-
1
-
-
0018199224
-
DNAse footprinting: A simple method for the detection of protein-DNA binding specificity
-
Galas, D.J. & Schmitz, A. DNAse footprinting: A simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res. 5, 3157-3170 (1978).
-
(1978)
Nucleic Acids Res
, vol.5
, pp. 3157-3170
-
-
Galas, D.J.1
Schmitz, A.2
-
2
-
-
0024359787
-
Defining the inside and outside of a catalytic RNA molecule
-
Latham, J.A. & Cech, T.R. Defining the inside and outside of a catalytic RNA molecule. Science 245, 276-282 (1989).
-
(1989)
Science
, vol.245
, pp. 276-282
-
-
Latham, J.A.1
Cech, T.R.2
-
3
-
-
0031013756
-
Quantitative nucleic acids footprinting: Thermodynamic and kinetic approaches
-
Petri, V. & Brenowitz, M. Quantitative nucleic acids footprinting: thermodynamic and kinetic approaches. Curr. Opin. Biotechnol. 8 36-44 (1997).
-
(1997)
Curr. Opin. Biotechnol
, vol.8
, pp. 36-44
-
-
Petri, V.1
Brenowitz, M.2
-
4
-
-
84918833988
-
Critical review of rate constants for reactions of hydrated electrons, hydrogen atoms and hydroxyl radicals in aqueous solution
-
Buxton, G.V., Greenstock, C.L., Heiman, W.P. & Ross, A.B. Critical review of rate constants for reactions of hydrated electrons, hydrogen atoms and hydroxyl radicals in aqueous solution. J. Phys. Chem. Ref. Data 17, 513-886 (1988).
-
(1988)
J. Phys. Chem. Ref. Data
, vol.17
, pp. 513-886
-
-
Buxton, G.V.1
Greenstock, C.L.2
Heiman, W.P.3
Ross, A.B.4
-
5
-
-
0001268975
-
Hydroxyl radical 'footprinting': High-resolution information about DNA-protein contacts and application to Lambda repressor and Cro protein
-
Tullius, T.D. & Dombroski, B.A. Hydroxyl radical 'footprinting': high-resolution information about DNA-protein contacts and application to Lambda repressor and Cro protein. Proc. Natl. Acad. Sci. USA 83, 5469-5473 (1986).
-
(1986)
Proc. Natl. Acad. Sci. USA
, vol.83
, pp. 5469-5473
-
-
Tullius, T.D.1
Dombroski, B.A.2
-
6
-
-
0029806242
-
Quantitative kinetics footprinting of protein-DNA association reactions
-
Hsieh, M. & Brenowitz, M. Quantitative kinetics footprinting of protein-DNA association reactions. Methods Enzymol. 274, 478-492 (1996).
-
(1996)
Methods Enzymol
, vol.274
, pp. 478-492
-
-
Hsieh, M.1
Brenowitz, M.2
-
7
-
-
18544384019
-
The oxidation of tartaric acid in presence of iron
-
Fenton, H.J.H. The oxidation of tartaric acid in presence of iron. J. Chem. Soc. 65, 899-910 (1894).
-
(1894)
J. Chem. Soc
, vol.65
, pp. 899-910
-
-
Fenton, H.J.H.1
-
8
-
-
33645819791
-
Fast Fenton footprinting: A Laboratory-based method for the time-resolved analysis of DNA, RNA and proteins
-
Shcherbakova, I., Mitra, S., Beer, R.H. & Brenowitt, M. Fast Fenton footprinting: A Laboratory-based method for the time-resolved analysis of DNA, RNA and proteins. Nucleic Acids Res. 34, e48 (2006).
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Shcherbakova, I.1
Mitra, S.2
Beer, R.H.3
Brenowitt, M.4
-
9
-
-
35448978228
-
Following molecular transitions with single residue spatial and millisecond time resolution
-
eds. Correia, J.J. & Detrich, H.W, Elsevier/Academic Press, New York
-
Shcherbakova, I., Mitra, S., Beer, R.H. & Brenowitz, M. Following molecular transitions with single residue spatial and millisecond time resolution. in Methods in Cell Biology, Vol. 84 (eds. Correia, J.J. & Detrich, H.W.) 589-615 (Elsevier/Academic Press, New York, 2008).
-
(2008)
Methods in Cell Biology
, vol.84
, pp. 589-615
-
-
Shcherbakova, I.1
Mitra, S.2
Beer, R.H.3
Brenowitz, M.4
-
10
-
-
0022382116
-
Iron(II) EDTA used to measure the helical twist along any DNA molecule
-
Tullius, T.D. & Dombroski, B.A. Iron(II) EDTA used to measure the helical twist along any DNA molecule. Science 230, 679-681 (1985).
-
(1985)
Science
, vol.230
, pp. 679-681
-
-
Tullius, T.D.1
Dombroski, B.A.2
-
11
-
-
0032549780
-
RNA folding at millisecond intervals by synchrotron hydroxyl, radical foutprinting
-
Sclavi, B., Sullivan, M., Chance, M.R., Brenowitz, M. & Woodson, S.A. RNA folding at millisecond intervals by synchrotron hydroxyl, radical foutprinting. Science 279, 1940-1943 (1998).
-
(1998)
Science
, vol.279
, pp. 1940-1943
-
-
Sclavi, B.1
Sullivan, M.2
Chance, M.R.3
Brenowitz, M.4
Woodson, S.A.5
-
12
-
-
0033644180
-
Time-resolved synchrotron X-ray footprinting and its application to RNA folding
-
Ralston, C.Y. et al. Time-resolved synchrotron X-ray footprinting and its application to RNA folding. Methods Enzymol. 317, 353-368 (2000).
-
(2000)
Methods Enzymol
, vol.317
, pp. 353-368
-
-
Ralston, C.Y.1
-
13
-
-
0036816641
-
Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl. radicaL 'footprinting
-
Brenowitz, M., Chance, M.R., Dhavan, G. & Takamoto, K. Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl. radicaL 'footprinting. Curr. Opin. Struct. Biol. 12, 648-653 (2002).
-
(2002)
Curr. Opin. Struct. Biol
, vol.12
, pp. 648-653
-
-
Brenowitz, M.1
Chance, M.R.2
Dhavan, G.3
Takamoto, K.4
-
14
-
-
24944566705
-
Nanosecond laser-induced photochemical oxidation method for protein surface mapping with mass spectrometry
-
Aye, T.T., Low, T.Y. & Sze, S.K. Nanosecond laser-induced photochemical oxidation method for protein surface mapping with mass spectrometry. Anal. Chem. 77, 5814-5822 (2005).
-
(2005)
Anal. Chem
, vol.77
, pp. 5814-5822
-
-
Aye, T.T.1
Low, T.Y.2
Sze, S.K.3
-
15
-
-
27844593258
-
Laser flash photolysis of hydrogen peroxide to oxidize protein solvent-accessible residues on the microsecond timescale
-
HambLy, D.M. & Gross, M.L. Laser flash photolysis of hydrogen peroxide to oxidize protein solvent-accessible residues on the microsecond timescale. J. Am. Soc. Mass Spectrom. 16, 2057-2063 (2005).
-
(2005)
J. Am. Soc. Mass Spectrom
, vol.16
, pp. 2057-2063
-
-
HambLy, D.M.1
Gross, M.L.2
-
16
-
-
0029836226
-
Determinants of RNA polymerase aloha subunit for interaction with beta, beta', and sigma subunits: Hydroxyl-radical protein footprinting
-
Heyduk, T., Heyduk, E., Severinov, K., Tang, H. & Ebright, R.H. Determinants of RNA polymerase aloha subunit for interaction with beta, beta', and sigma subunits: Hydroxyl-radical protein footprinting. Proc. Natl. Acad. Sci. USA 93, 10162-10166 (1996).
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 10162-10166
-
-
Heyduk, T.1
Heyduk, E.2
Severinov, K.3
Tang, H.4
Ebright, R.H.5
-
17
-
-
0037442729
-
Protein surface mapping by chemical oxidation: Structural analysis by mass spectrometry
-
Sharp, J.S., Becker, J.M. & Hettich, R.L. Protein surface mapping by chemical oxidation: Structural analysis by mass spectrometry. Anal. Biochem. 313, 216-225 (2003).
-
(2003)
Anal. Biochem
, vol.313
, pp. 216-225
-
-
Sharp, J.S.1
Becker, J.M.2
Hettich, R.L.3
-
18
-
-
33745041235
-
Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes
-
Takamoto, K. & Chance, M.R. Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes. Annu. Rev. Biohys. Biomol. Struct. 35, 521-276 (2006).
-
(2006)
Annu. Rev. Biohys. Biomol. Struct
, vol.35
, pp. 521-276
-
-
Takamoto, K.1
Chance, M.R.2
-
19
-
-
16344376192
-
-
Sclavi, B. et al. 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. USA 102 1706-4711 (2005).
-
Sclavi, B. et al. 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. USA 102 1706-4711 (2005).
-
-
-
-
20
-
-
0024285808
-
Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: Enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes
-
Zaug, A.J., Grosshans, C.A. & Cech, T.R. Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: Enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes. Biochemistry 27, 8924-8931 (1988).
-
(1988)
Biochemistry
, vol.27
, pp. 8924-8931
-
-
Zaug, A.J.1
Grosshans, C.A.2
Cech, T.R.3
-
21
-
-
0029963656
-
A simple method for 3′-labeling of RNA
-
Huang, Z. & Szostak, J.W. A simple method for 3′-labeling of RNA. Nucleic Acids Res. 24, 4360-4361 (1996).
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 4360-4361
-
-
Huang, Z.1
Szostak, J.W.2
-
22
-
-
4444370899
-
Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme
-
Shcherbakova, I., Gupta, S., Chance, M.R. & Brenowitz, M. Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme. J. Mol. Biol. 342, 1431-1442 (2004).
-
(2004)
J. Mol. Biol
, vol.342
, pp. 1431-1442
-
-
Shcherbakova, I.1
Gupta, S.2
Chance, M.R.3
Brenowitz, M.4
-
23
-
-
0034019929
-
Custom fluorescent-nucleotide synthesis as an alternative method for nucleic acid labeling
-
Henegariu, O., Bray-Ward, P. & Ward, D.C. Custom fluorescent-nucleotide synthesis as an alternative method for nucleic acid labeling. Nat. Biotechnol. 28, 345-348 (2000).
-
(2000)
Nat. Biotechnol
, vol.28
, pp. 345-348
-
-
Henegariu, O.1
Bray-Ward, P.2
Ward, D.C.3
-
24
-
-
33745279107
-
Following the dynamics of changes in solvent accessibility of 16 S and 23 S rRNA during ribosomal subunit association using synchrotron-generated hydroxyl. radicals
-
Nguyenle, T., Laurberg, M., Brenowitz, M. & Noller, H.F. Following the dynamics of changes in solvent accessibility of 16 S and 23 S rRNA during ribosomal subunit association using synchrotron-generated hydroxyl. radicals. J. Mol. Biol. 359, 1235-1248 (2006).
-
(2006)
J. Mol. Biol
, vol.359
, pp. 1235-1248
-
-
Nguyenle, T.1
Laurberg, M.2
Brenowitz, M.3
Noller, H.F.4
-
25
-
-
22544466402
-
Protein-independent folding pathway of the 16S rRNA 5′ domain
-
Adilakshmi, T., Ramaswamy, P. & Woodson, S.A. Protein-independent folding pathway of the 16S rRNA 5′ domain. J. Mol. Biol. 351 508-519 (2005).
-
(2005)
J. Mol. Biol
, vol.351
, pp. 508-519
-
-
Adilakshmi, T.1
Ramaswamy, P.2
Woodson, S.A.3
-
26
-
-
0022437260
-
Quantitative DNase footprint titration: A method for studying protein-DNA interactions
-
Brenowitz, M., Senear, D.F., Shea, M.A. & Ackers, G.K., Quantitative DNase footprint titration: A method for studying protein-DNA interactions. Methods Enzymol. 130, 132-181 (1986).
-
(1986)
Methods Enzymol
, vol.130
, pp. 132-181
-
-
Brenowitz, M.1
Senear, D.F.2
Shea, M.A.3
Ackers, G.K.4
-
27
-
-
0032319210
-
Following the folding of RNA with time-resolved synchrotron X-ray footprinting
-
Sclavi, B., Woodson, S., Sullivan, M., Chance, M. & Brenowitz, M. Following the folding of RNA with time-resolved synchrotron X-ray footprinting. Methods Enzymol. 295, 379-402 (1998).
-
(1998)
Methods Enzymol
, vol.295
, pp. 379-402
-
-
Sclavi, B.1
Woodson, S.2
Sullivan, M.3
Chance, M.4
Brenowitz, M.5
-
28
-
-
13944278373
-
Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments
-
Das, R., Laederach, A., Pearlman, S.M., Herschlag, D. & Altman, R.B. SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA 11 344-354 (2005).
-
(2005)
RNA
, vol.11
, pp. 344-354
-
-
Das, R.1
Laederach, A.2
Pearlman, S.M.3
Herschlag, D.4
Altman, R.B.S.5
-
29
-
-
33646089899
-
Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule
-
Laederach, A., Shcherbakova, I., Liang, M.P., Brenowitz, M. & Altman, R.B. Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule. J. Mol. Biol. 358, 1179-1190 (2006).
-
(2006)
J. Mol. Biol
, vol.358
, pp. 1179-1190
-
-
Laederach, A.1
Shcherbakova, I.2
Liang, M.P.3
Brenowitz, M.4
Altman, R.B.5
-
30
-
-
0842283944
-
Analysis of protein solvent accessible surfaces by photochemical oxidation and mass spectrometry
-
Sharp, J.S., Becker, J.M. & Hettich, R.L. Analysis of protein solvent accessible surfaces by photochemical oxidation and mass spectrometry. Anal. Chem. 76, 672-683 (2004).
-
(2004)
Anal. Chem
, vol.76
, pp. 672-683
-
-
Sharp, J.S.1
Becker, J.M.2
Hettich, R.L.3
-
31
-
-
38449119903
-
DMS footprinting of structured RNAs and RNA-protein complexes
-
Tijerina, P., Mohr, S. & Russell, R. DMS footprinting of structured RNAs and RNA-protein complexes. Nat. Protoc. 2, 2608-2623 (2007).
-
(2007)
Nat. Protoc
, vol.2
, pp. 2608-2623
-
-
Tijerina, P.1
Mohr, S.2
Russell, R.3
-
32
-
-
0031566962
-
Time-resolved synchrotron X-ray 'footprinting', a new approach to the study of nucleic acid structure and function: Application to protein-DRA interactions and RNA folding
-
Sclavi, B., Woodson, S., Sullivan, M., Chance, M.R. & Brenowitz, M. Time-resolved synchrotron X-ray 'footprinting', a new approach to the study of nucleic acid structure and function: Application to protein-DRA interactions and RNA folding. J. Mol. Biol. 266, 144-159 (1997).
-
(1997)
J. Mol. Biol
, vol.266
, pp. 144-159
-
-
Sclavi, B.1
Woodson, S.2
Sullivan, M.3
Chance, M.R.4
Brenowitz, M.5
-
33
-
-
34249850484
-
Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding
-
Laederach, A., Shcherbakova, I., Jonikas, M.A., Altman, R.B. & Brenowitz, M. Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding. Proc. Natl. Acad. Sci. USA 104, 7045-7050 (2007).
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 7045-7050
-
-
Laederach, A.1
Shcherbakova, I.2
Jonikas, M.A.3
Altman, R.B.4
Brenowitz, M.5
|