-
1
-
-
0032549780
-
RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting
-
Sclavi, B., Sullivan, M., Chance, M.R., Brenowitz, M. and Woodson, S.A. (1998) RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science 279, 1940-1943
-
(1998)
Science
, vol.279
, pp. 1940-1943
-
-
Sclavi, B.1
Sullivan, M.2
Chance, M.R.3
Brenowitz, M.4
Woodson, S.A.5
-
2
-
-
35448978228
-
Following molecular transitions with single residue spatial and millisecond time resolution
-
Shcherbakova, I., Mitra, S., Beer, R. and Brenowitz, M. (2008) Following molecular transitions with single residue spatial and millisecond time resolution. Methods Cell Biol. 84, 589-615
-
(2008)
Methods Cell Biol
, vol.84
, pp. 589-615
-
-
Shcherbakova, I.1
Mitra, S.2
Beer, R.3
Brenowitz, M.4
-
3
-
-
33745041235
-
Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes
-
Takamoto, K. and Chance, M.R. (2006) Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes. Annu. Rev. Biophys. Biomol. Struct. 35, 251-276
-
(2006)
Annu. Rev. Biophys. Biomol. Struct
, vol.35
, pp. 251-276
-
-
Takamoto, K.1
Chance, M.R.2
-
4
-
-
0242435017
-
Rapid 'footprinting' on supercoiled DNA
-
Gralla, J.D. (1985) Rapid 'footprinting' on supercoiled DNA. Proc. Natl. Acad Sci. U.S.A. 82, 3078-3081
-
(1985)
Proc. Natl. Acad Sci. U.S.A
, vol.82
, pp. 3078-3081
-
-
Gralla, J.D.1
-
5
-
-
0037127286
-
In vivo UV-laser footprinting of the Pseudomonas putida s54 Pu promoter reveals that IHF couples transcriptional activity to growth phase
-
Valls, M., Buckle, M. and De Lorenzo, V. (2001) In vivo UV-laser footprinting of the Pseudomonas putida s54 Pu promoter reveals that IHF couples transcriptional activity to growth phase. J. Biol. Chem. 277, 2169-2175
-
(2001)
J. Biol. Chem
, vol.277
, pp. 2169-2175
-
-
Valls, M.1
Buckle, M.2
De Lorenzo, V.3
-
6
-
-
0034697671
-
High-resolution in vivo footprinting of a protein-DNA complex using γ-radiation
-
Ottinger, L.M. and Tullius, T.D. (2000) High-resolution in vivo footprinting of a protein-DNA complex using γ-radiation. J. Am. Chem. Soc. 122, 5901-5902
-
(2000)
J. Am. Chem. Soc
, vol.122
, pp. 5901-5902
-
-
Ottinger, L.M.1
Tullius, T.D.2
-
7
-
-
0031013756
-
Quantitative nucleic acids footprinting: Thermodynamic and kinetic approaches
-
Petri, V. and Brenowitz, M. (1997) Quantitative nucleic acids footprinting: thermodynamic and kinetic approaches. Curr. Opin. Biotechnol. 8, 36-44
-
(1997)
Curr. Opin. Biotechnol
, vol.8
, pp. 36-44
-
-
Petri, V.1
Brenowitz, M.2
-
8
-
-
0026354983
-
DNase I-induced DNA conformation: 2 Å structure of a DNase I-octamer complex
-
Lahm, A. and Suck, D. (1991) DNase I-induced DNA conformation: 2 Å structure of a DNase I-octamer complex. J. Mol. Biol. 222, 645-667
-
(1991)
J. Mol. Biol
, vol.222
, pp. 645-667
-
-
Lahm, A.1
Suck, D.2
-
9
-
-
49349107230
-
-
Brenowitz, M., Senear, D.F. and Kingston, R.F. (2001) DNase I footprint analysis of protein-DNA binding. in Current Protocols in molecular Biology (Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. and Struhl, K., eds.), chapter 12, unit 12.4, John Wiley and Sons, New York
-
Brenowitz, M., Senear, D.F. and Kingston, R.F. (2001) DNase I footprint analysis of protein-DNA binding. in Current Protocols in molecular Biology (Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. and Struhl, K., eds.), chapter 12, unit 12.4, John Wiley and Sons, New York
-
-
-
-
10
-
-
16244389281
-
Mapping nucleic acid structure by hydroxyl radical cleavage
-
Tullius, T. and Greenbaum, J. (2005) Mapping nucleic acid structure by hydroxyl radical cleavage. Curr. Opin. Chem. Biol. 9, 127-134
-
(2005)
Curr. Opin. Chem. Biol
, vol.9
, pp. 127-134
-
-
Tullius, T.1
Greenbaum, J.2
-
11
-
-
0032544035
-
DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone
-
Balasubramanian, B., Pogozelski, W. and Tullius, T. (1998) DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone. Proc. Natl. Acad. Sci. U.S.A. 95, 9738-9743
-
(1998)
Proc. Natl. Acad. Sci. U.S.A
, vol.95
, pp. 9738-9743
-
-
Balasubramanian, B.1
Pogozelski, W.2
Tullius, T.3
-
12
-
-
0037123602
-
Structural basis of transcription initiation: An RNA polymerase holoenzyme-DNA complex
-
Murakami, K.S., Masuda, S., Campbell, F.A., Muzzin, O. and Darst, S.A. (2002) Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science 296, 1285-1290
-
(2002)
Science
, vol.296
, pp. 1285-1290
-
-
Murakami, K.S.1
Masuda, S.2
Campbell, F.A.3
Muzzin, O.4
Darst, S.A.5
-
13
-
-
0030452773
-
New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: A complete 3D model of the Tetrahymena thermophila ribozyme
-
Lehnert, V., Jaeger, L., Michel, F. and Westhof, E. (1996) New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem. Biol. 3, 993-1009
-
(1996)
Chem. Biol
, vol.3
, pp. 993-1009
-
-
Lehnert, V.1
Jaeger, L.2
Michel, F.3
Westhof, E.4
-
14
-
-
0034635167
-
Characterization of the Tetrahymena ribozyme folding pathway using the kinetic footprinting reagent peroxynitrous acid
-
Chaulk, S.G. and MacMillan, A.M. (2000) Characterization of the Tetrahymena ribozyme folding pathway using the kinetic footprinting reagent peroxynitrous acid. Biochemistry 39, 2-8
-
(2000)
Biochemistry
, vol.39
, pp. 2-8
-
-
Chaulk, S.G.1
MacMillan, A.M.2
-
15
-
-
33645819791
-
Fast fenton footprinting: A laboratory-based method for the time-resolved analysis of DNA, RNA and proteins
-
Shcherbakova, I., Mitra, S., Beer, R. and Brenowitz, M. (2006) Fast fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins. Nucleic Acids Res. 34, e48
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Shcherbakova, I.1
Mitra, S.2
Beer, R.3
Brenowitz, M.4
-
16
-
-
0031056544
-
The two α subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element
-
Murakami, K., Kimura, M., Owens, J.T., Meares, C.F. and Ishihama, A. (1997) The two α subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element. Proc. Natl. Acad. Sci. U.S.A. 94, 1709-1714
-
(1997)
Proc. Natl. Acad. Sci. U.S.A
, vol.94
, pp. 1709-1714
-
-
Murakami, K.1
Kimura, M.2
Owens, J.T.3
Meares, C.F.4
Ishihama, A.5
-
17
-
-
0033619725
-
Targeted protein footprinting: Where different transcription factors bind to RNA polymerase
-
Traviglia, S.L., Datwyler, S.A., Yan, D., Ishihama, A. and Meares, C.F. (1999) Targeted protein footprinting: where different transcription factors bind to RNA polymerase. Biochemistry 38, 15774-15778
-
(1999)
Biochemistry
, vol.38
, pp. 15774-15778
-
-
Traviglia, S.L.1
Datwyler, S.A.2
Yan, D.3
Ishihama, A.4
Meares, C.F.5
-
18
-
-
33646841501
-
Hydroxyl radical footpfinting in vivo: Mapping macromolecular structures with synchrotron radiation
-
Adilakshmi, T., Lease, R. and Woodson, S. (2006) Hydroxyl radical footpfinting in vivo: mapping macromolecular structures with synchrotron radiation. Nucleic Acids Res. 34, e64
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Adilakshmi, T.1
Lease, R.2
Woodson, S.3
-
19
-
-
2142777597
-
Laser UV cross-linking of nucleoprotein complexes in vitro
-
Buckle, M. and Travers, A, eds, pp, Oxford University Press, Oxford
-
Buckle, M., Place, C. and Pemberton, I.K. (2000) Laser UV cross-linking of nucleoprotein complexes in vitro. in Protein-DNA Interactions: A Practical Approach (Buckle, M. and Travers, A., eds.), pp. 189-200, Oxford University Press, Oxford
-
(2000)
Protein-DNA Interactions: A Practical Approach
, pp. 189-200
-
-
Buckle, M.1
Place, C.2
Pemberton, I.K.3
-
20
-
-
0032509089
-
A quantitative UV laser footprinting analysis of the interaction of IHF with specific binding sites: Re-evaluation of the effective concentration of IHF in the cell
-
Murtin, C., Engelhorn, M., Gelselmann, J. and Boccard, F. (1998) A quantitative UV laser footprinting analysis of the interaction of IHF with specific binding sites: re-evaluation of the effective concentration of IHF in the cell. J. Mol. Biol. 284, 949-961
-
(1998)
J. Mol. Biol
, vol.284
, pp. 949-961
-
-
Murtin, C.1
Engelhorn, M.2
Gelselmann, J.3
Boccard, F.4
-
21
-
-
0034625251
-
Structural organization of the RNA polymerase-promoter open complex
-
Naryshkin, N., Revyakin, A., Kim, Y., Mekler, V. and Elbright, R.H. (2000) Structural organization of the RNA polymerase-promoter open complex. Cell 101, 601-611
-
(2000)
Cell
, vol.101
, pp. 601-611
-
-
Naryshkin, N.1
Revyakin, A.2
Kim, Y.3
Mekler, V.4
Elbright, R.H.5
-
22
-
-
0020757474
-
Mapping of single-stranded regions in duplex DNA at the sequence level: Single-strand-specific cytosine methylation in RNA polymerase-promoter complexes
-
Kirkegaard, K., Buc, H., Spassky, A. and Wang, J.C. (1983) Mapping of single-stranded regions in duplex DNA at the sequence level: single-strand-specific cytosine methylation in RNA polymerase-promoter complexes. Proc. Natl. Acad. Sci. U.S.A. 80, 2544-2548
-
(1983)
Proc. Natl. Acad. Sci. U.S.A
, vol.80
, pp. 2544-2548
-
-
Kirkegaard, K.1
Buc, H.2
Spassky, A.3
Wang, J.C.4
-
24
-
-
0024314892
-
Fine mapping of DNA single-stranded regions using base-specific chemical probes: Study of an open complex formed between RNA polymerase and the lac UV5 promoter
-
Buckle, M. and Buc, H. (1989) Fine mapping of DNA single-stranded regions using base-specific chemical probes: study of an open complex formed between RNA polymerase and the lac UV5 promoter. Biochemistry 28, 4388-4396
-
(1989)
Biochemistry
, vol.28
, pp. 4388-4396
-
-
Buckle, M.1
Buc, H.2
-
26
-
-
16344376192
-
Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter
-
Sclavi, B., Zaychikov, E., Rogozina, A., Walther, F., Buckle, M. and Heumann, H. (2005) Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter. Proc. Natl. Acad. Sci. U.S.A. 102, 4706-4711
-
(2005)
Proc. Natl. Acad. Sci. U.S.A
, vol.102
, pp. 4706-4711
-
-
Sclavi, B.1
Zaychikov, E.2
Rogozina, A.3
Walther, F.4
Buckle, M.5
Heumann, H.6
-
27
-
-
0036304119
-
Concerted binding and bending of DNA by Escherichia coli integration host factor
-
Dhavan, G.M., Crothers, D.M., Chance, M.R. and Brenowitz, M. (2002) Concerted binding and bending of DNA by Escherichia coli integration host factor. J. Mol. Biol. 315, 1027-1037
-
(2002)
J. Mol. Biol
, vol.315
, pp. 1027-1037
-
-
Dhavan, G.M.1
Crothers, D.M.2
Chance, M.R.3
Brenowitz, M.4
-
28
-
-
0022429106
-
The OR control system of bacteroophage lambda: A physical-chemical model for gene regulation
-
Shea, M. and Ackers, G. (1985) The OR control system of bacteroophage lambda: a physical-chemical model for gene regulation. J. Mol. Biol. 181, 211-230
-
(1985)
J. Mol. Biol
, vol.181
, pp. 211-230
-
-
Shea, M.1
Ackers, G.2
|