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1

Mechanism of Bacterial Transcription Initiation: RNA Polymerase - Promoter Binding, Isomerization to Initiation-Competent Open Complexes, and Initiation of RNA Synthesis

Ruth M. Saecker, M. Thomas Record Jr., Pieter L. deHaseth

Journal:

Journal of Molecular Biology

Year:

2011

Language:

english

File:

PDF, 894 KB

english, 2011

2

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

Hong, Jiang, Capp, Michael W., Anderson, Charles F., Saecker, Ruth M., Felitsky, Daniel J., Anderson, Melissa W., Record, M. Thomas

Journal:

Year:

2004

Language:

english

File:

PDF, 193 KB

english, 2004

3

Protein surface salt bridges and paths for DNA wrapping

Ruth M Saecker, M.Thomas Record Jr

Journal:

Current Opinion in Structural Biology

Year:

2002

Language:

english

File:

PDF, 1.01 MB

english, 2002

4

Compensating Effects of Opposing Changes in Putrescine (2+) and K+Concentrations onlacRepressor-lacOperator Binding:in VitroThermodynamic Analysis andin VivoRelevance

Michael W. Capp, Scott D. Cayley, Wentao Zhang, Harry J. Guttman, Sonya E. Melcher, Ruth M. Saecker, Charles F. Anderson, Thomas M. Record, Jr

Journal:

Journal of Molecular Biology

Year:

1996

Language:

english

File:

PDF, 514 KB

english, 1996

5

Cooperative and Anticooperative Effects in Binding of the First and Second Plasmid OsymOperators to a LacI Tetramer: Evidence for Contributions of Non-operator DNA Binding by Wrapping and Looping

Mark M. Levandoski, Oleg V. Tsodikov, Diane E. Frank, Sonya E. Melcher, Ruth M. Saecker, Thomas M. Record Jr

Journal:

Journal of Molecular Biology

Year:

1996

Language:

english

File:

PDF, 624 KB

english, 1996

6

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

Diane E. Frank, Ruth M. Saecker, Jeffrey P. Bond, Michael W. Capp, Oleg V. Tsodikov, Sonya E. Melcher, Mark M. Levandoski, M.Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

1997

Language:

english

File:

PDF, 510 KB

english, 1997

7

Quantitative analysis of multiple-hit footprinting studies to characterize DNA conformational changes in protein-DNA complexes: application to DNA opening by Eσ70 RNA polymerase

Oleg V. Tsodikov, Maria L. Craig, Ruth M. Saecker, M.Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

1998

Language:

english

File:

PDF, 385 KB

english, 1998

8

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

Maria L. Craig, Oleg V. Tsodikov, Kristi L. McQuade, Peter E. Schlax Jr, Michael W. Capp, Ruth M. Saecker, M.Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

1998

Language:

english

File:

PDF, 494 KB

english, 1998

9

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

Oleg V. Tsodikov, Ruth M. Saecker, Sonya E. Melcher, Mark M. Levandoski, Diane E. Frank, Michael W. Capp, M.Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

1999

Language:

english

File:

PDF, 420 KB

english, 1999

10

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

Jill A. Holbrook, Oleg V. Tsodikov, Ruth M. Saecker, M.Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 600 KB

english, 2001

11

Do Sigma Factors Need Help with a Meltdown?

Ruth M. Saecker, Caroline A. Davis, M.T. Record Jr.

Journal:

Year:

2006

Language:

english

File:

PDF, 265 KB

english, 2006

12

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

Kirk A. Vander Meulen, Ruth M. Saecker, M. Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

2008

Language:

english

File:

PDF, 1.60 MB

english, 2008

13

Late Steps in the Formation of E. coli RNA Polymerase—λPR Promoter Open Complexes: Characterization of Conformational Changes by Rapid [Perturbant] Upshift Experiments

Wayne S. Kontur, Ruth M. Saecker, Michael W. Capp, M. Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

2008

Language:

english

File:

PDF, 331 KB

english, 2008

14

DNA Binding Mode Transitions of Escherichia coli HUαβ: Evidence for Formation of a Bent DNA — Protein Complex on Intact, Linear Duplex DNA

Junseock Koh, Ruth M. Saecker, M. Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

2008

Language:

english

File:

PDF, 1.26 MB

english, 2008

15

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

Lisa A. Schroeder, Theodore J. Gries, Ruth M. Saecker, M. Thomas Record Jr, Michael E. Harris, Pieter L. deHaseth

Journal:

Journal of Molecular Biology

Year:

2009

Language:

english

File:

PDF, 678 KB

english, 2009

16

Nonspecific DNA Binding and Bending by HUαβ: Interfaces of the Three Binding Modes Characterized by Salt-Dependent Thermodynamics

Junseock Koh, Irina Shkel, Ruth M. Saecker, M. Thomas Record Jr.

Journal:

Journal of Molecular Biology

Year:

2011

Language:

english

File:

PDF, 1.11 MB

english, 2011

17

Kinetic Studies and Structural Models of the Association of E. coli σ70 RNA Polymerase with the λPR Promoter: Large Scale Conformational Changes in Forming the Kinetically Significant Intermediates

Ruth M Saecker, Oleg V Tsodikov, Kristi L McQuade, Peter E Schlax Jr, Michael W Capp, M Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 580 KB

english, 2002

18

Rapid-Quench Mixing and Use of Fast Footprinting to Characterize DNA Opening in the Late Steps of Open Complex Formation at λPR by E. coli RNA Polymerase

Gries, Theodore J., Kontur, Wayne S., Capp, Michael W., Davis, Caroline A., Drennan, Amanda C., Saecker, Ruth M., Record, M. Thomas

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 73 KB

english, 2009

19

Thermodynamics of Interactions between Histone-like Proteins from Escherichia coli (HU and IHF) and Intact Duplex DNA

Koh, Junseock, Saecker, Ruth M., Record, M. Thomas

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 43 KB

english, 2009

20

Probing DNA Binding, DNA Opening and Assembly of a Downstream Clamp During Transcription Initiation by E. coli RNA Polymerase at the λPR Promoter

Drennan, Amanda, Gries, Theodore, Heitkamp, Sara, Ruff, Emily, Saecker, Ruth, Record, M. Thomas

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 38 KB

english, 2011

21

[Methods in Enzymology] RNA Polymerases and Associated Factors, Part C Volume 370 || Rapid Quench Mixing to Quantify Kinetics of Steps in Association of Escherichia coli RNA Polymerase with Promoter DNA

Saecker, Ruth M.

Year:

2003

Language:

english

File:

PDF, 126 KB

english, 2003

22

E. Coli RNA Polymerase: A Molecular DNA Opening Machine

Drennan, Amanda, Saecker, Ruth, Heitkamp, Sara, Capp, Michael, Kraemer, Mark, Bellissimo, Dana, Gries, Theodore, Ruff, Emily, Sheppard, Carol, Wigneshweraraj, Siva, Artsimovitch, Irina, Record, M. Tho

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 40 KB

english, 2012

23

Use of Fast DNA Footprinting and Real-Time Fluorescence Spectroscopy to Characterize Novel, Biologically Revlevant Transcription Initiation Intermediates for E. Coli RNA Polymerase

Heitkamp, Sara, Lingeman, Emily, Capp, Mike, Saecker, Ruth, Record, M. Thomas

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 40 KB

english, 2012

24

Solute Probes of Conformational Changes in Open Complex (RP o ) Formation by Escherichia coli RNA Polymerase at the λP 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 o†

Kontur, Wayne S., Saecker, Ruth M., Davis, Caroline A., Capp, Michael W., Record, M. Thomas

Journal:

Year:

2006

Language:

english

File:

PDF, 510 KB

english, 2006

25

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

Hong, Jiang, Capp, Mike W., Saecker, Ruth M., Record, M. Thomas

Journal:

Year:

2005

Language:

english

File:

PDF, 383 KB

english, 2005

26

Interactions of the Osmolyte Glycine Betaine with Molecular Surfaces in Water: Thermodynamics, Structural Interpretation, and Prediction of m -Values

Capp, Michael W., Pegram, Laurel M., Saecker, Ruth M., Kratz, Megan, Riccardi, Demian, Wendorff, Timothy, Cannon, Jonathan G., Record, M. Thomas

Journal:

Year:

2009

Language:

english

File:

PDF, 1.21 MB

english, 2009

27

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 †

Holbrook, Jill A., Capp, Michael W., Saecker, Ruth M., Record, M. Thomas

Journal:

Year:

1999

Language:

english

File:

PDF, 141 KB

english, 1999

28

Probing DNA Binding, DNA Opening, and Assembly of a Downstream Clamp/Jaw in Escherichia coli RNA Polymerase−λP R Promoter Complexes Using Salt and the Physiological Anion Glutamate

Kontur, Wayne S., Capp, Michael W., Gries, Theodore J., Saecker, Ruth M., Record, M. Thomas

Journal:

Year:

2010

Language:

english

File:

PDF, 1.78 MB

english, 2010

29

One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex

Theodore J. Gries, Wayne S. Kontur, Michael W. Capp, Ruth M. Saecker, M. Thomas Record, Jr. and E. Peter Geiduschek

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 1.49 MB

english, 2010

30

FRET Characterization of DNA Wrapping in Closed and Open Escherichia coli RNA Polymerase - λP R Promoter Complexes

Sreenivasan, Raashi, Heitkamp, Sara, Chhabra, Munish, Saecker, Ruth Margaret, Lingeman, Emily, Poulos, Mikaela, McCaslin, Darrell R, Capp, Michael W., Artsimovitch, Irina, Record, M. Thomas

Journal:

Year:

2016

Language:

english

File:

PDF, 1.22 MB

english, 2016

31

Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA

Hubin, Elizabeth A, Fay, Allison, Xu, Catherine, Bean, James M, Saecker, Ruth M, Glickman, Michael S, Darst, Seth A, Campbell, Elizabeth A

Journal:

Year:

2017

Language:

english

File:

PDF, 7.51 MB

english, 2017

32

Transcription initiation in mycobacteria: a biophysical perspective

Boyaci, Hande, Saecker, Ruth M., Campbell, Elizabeth A.

Journal:

Year:

2019

Language:

english

File:

PDF, 2.74 MB

english, 2019

33

Transcription initiation in mycobacteria: a biophysical perspective

Boyaci, Hande, Saecker, Ruth M., Campbell, Elizabeth A.

Journal:

Year:

2019

File:

PDF, 2.74 MB

2019

34

Stepwise Promoter Melting by Bacterial RNA Polymerase

Chen, James, Chiu, Courtney, Gopalkrishnan, Saumya, Chen, Albert Y., Olinares, Paul Dominic B., Saecker, Ruth M., Winkelman, Jared T., Maloney, Michael F., Chait, Brian T., Ross, Wilma, Gourse, Richar

Journal:

Year:

2020

File:

PDF, 4.70 MB

2020

35

Native Mass Spectrometry-Based Screening for Optimal Sample Preparation in Single-Particle Cryo-EM

Olinares, Paul Dominic B., Kang, Jin Young, Llewellyn, Eliza, Chiu, Courtney, Chen, James, Malone, Brandon, Saecker, Ruth M., Campbell, Elizabeth A., Darst, Seth A., Chait, Brian T.

Journal:

Year:

2020

File:

PDF, 777 KB

2020