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1

Effects of Na+ and Mg++ ions on the helix–coil transition of DNA

M. Thomas Record Jr.

Journal:

Year:

1975

Language:

english

File:

PDF, 1.03 MB

english, 1975

2

Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature

Oleg V. Tsodikov, M. Thomas Record Jr., Yuri V. Sergeev

Journal:

Journal of Computational Chemistry

Year:

2002

Language:

english

File:

PDF, 115 KB

english, 2002

3

Responses of E. coli to osmotic stress: large changes in amounts of cytoplasmic solutes and water

M.Thomas Record Jr, Elizabeth S. Courtenay, D.Scott Cayley, Harry J. Guttman

Journal:

Trends in Biochemical Sciences

Year:

1998

Language:

english

File:

PDF, 135 KB

english, 1998

4

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

5

Polypeptides containing highly conserved regions of transcription initiation factor σ70 exhibit specificity of binding to promoter DNA

Alicia J. Dombroski, William A. Walter, M.Thomas Record Jr., Deborah A. Slegele, Carol A. Gross

Journal:

Year:

1992

Language:

english

File:

PDF, 1.34 MB

english, 1992

6

Electrostatic effects on polynucleotide transitions. I. Behavior at neutral pH

M. Thomas Record Jr.

Journal:

Year:

1967

Language:

english

File:

PDF, 961 KB

english, 1967

7

Electrostatic effects on polynucleotide transitions. II. Behavior of titrated systems

M. Thomas Record Jr.

Journal:

Year:

1967

Language:

english

File:

PDF, 806 KB

english, 1967

8

The strand-separation transition of T7 DNA

Michael Kallay, M. Thomas Record Jr.

Journal:

Year:

1974

Language:

english

File:

PDF, 774 KB

english, 1974

9

The strand-separation transition of T2 bacteriophage DNA

Elliot L. Elson, M. Thomas Record Jr.

Journal:

Year:

1974

Language:

english

File:

PDF, 1.40 MB

english, 1974

10

Characterization of rodlike DNA fragments

M. Record Thomas Jr., Charles P. Woodbury, Ross B. Inman

Journal:

Year:

1975

Language:

english

File:

PDF, 901 KB

english, 1975

11

Intermediates in the strand-separation transition of T7 DNA

C. Glen Wensley, M. Thomas Record Jr.

Journal:

Year:

1976

Language:

english

File:

PDF, 623 KB

english, 1976

12

Na+ effects on transitions of DNA and polynucleotides of variable linear charge density

M. Thomas Record Jr., Charles P. Woodbury, Timothy M. Lohman

Journal:

Year:

1976

Language:

english

File:

PDF, 1.07 MB

english, 1976

13

Comparison of Poisson-Boltzmann and condensation model expression for the colligative properties of cylindrical polyions

Barbara Kure Klein, Charles F. Anderson, M. Thomas Record Jr.

Journal:

Year:

1981

Language:

english

File:

PDF, 985 KB

english, 1981

14

23Na-nmr investigations of counterion exchange reactions of helical DNA

W. H. Braunlin, C. F. Anderson, M. Thomas Record Jr.

Journal:

Year:

1986

Language:

english

File:

PDF, 646 KB

english, 1986

15

Kinetics of nonspecific binding reactions of proteins with DNA flexible coils: Site-based and molecule-based association reactions

Sharlyn J. Mazur, M. Thomas Record Jr.

Journal:

Year:

1986

Language:

english

File:

PDF, 1.27 MB

english, 1986

16

Counterion exchange reactions on DNA: Monte Carlo and Poisson–Boltzmann analysis

Mark D. Paulsen, Charles F. Anderson, M. Thomas Record Jr.

Journal:

Year:

1988

Language:

english

File:

PDF, 1.08 MB

english, 1988

17

Association kinetics of site-specific protein-DNA interactions: Roles of nonspecific DNA sites and of the molecular location of the specific site

Sharlyn J. Mazur, M. Thomas Record Jr.

Journal:

Year:

1989

Language:

english

File:

PDF, 1.32 MB

english, 1989

18

Association kinetics of site-specific protein-DNA interactions: Roles of nonspecific DNA sites and of the molecular location of the specific site

Sharlyn J. Mazur, M. Thomas Record Jr.

Journal:

Year:

1990

Language:

english

File:

PDF, 67 KB

english, 1990

19

Importance of oligoelectrolyte end effects for the thermodynamics of conformational transitions of nucleic acid oligomers: A grand canonical Monte Carlo analysis

Martha C. Olmsted, Charles F. Anderson, M. Thomas Record Jr.

Journal:

Year:

1991

Language:

english

File:

PDF, 1.05 MB

english, 1991

20

Large changes in cytoplasmic biopolymer concentration with osmolality indicate that macromolecular crowding may regulate protein–DNA interactions and growth rate in osmotically stressed Escherichia coli K-12

Scott Cayley, M. Thomas Record Jr

Journal:

Journal of Molecular Recognition

Year:

2004

Language:

english

File:

PDF, 194 KB

english, 2004

21

Monte carlo simulations of counterion accumulation near helical DNA

Pamela Mills, Mark D. Paulsen, Charles F. Anderson, M.Thomas Record Jr.

Journal:

Chemical Physics Letters

Year:

1986

Language:

english

File:

PDF, 402 KB

english, 1986

22

The salt dependence of the preferential interaction coefficient in dna solutions as determined by grand canonical monte carlo simulations

Mark D. Paulsen, Brough Richey, Charles F. Anderson, M.Thomas Record Jr.

Journal:

Chemical Physics Letters

Year:

1987

Language:

english

File:

PDF, 495 KB

english, 1987

23

Analysis of ion concentration effects on the kinetics of protein-nucleic acid interactions: Application to lac repressor-operator interactions

Timothy M. Lohman, Pietsr L. DeHaseth, M.Thomas Record Jr.

Journal:

Biophysical Chemistry

Year:

1978

Language:

english

File:

PDF, 1.60 MB

english, 1978

24

The relationship between the poisson-boltzmann model and the condensation hypothesis: an analysis based on the low salt form of the donnan coefficient

Charles F. Anderson, M.Thomas Record Jr.

Journal:

Biophysical Chemistry

Year:

1980

Language:

english

File:

PDF, 847 KB

english, 1980

25

Gibbs–Duhem-based relationships among derivatives expressing the concentration dependences of selected chemical potentials for a multicomponent system

Charles F. Anderson, M. Thomas Record Jr.

Journal:

Biophysical Chemistry

Year:

2004

Language:

english

File:

PDF, 176 KB

english, 2004

26

Generalized derivation of an exact relationship linking different coefficients that characterize thermodynamic effects of preferential interactions

Charles F. Anderson, Daniel J. Felitsky, Jiang Hong, M. Thomas Record Jr

Journal:

Biophysical Chemistry

Year:

2002

Language:

english

File:

PDF, 220 KB

english, 2002

27

Preferential interactions in aqueous solutions of urea and KCl

Jiang Hong, Michael W Capp, Charles F Anderson, M.Thomas Record Jr.

Journal:

Biophysical Chemistry

Year:

2003

Language:

english

File:

PDF, 229 KB

english, 2003

28

Thermodynamics of interactions of urea and guanidinium salts with protein surface: Relationship between solute effects on protein processes and changes in water-accessible surface area

Elizabeth S. Courtenay, Michael W. Capp, M. Thomas Record Jr.

Journal:

Protein Science

Year:

2001

Language:

english

File:

PDF, 239 KB

english, 2001

29

K+-Ribosome interactions determine the large enhancements of 39K NMR transverse relaxation rates in the cytoplasm of Escherichia coli K-12

Guttman, Harry J., Cayley, Scott, Li, Man, Anderson, Charles F., Record, M. Thomas Jr.

Journal:

Year:

1995

Language:

english

File:

PDF, 1.55 MB

english, 1995

30

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

31

Biophysical compensation mechanisms buffering E. coli protein–nucleic acid interactions against changing environments

M.Thomas Record Jr, Elizabeth S Courtenay, Scott Cayley, Harry J Guttman

Journal:

Trends in Biochemical Sciences

Year:

1998

Language:

english

File:

PDF, 142 KB

english, 1998

32

In Vivo Thermodynamic Analysis of Repression with and without Looping in lac Constructs: Estimates of Free and Local lac Repressor Concentrations and of Physical Properties of a Region of Supercoiled Plasmid DNA in Vivo

Scott M. Law, Gregory R. Bellomy, Paula J. Schlax, M.Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

1993

File:

PDF, 859 KB

1993

33

Inhibition of Transcription Initiation buIacRepressor

Paula J. Schlax, Michael W. Capp, Thomas M. Record Jr

Journal:

Journal of Molecular Biology

Year:

1995

Language:

english

File:

PDF, 941 KB

english, 1995

34

Factor Independent Activation of rrnB P1: An "Extended" Promoter with an Upstream Element that Dramatically Increases Promoter Strength

Lin Rao, Wilma Ross, J.Alex Appleman, Tamas Gaal, Sigrid Leirmo, Paula J. Schlax, M.Thomas Record Jr, Richard L. Gourse

Journal:

Journal of Molecular Biology

Year:

1994

File:

PDF, 982 KB

1994

35

Thermodynamic Investigation of Hirudin Binding to the Slow and Fast Forms of Thrombin: Evidence for Folding Transitions in the Inhibitor and Protease Coupled to Binding

Youhna M. Ayala, Alessandro Vindigni, Murad Nayal, Ruth S. Spolar, Thomas M. Record, Jr, Enrico Di Cera

Journal:

Journal of Molecular Biology

Year:

1995

Language:

english

File:

PDF, 1.90 MB

english, 1995

36

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

37

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

38

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

39

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

40

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

41

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

42

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

43

Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity: Implications for protein-DNA interactions in vivo

Scott Cayley, Barbara A. Lewis, Harry J. Guttman, M.Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

1991

Language:

english

File:

PDF, 2.56 MB

english, 1991

44

Thermodynamic stoichiometries of participation of water, cations and anions in specific and non-specific binding of lac repressor to DNA: Possible thermodynamic origins of the “glutamate effect” on protein-DNA interactions

Jeung-Hoi Ha, Michael W. Capp, Mark D. Hohenwalter, Mark Baskerville, M.Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

1992

Language:

english

File:

PDF, 1.54 MB

english, 1992

45

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

46

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

47

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

48

Thermodynamics and Folding Pathway of Tetraloop Receptor-Mediated RNA Helical Packing

Kirk A. Vander Meulen, Jared H. Davis, Trenton R. Foster, M. Thomas Record Jr, Samuel E. Butcher

Journal:

Journal of Molecular Biology

Year:

2008

Language:

english

File:

PDF, 767 KB

english, 2008

49

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

50

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

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