-
1
-
-
0025228644
-
Determination of the extent of DNA bending by an adenine-thymine tract
-
Koo H.S., Drak J., Rice J.A., Crothers D.M. Determination of the extent of DNA bending by an adenine-thymine tract. Biochemistry. 29:1990;4227-4234
-
(1990)
Biochemistry
, vol.29
, pp. 4227-4234
-
-
Koo, H.S.1
Drak, J.2
Rice, J.A.3
Crothers, D.M.4
-
2
-
-
0027490778
-
Thermodynamics and premelting conformational changes of phased (dA)5 tracts
-
Chan S.S., Breslauer K.J., Austin R.H., Hogan M.E. Thermodynamics and premelting conformational changes of phased (dA)5 tracts. Biochemistry. 32:1993;11776-11784
-
(1993)
Biochemistry
, vol.32
, pp. 11776-11784
-
-
Chan, S.S.1
Breslauer, K.J.2
Austin, R.H.3
Hogan, M.E.4
-
4
-
-
0037459036
-
Topological measurement of the A-tract bend angle: Comparison of bent and straightened states
-
Tchernaenko V., Radlinska M., Drabik C.E., Bujnicki J.M., Halvorson H.R., Lutter L.C. Topological measurement of the A-tract bend angle: comparison of bent and straightened states. J. Mol. Biol. 326:2003;737-749
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 737-749
-
-
Tchernaenko, V.1
Radlinska, M.2
Drabik, C.E.3
Bujnicki, J.M.4
Halvorson, H.R.5
Lutter, L.C.6
-
5
-
-
0037459086
-
Topological measurement of the A-tract bend angle: Variation of duplex winding
-
Tchernaenko V., Halvorson H.R., Lutter L.C. Topological measurement of the A-tract bend angle: variation of duplex winding. J. Mol. Biol. 326:2003;751-760
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 751-760
-
-
Tchernaenko, V.1
Halvorson, H.R.2
Lutter, L.C.3
-
6
-
-
0035830968
-
Solution structure of an A-tract DNA bend
-
MacDonald D., Herbert K., Zhang X., Pologruto T., Lu P. Solution structure of an A-tract DNA bend. J. Mol. Biol. 306:2001;1081-1098
-
(2001)
J. Mol. Biol.
, vol.306
, pp. 1081-1098
-
-
MacDonald, D.1
Herbert, K.2
Zhang, X.3
Pologruto, T.4
Lu, P.5
-
7
-
-
0001106657
-
Curved DNA design, synthesis, and circularization
-
Ulanovsky L., Bodner M., Trifonov E.N., Choder M. Curved DNA design, synthesis, and circularization. Proc. Natl Acad. Sci. USA. 83:1986;862-866
-
(1986)
Proc. Natl Acad. Sci. USA
, vol.83
, pp. 862-866
-
-
Ulanovsky, L.1
Bodner, M.2
Trifonov, E.N.3
Choder, M.4
-
8
-
-
0001975345
-
DNA bending by sequence and proteins
-
D.M.J. Lilley. Oxford: Oxford University Press
-
Travers A.A. DNA bending by sequence and proteins. Lilley D.M.J. DNA-Protein: Structural Interactions. 1995;49-75 Oxford University Press, Oxford
-
(1995)
DNA-Protein: Structural Interactions
, pp. 49-75
-
-
Travers, A.A.1
-
9
-
-
0000388872
-
DNA bending by adenine-thymine tracts
-
S. Neidle. Oxford: Oxford University Press
-
Crothers D.M., Shakked Z. DNA bending by adenine-thymine tracts. Neidle S. Oxford Handbook of Nucleic Acid Structure. 1999;455-469 Oxford University Press, Oxford
-
(1999)
Oxford Handbook of Nucleic Acid Structure
, pp. 455-469
-
-
Crothers, D.M.1
Shakked, Z.2
-
10
-
-
0025312950
-
Sequence-directed curvature of DNA
-
Hagerman P.J. Sequence-directed curvature of DNA. Annu. Rev. Biochem. 59:1990;755-781
-
(1990)
Annu. Rev. Biochem.
, vol.59
, pp. 755-781
-
-
Hagerman, P.J.1
-
11
-
-
0027327815
-
Studies of DNA bending and flexibility using gel electrophoresis
-
Harrington R.E. Studies of DNA bending and flexibility using gel electrophoresis. Electrophoresis. 14:1993;732-746
-
(1993)
Electrophoresis
, vol.14
, pp. 732-746
-
-
Harrington, R.E.1
-
13
-
-
0038677710
-
Cre induces an asymmetric DNA bend in its target loxP site
-
Lee L., Chu L.C.H., Sadowski P.D. Cre induces an asymmetric DNA bend in its target loxP site. J. Biol. Chem. 278:2003;23118-23129
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 23118-23129
-
-
Lee, L.1
Chu, L.C.H.2
Sadowski, P.D.3
-
14
-
-
0037657677
-
A-tract polarity dominate the curvature in flanking sequences
-
Merling A., Sagaydakova N., Haran T.E. A-tract polarity dominate the curvature in flanking sequences. Biochemistry. 42:2003;4978-4984
-
(2003)
Biochemistry
, vol.42
, pp. 4978-4984
-
-
Merling, A.1
Sagaydakova, N.2
Haran, T.E.3
-
15
-
-
0037424628
-
Visualizing RNA extrusion and DNA wrapping in transcription elongation complexes of bacterial and eukaryotic RNA polymerases
-
Rivetti C., Codeluppi S., Dieci G., Bustamante C. Visualizing RNA extrusion and DNA wrapping in transcription elongation complexes of bacterial and eukaryotic RNA polymerases. J. Mol. Biol. 326:2003;1413-1426
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 1413-1426
-
-
Rivetti, C.1
Codeluppi, S.2
Dieci, G.3
Bustamante, C.4
-
16
-
-
0037129935
-
DNA bending by bZIP charge variants: A unified study using electrophoretic phasing and fluorescence resonance energy transfer
-
Hardwidge P.R., Wu J., Williams S.L., Parkhurst K.M., Parkhurst L.J., Maher L.J. III. DNA bending by bZIP charge variants: a unified study using electrophoretic phasing and fluorescence resonance energy transfer. Biochemistry. 41:2002;7732-7742
-
(2002)
Biochemistry
, vol.41
, pp. 7732-7742
-
-
Hardwidge, P.R.1
Wu, J.2
Williams, S.L.3
Parkhurst, K.M.4
Parkhurst, L.J.5
Maher III, L.J.6
-
17
-
-
0033568357
-
Escherichia coli RNA polymerase translocation is accompanied by periodic bending of the DNA
-
Zaychikov E., Denissova L., Guckenberger R., Heumann H. Escherichia coli RNA polymerase translocation is accompanied by periodic bending of the DNA. Nucl. Acids Res. 27:1999;3645-3652
-
(1999)
Nucl. Acids Res.
, vol.27
, pp. 3645-3652
-
-
Zaychikov, E.1
Denissova, L.2
Guckenberger, R.3
Heumann, H.4
-
18
-
-
0034602929
-
Evidence for DNA bending at the T7 RNA polymerase promoter
-
Ujvari A., Martin C.T. Evidence for DNA bending at the T7 RNA polymerase promoter. J. Mol. Biol. 295:2000;1173-1184
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 1173-1184
-
-
Ujvari, A.1
Martin, C.T.2
-
19
-
-
0034696584
-
Determining the DNA bending angle induced by non-specific high mobility group-1 (HMG-1) proteins: A novel method
-
Tang L., Li J., Katz D.S., Feng J.A. Determining the DNA bending angle induced by non-specific high mobility group-1 (HMG-1) proteins: a novel method. Biochemistry. 39:2000;3052-3060
-
(2000)
Biochemistry
, vol.39
, pp. 3052-3060
-
-
Tang, L.1
Li, J.2
Katz, D.S.3
Feng, J.A.4
-
20
-
-
0033515035
-
P53-induced DNA bending and twisting: P53 tetramer binds on the outer side of a DNA loop and increases DNA twisting
-
Nagaich A.K., Zhurkin V.B., Durell S.R., Jernigan R.L., Appella E., Harrington R.E. p53-induced DNA bending and twisting: p53 tetramer binds on the outer side of a DNA loop and increases DNA twisting. Proc. Natl Acad. Sci. USA. 96:1999;1875-1880
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 1875-1880
-
-
Nagaich, A.K.1
Zhurkin, V.B.2
Durell, S.R.3
Jernigan, R.L.4
Appella, E.5
Harrington, R.E.6
-
21
-
-
0033575742
-
Wrapping of DNA around the E. coli RNA polymerase open promoter complex
-
Rivetti C., Guthold M., Bustamante C. Wrapping of DNA around the E. coli RNA polymerase open promoter complex. EMBO J. 18:1999;4464-4475
-
(1999)
EMBO J.
, vol.18
, pp. 4464-4475
-
-
Rivetti, C.1
Guthold, M.2
Bustamante, C.3
-
22
-
-
0030876348
-
Comparison of DNA bending by Fos-Jun and phased a tracts by multifactorial phasing analysis
-
Kerppola T.K. Comparison of DNA bending by Fos-Jun and phased A tracts by multifactorial phasing analysis. Biochemistry. 36:1997;10872-10884
-
(1997)
Biochemistry
, vol.36
, pp. 10872-10884
-
-
Kerppola, T.K.1
-
23
-
-
0025008815
-
Comparative gel electrophoresis measurement of the DNA bend angle induced by the catabolite activator protein
-
Zinkel S.S., Crothers D.M. Comparative gel electrophoresis measurement of the DNA bend angle induced by the catabolite activator protein. Biopolymers. 29:1990;29-38
-
(1990)
Biopolymers
, vol.29
, pp. 29-38
-
-
Zinkel, S.S.1
Crothers, D.M.2
-
24
-
-
0023771741
-
Empirical estimation of protein-induced DNA bending angles: Applications to lambda site-specific recombination complexes
-
Thompson J.F., Landy A. Empirical estimation of protein-induced DNA bending angles: applications to lambda site-specific recombination complexes. Nucl. Acids Res. 16:1988;9687-9705
-
(1988)
Nucl. Acids Res.
, vol.16
, pp. 9687-9705
-
-
Thompson, J.F.1
Landy, A.2
-
26
-
-
0037008044
-
Dominant effect of protein charge rather than protein shape in apparent DNA bending by engineered bZIP domains
-
Hardwidge P.R., Kahn J.D., Maher L.J. III. Dominant effect of protein charge rather than protein shape in apparent DNA bending by engineered bZIP domains. Biochemistry. 41:2002;8277-8288
-
(2002)
Biochemistry
, vol.41
, pp. 8277-8288
-
-
Hardwidge, P.R.1
Kahn, J.D.2
Maher III, L.J.3
-
27
-
-
0035910276
-
Long-range electrostatic interactions influence the orientation of Fos-Jun binding at AP-1 sites
-
Ramirez-Carrozzi V.R., Kerppola T.K. Long-range electrostatic interactions influence the orientation of Fos-Jun binding at AP-1 sites. J. Mol. Biol. 305:2001;411-427
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 411-427
-
-
Ramirez-Carrozzi, V.R.1
Kerppola, T.K.2
-
28
-
-
0030831193
-
DNA binding and phasing analyses of Tn5 transposase and a monomeric variant
-
York D., Reznikoff W.S. DNA binding and phasing analyses of Tn5 transposase and a monomeric variant. Nucl. Acids Res. 25:1997;2153-2160
-
(1997)
Nucl. Acids Res.
, vol.25
, pp. 2153-2160
-
-
York, D.1
Reznikoff, W.S.2
-
29
-
-
0027050007
-
Myc/Max and other helix-loop-helix/leucine zipper proteins bend DNA toward the minor groove
-
Fisher D.E., Parent L.A., Sharp P.A. Myc/Max and other helix-loop-helix/leucine zipper proteins bend DNA toward the minor groove. Proc. Natl Acad. Sci. USA. 89:1992;11779-11783
-
(1992)
Proc. Natl Acad. Sci. USA
, vol.89
, pp. 11779-11783
-
-
Fisher, D.E.1
Parent, L.A.2
Sharp, P.A.3
-
30
-
-
0026630130
-
Intrinsically bent DNA flanks both sides of an RNA polymerase I transcription start site. Both regions display novel electrophoretic mobility
-
Schroth G.P., Siino J.S., Cooney C.A., Th'ng J.P., Ho P.S., Bradbury E.M. Intrinsically bent DNA flanks both sides of an RNA polymerase I transcription start site. Both regions display novel electrophoretic mobility. J. Biol. Chem. 267:1992;9958-9964
-
(1992)
J. Biol. Chem.
, vol.267
, pp. 9958-9964
-
-
Schroth, G.P.1
Siino, J.S.2
Cooney, C.A.3
Th'Ng, J.P.4
Ho, P.S.5
Bradbury, E.M.6
-
31
-
-
0029790141
-
Do basic region-leucine zipper proteins bend their DNA targets... does it matter?
-
Hagerman P.J. Do basic region-leucine zipper proteins bend their DNA targets... does it matter? Proc. Natl Acad. Sci. USA. 93:1996;9993-9996
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 9993-9996
-
-
Hagerman, P.J.1
-
32
-
-
0028230588
-
Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA
-
Brukner I., Susic S., Dlakic M., Savic A., Pongor S. Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA. J. Mol. Biol. 236:1994;26-32
-
(1994)
J. Mol. Biol.
, vol.236
, pp. 26-32
-
-
Brukner, I.1
Susic, S.2
Dlakic, M.3
Savic, A.4
Pongor, S.5
-
33
-
-
0029981193
-
The effects of sequence context on DNA curvature
-
Dlakic M., Harrington R.E. The effects of sequence context on DNA curvature. Proc. Natl Acad. Sci. USA. 93:1996;3847-3852
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 3847-3852
-
-
Dlakic, M.1
Harrington, R.E.2
-
34
-
-
0023651638
-
Temperature and salt dependence of the gel migration anomaly of curved DNA fragments
-
Diekmann S. Temperature and salt dependence of the gel migration anomaly of curved DNA fragments. Nucl. Acids Res. 15:1987;247-265
-
(1987)
Nucl. Acids Res.
, vol.15
, pp. 247-265
-
-
Diekmann, S.1
-
35
-
-
0022359711
-
On the sequence determinants and flexibility of the kinetoplast DNA fragment with abnormal gel electrophoretic mobilities
-
Diekmann S., Wang J.C. On the sequence determinants and flexibility of the kinetoplast DNA fragment with abnormal gel electrophoretic mobilities. J. Mol. Biol. 186:1985;1-11
-
(1985)
J. Mol. Biol.
, vol.186
, pp. 1-11
-
-
Diekmann, S.1
Wang, J.C.2
-
36
-
-
0035822621
-
Magnesium increases the curvature of duplex DNA that contains dA tracts
-
Jerkovic B., Bolton P.H. Magnesium increases the curvature of duplex DNA that contains dA tracts. Biochemistry. 40:2001;9406-9411
-
(2001)
Biochemistry
, vol.40
, pp. 9406-9411
-
-
Jerkovic, B.1
Bolton, P.H.2
-
37
-
-
0342828135
-
Influence of temperature and ionic strength on electrophoretic mobility of synthetic DNA fragments
-
Shlyakhtenko L.S., Lyubchenko Y.L., Chernov B.K., Zhurkin V.B. Influence of temperature and ionic strength on electrophoretic mobility of synthetic DNA fragments. Mol. Biol. 24:1990;66-81
-
(1990)
Mol. Biol.
, vol.24
, pp. 66-81
-
-
Shlyakhtenko, L.S.1
Lyubchenko, Y.L.2
Chernov, B.K.3
Zhurkin, V.B.4
-
38
-
-
0942279698
-
Direct comparison of A- and T-strand minor groove interactions in DNA curvature at a tracts
-
Maki A.S., Kim T., Kool E.T. Direct comparison of A- and T-strand minor groove interactions in DNA curvature at A tracts. Biochemistry. 43:2004;1102-1110
-
(2004)
Biochemistry
, vol.43
, pp. 1102-1110
-
-
Maki, A.S.1
Kim, T.2
Kool, E.T.3
-
39
-
-
0017820499
-
Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: The roles of ion association or release, screening, and ion effects on water activity
-
Record M.T. Jr. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Quart. Rev. Biophys. 11:1978;103-178
-
(1978)
Quart. Rev. Biophys.
, vol.11
, pp. 103-178
-
-
Record Jr., M.T.1
-
40
-
-
0025902328
-
Fos-Jun heterodimers and Jun homodimers bend DNA in opposite orientations: Implications for transcription factor cooperativity
-
Kerppola T.K., Curran T. Fos-Jun heterodimers and Jun homodimers bend DNA in opposite orientations: implications for transcription factor cooperativity. Cell. 66:1991;317-326
-
(1991)
Cell
, vol.66
, pp. 317-326
-
-
Kerppola, T.K.1
Curran, T.2
-
41
-
-
0030572622
-
Topological measurement of protein-induced DNA bend angles
-
Lutter L.C., Halvorson H.R., Calladine C.R. Topological measurement of protein-induced DNA bend angles. J. Mol. Biol. 261:1996;620-633
-
(1996)
J. Mol. Biol.
, vol.261
, pp. 620-633
-
-
Lutter, L.C.1
Halvorson, H.R.2
Calladine, C.R.3
-
42
-
-
0026809001
-
Analyzing DNA curvature in polyacrylamide gels
-
Diekmann S. Analyzing DNA curvature in polyacrylamide gels. Methods Enzymol. 212:1992;30-46
-
(1992)
Methods Enzymol.
, vol.212
, pp. 30-46
-
-
Diekmann, S.1
-
43
-
-
0032575760
-
Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn
-
Young M.A., Beveridge D.L. Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn. J. Mol. Biol. 281:1998;675-687
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 675-687
-
-
Young, M.A.1
Beveridge, D.L.2
-
44
-
-
0017895903
-
The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
-
Manning G.S. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Quart. Rev. Biophys. 11:1978;179-246
-
(1978)
Quart. Rev. Biophys.
, vol.11
, pp. 179-246
-
-
Manning, G.S.1
-
45
-
-
0024121469
-
Calibration of DNA curvature and a unified description of sequence-directed bending
-
Koo H.S., Crothers D.M. Calibration of DNA curvature and a unified description of sequence-directed bending. Proc. Natl Acad. Sci. USA. 85:1988;1763-1767
-
(1988)
Proc. Natl Acad. Sci. USA
, vol.85
, pp. 1763-1767
-
-
Koo, H.S.1
Crothers, D.M.2
-
46
-
-
0002890451
-
Use of topology to measure protein-induced DNA bend and unwinding angles
-
A.A. Travers, & M. Buckle. Oxford: Oxford University Press
-
Lutter L.C., Drabik C.E., Halvorson H.R. Use of topology to measure protein-induced DNA bend and unwinding angles. Travers A.A., Buckle M. Protein-DNA Interactions: A Practical Approach. 2000;47-64 Oxford University Press, Oxford
-
(2000)
Protein-DNa Interactions: A Practical Approach
, pp. 47-64
-
-
Lutter, L.C.1
Drabik, C.E.2
Halvorson, H.R.3
-
48
-
-
0041829746
-
DNA curvature in solution measured by fluorescence resonance energy transfer
-
Toth K., Sauermann V., Langowski J. DNA curvature in solution measured by fluorescence resonance energy transfer. Biochemistry. 37:1998;8173-8179
-
(1998)
Biochemistry
, vol.37
, pp. 8173-8179
-
-
Toth, K.1
Sauermann, V.2
Langowski, J.3
-
49
-
-
0000744136
-
Conformational fluctuations of DNA helix
-
Depew D.E., Wang J.C. Conformational fluctuations of DNA helix. Proc. Natl Acad. Sci. USA. 72:1975;4275-4279
-
(1975)
Proc. Natl Acad. Sci. USA
, vol.72
, pp. 4275-4279
-
-
Depew, D.E.1
Wang, J.C.2
-
50
-
-
0017835311
-
Supercoiling in closed circular DNA: Dependence upon ion type and concentration
-
Anderson P., Bauer W. Supercoiling in closed circular DNA: dependence upon ion type and concentration. Biochemistry. 17:1978;594-601
-
(1978)
Biochemistry
, vol.17
, pp. 594-601
-
-
Anderson, P.1
Bauer, W.2
-
51
-
-
0026642548
-
Straightening out the bends in curved DNA
-
Hagerman P.J. Straightening out the bends in curved DNA. Biochim. Biophys. Acta. 1131:1992;125-132
-
(1992)
Biochim. Biophys. Acta
, vol.1131
, pp. 125-132
-
-
Hagerman, P.J.1
-
52
-
-
0038713237
-
A unified model for the origin of DNA sequence-directed curvature
-
Hud N.V., Plavec J. A unified model for the origin of DNA sequence-directed curvature. Biopolymers. 69:2003;144-158
-
(2003)
Biopolymers
, vol.69
, pp. 144-158
-
-
Hud, N.V.1
Plavec, J.2
|