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Preferential Interactions of Glycine Betaine and of Urea with DNA: Implications for DNA Hydration and for Effects of These Solutes on DNA Stability

Biochemistry (Easton), 2004-11, Vol.43 (46), p.14744-14758

2004

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Enthalpy and Heat Capacity Changes for Formation of an Oligomeric DNA Duplex: Interpretation in Terms of Coupled Processes of Formation and Association of Single-Stranded Helices

Biochemistry (Easton), 1999-06, Vol.38 (26), p.8409-8422

1999

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Protein surface salt bridges and paths for DNA wrapping

Current Opinion in Structural Biology, 2002-06, Vol.12 (3), p.311-319

2002

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Specific and non-specific interactions of integration host factor with DNA: thermodynamic evidence for disruption of multiple IHF surface salt-bridges coupled to DNA binding

Journal of molecular biology, 2001-07, Vol.310 (2), p.379-401

2001

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Thermodynamic analysis of interactions between denaturants and protein surface exposed on unfolding: Interpretation of urea and guanidinium chloride m-values and their correlation with changes in accessible surface area (ASA) using preferential interaction coefficients and the local-bulk domain model

Proteins, structure, function, and bioinformatics, 2000, Vol.41 (S4), p.72-85

2000

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DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA

Journal of molecular biology, 1998-11, Vol.283 (4), p.741-756

1998

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Formation of a Wrapped DNA–Protein Interface: Experimental Characterization and Analysis of the Large Contributions of Ions and Water to the Thermodynamics of Binding IHF to H′ DNA

Journal of molecular biology, 2008-03, Vol.377 (1), p.9-27

2008

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Thermodynamics of the interactions of Lac repressor with variants of the symmetric Lac operator: effects of converting a consensus site to a non-specific site

Journal of molecular biology, 1997-04, Vol.267 (5), p.1186-1206

1997

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Evidence for a Tyrosine–Adenine Stacking Interaction and for a Short-lived Open Intermediate Subsequent to Initial Binding of Escherichia coli RNA Polymerase to Promoter DNA

Journal of molecular biology, 2009-01, Vol.385 (2), p.339-349

2009

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Use of Urea and Glycine Betaine To Quantify Coupled Folding and Probe the Burial of DNA Phosphates in Lac Repressor−Lac Operator Binding

Biochemistry (Easton), 2005-12, Vol.44 (51), p.16896-16911

2005

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Wrapping of flanking non-operator DNA in lac repressor-operator complexes: implications for DNA looping

Journal of molecular biology, 1999-12, Vol.294 (3), p.639-655

1999

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Structural stability of binding sites: Consequences for binding affinity and allosteric effects

Proteins, structure, function, and bioinformatics, 2000, Vol.41 (S4), p.63-71

2000

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DNA Binding Mode Transitions of Escherichia coli HU sub(a) sub(b): Evidence for Formation of a Bent DNA - Protein Complex on Intact, Linear Duplex DNA

Journal of molecular biology, 2008-11, Vol.383 (2), p.324-346

2008

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Compensating effects of opposing changes in putrescine (2+) and K+ concentrations on lac repressor-lac operator binding: in vitro thermodynamic analysis and in vivo relevance

Journal of molecular biology, 1996-04, Vol.258 (1), p.25-36

1996

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Quantitative Analysis of Multiple-hit Footprinting Studies to Characterize DNA Conformational Changes in Protein-DNA Complexes: Application to DNA Opening by E sigma RNA Polymerase

Journal of molecular biology, 1998-11, Vol.283 (4), p.757-769

1998

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The Effects of Upstream DNA on Open Complex Formation by Escherichia coli RNA Polymerase

Proceedings of the National Academy of Sciences - PNAS, 2005-01, Vol.102 (2), p.285-290

2005

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Late Steps in the Formation of E. coli RNA Polymerase-lP sub(R) Promoter Open Complexes: Characterization of Conformational Changes by Rapid [Perturbant] Upshift Experiments

Journal of molecular biology, 2008-02, Vol.376 (4), p.1034-1047

2008

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Solute Probes of Conformational Changes in Open Complex (RPo) Formation by Escherichia coli RNA Polymerase at the λPR Promoter: Evidence for Unmasking of the Active Site in the Isomerization Step and for Large-Scale Coupled Folding in the Subsequent Conversion to RPo

Biochemistry (Easton), 2006-02, Vol.45 (7), p.2161-2177

2006

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Solute Probes of Conformational Changes in Open Complex (RP sub(o)) Formation by Escherichia coli RNA Polymerase at the lambda P sub(r) Promoter: Evidence for Unmasking of the Active Site in the Isomerization Step and for Large-Scale Coupled Folding in the Subsequent Conversion to RP sub(o)

Biochemistry (Easton), 2006-02, Vol.45 (7), p.2161-2177

2006

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Thermodynamic analysis of interactions between denaturants and protein surface exposed on unfolding: interpretation of urea and guanidinium chloride m-values and their correlation with changes in accessible surface area (ASA) using preferential interaction coefficients and the local-bulk domain model

Proteins, structure, function, and bioinformatics, 2000-01, Vol.Suppl 4, p.72-85

2000

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Quantitative analysis of multiple-hit footprinting studies to characterize DNA conformational changes in protein-DNA complexes: application to DNA opening by Esigma70 RNA polymerase

Journal of molecular biology, 1998-11, Vol.283 (4), p.757-769

1998

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Rapid Quench Mixing to Quantify Kinetics of Steps in Association of Escherichia coli RNA Polymerase with Promoter DNA

Methods in Enzymology, 2003, Vol.370, p.535-546

2003

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Cooperative and anticooperative effects in binding of the first and second plasmid Osym operators to a LacI tetramer: evidence for contributions of non-operator DNA binding by wrapping and looping

Journal of molecular biology, 1996-08, Vol.260 (5), p.697-717

1996

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Cooperative and anticooperative effects in binding of the first and second plasmid O super(sym) operators to a LacI tetramer: Evidence for contributions of non-operator DNA binding by wrapping and looping

Journal of molecular biology, 1996-01, Vol.260 (5), p.697-717

1996

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Compensating effects of opposing changes in putrescine (2+) and K super(+) concentrations on lac repressor-lac operator binding: In vitro thermodynamic analysis and in vivo relevance

Journal of molecular biology, 1996-01, Vol.258 (1), p.25-36

1996

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Preferential Interactions of Glycine Betaine and of Urea with DNA: Implications for DNA Hydration and for Effects of These Solutes on DNA Stability

Enthalpy and Heat Capacity Changes for Formation of an Oligomeric DNA Duplex: Interpretation in Terms of Coupled Processes of Formation and Association of Single-Stranded Helices

Protein surface salt bridges and paths for DNA wrapping

Specific and non-specific interactions of integration host factor with DNA: thermodynamic evidence for disruption of multiple IHF surface salt-bridges coupled to DNA binding

DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA

Formation of a Wrapped DNA–Protein Interface: Experimental Characterization and Analysis of the Large Contributions of Ions and Water to the Thermodynamics of Binding IHF to H′ DNA

Thermodynamics of the interactions of Lac repressor with variants of the symmetric Lac operator: effects of converting a consensus site to a non-specific site

Evidence for a Tyrosine–Adenine Stacking Interaction and for a Short-lived Open Intermediate Subsequent to Initial Binding of Escherichia coli RNA Polymerase to Promoter DNA

Use of Urea and Glycine Betaine To Quantify Coupled Folding and Probe the Burial of DNA Phosphates in Lac Repressor−Lac Operator Binding

Wrapping of flanking non-operator DNA in lac repressor-operator complexes: implications for DNA looping

Structural stability of binding sites: Consequences for binding affinity and allosteric effects

DNA Binding Mode Transitions of Escherichia coli HU sub(a) sub(b): Evidence for Formation of a Bent DNA - Protein Complex on Intact, Linear Duplex DNA

Compensating effects of opposing changes in putrescine (2+) and K+ concentrations on lac repressor-lac operator binding: in vitro thermodynamic analysis and in vivo relevance

Quantitative Analysis of Multiple-hit Footprinting Studies to Characterize DNA Conformational Changes in Protein-DNA Complexes: Application to DNA Opening by E sigma RNA Polymerase

The Effects of Upstream DNA on Open Complex Formation by Escherichia coli RNA Polymerase

Late Steps in the Formation of E. coli RNA Polymerase-lP sub(R) Promoter Open Complexes: Characterization of Conformational Changes by Rapid [Perturbant] Upshift Experiments

Solute Probes of Conformational Changes in Open Complex (RPo) Formation by Escherichia coli RNA Polymerase at the λPR Promoter: Evidence for Unmasking of the Active Site in the Isomerization Step and for Large-Scale Coupled Folding in the Subsequent Conversion to RPo

Solute Probes of Conformational Changes in Open Complex (RP sub(o)) Formation by Escherichia coli RNA Polymerase at the lambda P sub(r) Promoter: Evidence for Unmasking of the Active Site in the Isomerization Step and for Large-Scale Coupled Folding in the Subsequent Conversion to RP sub(o)

Quantitative analysis of multiple-hit footprinting studies to characterize DNA conformational changes in protein-DNA complexes: application to DNA opening by Esigma70 RNA polymerase

Rapid Quench Mixing to Quantify Kinetics of Steps in Association of Escherichia coli RNA Polymerase with Promoter DNA

Cooperative and anticooperative effects in binding of the first and second plasmid Osym operators to a LacI tetramer: evidence for contributions of non-operator DNA binding by wrapping and looping

Cooperative and anticooperative effects in binding of the first and second plasmid O super(sym) operators to a LacI tetramer: Evidence for contributions of non-operator DNA binding by wrapping and looping

Compensating effects of opposing changes in putrescine (2+) and K super(+) concentrations on lac repressor-lac operator binding: In vitro thermodynamic analysis and in vivo relevance

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