solution: A site-directed spin labeling study
-
Qin,P. Z., Butcher,S. E., Feigon,J. and Hubbell,W. L. (2001) Quantitative analysis of the GAAA tetraloop/receptor interaction in solution: a site-directed spin labeling study. Biochemistry, 40, 6929-6936.
-
(2001)
Biochemistry
, vol.40
, pp. 6929-6936
-
-
Qin, P.Z.1
Butcher, S.E.2
Feigon, J.3
Hubbell, W.L.4
-
24
-
-
38449119116
-
Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe
-
Qin,P. Z., Haworth,I. S., Cai,Q., Kusnetzow,A. K., Grant,G. P. G., Price,E. A., Sowa,G. Z., Popova,A., Herreros,B. and He,H. (2007) Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe. Nat. Protocols, 2, 2354-2365.
-
(2007)
Nat. Protocols
, vol.2
, pp. 2354-2365
-
-
Qin, P.Z.1
Haworth, I.S.2
Cai, Q.3
Kusnetzow, A.K.4
Grant, G.P.G.5
Price, E.A.6
Sowa, G.Z.7
Popova, A.8
Herreros, B.9
He, H.10
-
25
-
-
77958476923
-
A nucleotide-independent nitroxide probe reports on site-specific stereomeric environment in DNA
-
Popova,A. M. and Qin,P. Z. (2010) A nucleotide-independent nitroxide probe reports on site-specific stereomeric environment in DNA. Biophys. J., 99, 2180-2189.
-
(2010)
Biophys. J.
, vol.99
, pp. 2180-2189
-
-
Popova, A.M.1
Qin, P.Z.2
-
26
-
-
84861875178
-
Nitroxide sensing of a DNA microenvironment: Mechanistic insights from EPR spectroscopy and molecular dynamics simulations
-
Popova,A. M., Hatmal,M. M., Frushicheva,M. P., Price,E. A., Qin,P. Z. and Haworth,I. S. (2012) Nitroxide sensing of a DNA microenvironment: mechanistic insights from EPR spectroscopy and molecular dynamics simulations. J. Phys. Chem. B, 116, 6387-6396.
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 6387-6396
-
-
Popova, A.M.1
Hatmal, M.M.2
Frushicheva, M.P.3
Price, E.A.4
Qin, P.Z.5
Haworth, I.S.6
-
27
-
-
42449114966
-
Transcriptional control of human p53-regulated genes
-
Riley,T., Sontag,E., Chen,P. and Levine,A. (2008) Transcriptional control of human p53-regulated genes. Nat. Rev. Mol. Cell. Biol., 9, 402-412.
-
(2008)
Nat. Rev. Mol. Cell. Biol.
, vol.9
, pp. 402-412
-
-
Riley, T.1
Sontag, E.2
Chen, P.3
Levine, A.4
-
28
-
-
70349438905
-
The expanding universe of p53 targets
-
Menendez,D., Inga,A. and Resnick,M. A. (2009) The expanding universe of p53 targets. Nat. Rev. Cancer, 9, 724-737.
-
(2009)
Nat. Rev. Cancer
, vol.9
, pp. 724-737
-
-
Menendez, D.1
Inga, A.2
Resnick, M.A.3
-
29
-
-
84884964169
-
Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion
-
Chen,Y., Zhang,X., Dantas Machado,A. C., Ding,Y., Chen,Z., Qin,P. Z., Rohs,R. and Chen,L. (2013) Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion. Nucleic Acids Res., 41, 8368-8376.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 8368-8376
-
-
Chen, Y.1
Zhang, X.2
Dantas Machado, A.C.3
Ding, Y.4
Chen, Z.5
Qin, P.Z.6
Rohs, R.7
Chen, L.8
-
30
-
-
84895833555
-
Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling
-
Zhang,X., Dantas Machado,A. C., Ding,Y., Chen,Y., Lu,Y., Duan,Y., Tham,K. W., Chen,L., Rohs,R. and Qin,P. Z. (2014) Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling. Nucleic Acids Res., 42, 2789-2797.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 2789-2797
-
-
Zhang, X.1
Dantas Machado, A.C.2
Ding, Y.3
Chen, Y.4
Lu, Y.5
Duan, Y.6
Tham, K.W.7
Chen, L.8
Rohs, R.9
Qin, P.Z.10
-
31
-
-
26544473673
-
Rotational-dynamics of rigid, symmetric top macromolecules-application to circular-cylinders
-
Tirado,M. M. and Garciadelatorre,J. (1980) Rotational-dynamics of rigid, symmetric top macromolecules-application to circular-cylinders. J. Chem. Phys., 73, 1986-1993.
-
(1980)
J. Chem. Phys.
, vol.73
, pp. 1986-1993
-
-
Tirado, M.M.1
Garciadelatorre, J.2
-
32
-
-
0029905422
-
Motion of spin-labeled side chains in T4 lysozyme,correlation with protein structure and dynamics
-
McHaourab,H. S., Lietzow,M. A., Hideg,K. and Hubbell,W. L. (1996) Motion of spin-labeled side chains in T4 lysozyme. Correlation with protein structure and dynamics. Biochemistry, 35, 7692-7704.
-
(1996)
Biochemistry
, vol.35
, pp. 7692-7704
-
-
McHaourab, H.S.1
Lietzow, M.A.2
Hideg, K.3
Hubbell, W.L.4
-
33
-
-
61949215199
-
Solute effects on spin labels at an aqueous-exposed site in the flap region of HIV-1 protease
-
Galiano,L., Blackburn,M. E., Veloro,A. M., Bonora,M. and Fanucci,G. E. (2009) Solute effects on spin labels at an aqueous-exposed site in the flap region of HIV-1 protease. J. Phys. Chem. B, 113, 1673-1680.
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 1673-1680
-
-
Galiano, L.1
Blackburn, M.E.2
Veloro, A.M.3
Bonora, M.4
Fanucci, G.E.5
-
34
-
-
33645098003
-
A model system for investigating lineshape/structure correlations in RNA site-directed spin labeling
-
Qin,P. Z., Iseri,J. and Oki,A. (2006) A model system for investigating lineshape/structure correlations in RNA site-directed spin labeling. Biochem. Biophys. Res. Commun., 343, 117-124.
-
(2006)
Biochem. Biophys. Res. Commun.
, vol.343
, pp. 117-124
-
-
Qin, P.Z.1
Iseri, J.2
Oki, A.3
-
35
-
-
33750212858
-
Site-directed spin labeling measurements of nanometer distances in nucleic acids using a sequence-independent nitroxide probe
-
Cai,Q., Kusnetzow,A. K., Hubbell,W. L., Haworth,I. S., Gacho,G. P. C., Van Eps,N., Hideg,K., Chambers,E. J. and Qin,P. Z. (2006) Site-directed spin labeling measurements of nanometer distances in nucleic acids using a sequence-independent nitroxide probe. Nucleic Acids Res., 34, 4722-4734.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 4722-4734
-
-
Cai, Q.1
Kusnetzow, A.K.2
Hubbell, W.L.3
Haworth, I.S.4
Gacho, G.P.C.5
Van Eps, N.6
Hideg, K.7
Chambers, E.J.8
Qin, P.Z.9
-
36
-
-
0034979126
-
Hydrogen bonding, base stacking, and steric effects in DNA replication
-
Kool,E. T. (2001) Hydrogen bonding, base stacking, and steric effects in dna replication. Ann. Rev. Biophys. Biomol. Struct., 30, 1-22.
-
(2001)
Ann. Rev. Biophys. Biomol. Struct.
, vol.30
, pp. 1-22
-
-
Kool, E.T.1
-
37
-
-
0034194135
-
Thermodynamic parameters for DNA sequences with dangling ends
-
Bommarito,S., Peyret,N. and SantaLucia,J. Jr. (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res., 28, 1929-1934.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 1929-1934
-
-
Bommarito, S.1
Peyret, N.2
SantaLucia, J.3
|