M Thomas Record, Jr.

Publications

DNA Wrapping
R. M. Saecker and M. T. Record, Jr. Protein Surface Salt Bridges and Paths for DNA Wrapping. Current Opinion in Structural Biology, 12, 311-319 (2002).

Coupled Folding
R. S. Spolar and M. T. Record, Jr., "Coupling of Local Folding to Site-Specific Binding of Proteins to DNA," Science 263, 777-784 (1994).

RNA Polymerase: Promoter
C. A. Davis, M. W. Capp, M. T. Record, Jr. and R. M. Saecker. "The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase." Proc. Natl. Acad. Sci. USA 102, 285-290 (2005).

Ruth M. Saecker, Oleg V. Tsodikov, Kristi L. McQuade, Peter E. Schlax, Jr., Michael W. Capp and M. Thomas Record, Jr. ?Kinetic Studies and Structural Models of the Association of E. coli RNA Polymerase with the LambdaPR Promoter: Large Scale Conformational Changes in Forming the Kinetically-Significant Intermediates?. Journal of Molecular Biology, 319, 649-671 (2002).

IHF: DNA
J. A. Holbrook, O. V. Tsodikov, R. M. Saecker and M. T. Record, Jr. "Specific and Nonspecific Interactions of Integration Host Factor with DNA: Thermodynamic Evidence for Disruption of Multiple IHF Surface Salt Bridges Coupled to DNA Binding. " J. Mol. Biol., 310(2), 379-401 (2001).

O. V. Tsodikov, J. A. Holbrook, I. A. Shkel and M. T. Record, Jr. "Analytical Binding Isotherms Describing Competitive Interactions of a Protein Ligand with Specific and Nonspecific Sites on a DNA Oligomer". Biophys. J., 81, 1960-1969 (2001).

Solute Effects on Protein Processes
J. Hong, M. W. Capp, R. M. Saecker & M. T. Record, Jr. "Use of Urea and Glycine Betaine to Quantify Coupled Folding and Probe the Burial of DNA Phosphates in Lac Repressor ? Lac Operator Binding." Biochemistry, 2005, submitted.

J. Hong, M. W. Capp, C. F. Anderson, R. M. Saecker, D. J. Felitsky, M. W. Anderson, and M. T. Record, Jr. "Preferential interactions of glycine betaine and of urea with DNA: implications for DNA hydration and for effects of these solutes on DNA stability." Biochemistry 43, 14744-14758 (2004).

D. J. Felitsky, J. G. Cannon, M. W. Capp, J. Hong, A. W. Van Wynsberghe, C. F. Anderson, and M. T. Record, Jr. "The exclusion of glycine betaine from anionic biopolymer surface: why glycine betaine is an effective osmoprotectant but also a compatible solute." Biochemistry 43, 14732-14743 (2004).

D. J. Felitsky & M. T. Record, Jr. "Thermal and urea-induced unfolding of the marginally stable lac repressor DNA-binding domain: a model system for analysis of solute effects on protein processes." Biochemistry 42, 2202-2217 (2003).

E. coli as an Osmotic System
S. Cayley and M. T. Record, Jr. "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."  J. Mol. Recognit. 17, 488-496 (2004).

S. Cayley and M. T. Record, Jr. "Roles of cytoplasmic osmolytes, water, and crowding in the response of Escherichia coli to osmotic stress: biophysical basis of osmoprotection by glycine betaine." Biochemistry 42, 12596-12609 (2003).

D. S. Cayley, H. J. Guttman and M. T. Record, Jr. "Biophysical Characterization of Changes in Amounts and Activity of Escherichia coli Cell and Compartment Water and Turgor Pressure in Response to Osmotic Stress. Biophys. J. 78(4), 1748-1764 (2000).

149.  C. A. Davis, M. W. Capp, M. T. Record, Jr. & R. M. Saecker. ?The Effects of Upstream DNA on Open Complex Formation.?  Proc. Natl. Acad. Sci. USA, 102: 285-290 (2005).

148.  C. F. Anderson & M. T. Record, Jr. ?Gibbs-Duhem-based relationships among derivatives expressing the concentration dependences of selected chemical potentials for a multicomponent system.?  Biophys Chem. 112(2-3):165-175 (2004).

147.  J. Hong, M. W. Capp, C. F. Anderson, R. M. Saecker, D. J. Felitsky, M. W. Anderson & M. T. Record, Jr.  ?Preferential interactions of glycine betaine and of urea with DNA: implications for DNA hydration and for effects of these solutes on DNA stability.? Biochemistry 43(46):14744-14758 (2004).

146. D. J. Felitsky, J. G. Cannon, M. W. Capp, J. Hong, A. W. Van Wynsberghe, C. F. Anderson & M. T. Record, Jr.  ?The exclusion of glycine betaine from anionic biopolymer surface: why glycine betaine is an effective osmoprotectant but also a compatible solute.?  Biochemistry 43(46):14732-14743 (2004).

145. D. S. Cayley and M. Thomas Record, Jr.  "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." Journal of Molecular Recognition, 17(5):488-496 (2004)

144. D. J. Felitsky & M. T. Record, Jr.  ?Application of the local-bulk partitioning and competitive binding models to interpret preferential interactions of glycine betaine and urea with protein.?  Biochemistry, 43(28):9276-9288 (2004).

143. J. D. Ballin, I. A. Shkel & M. T. Record, Jr.  ?Interactions of the KWK6 cationic peptide with short nucleic acid oligomers: demonstration of large Coulombic end effects on binding at 0.1-0.2 M salt.? Nucleic Acids Res. 32(11):3271-3281 (2004).

142. I. A. Shkel and M. T. Record, Jr.  ?Effect of the Number of Nucleic Acid Oligomer Charges on the Salt Dependence of Stability and Melting Temperature (Tm): NLPB Analysis of Experimental Data? Biochemistry 43(22):7090-7101 (2004).

141. R. M. Saecker, O. V. Tsodikov, M. W. Capp, and M. T. Record, Jr.  ?Rapid Quench Mixing to Quantify Kinetics of Steps in Association of Escherichia coli RNA Polymerase with Promoter DNA.?  Methods in Enzymology 370, 535-546 (2003).

140. S. Cayley and M. T. Record, Jr.  ?Roles of Cytoplasmic Osmolytes, Water and Crowding in the Response of Escherichia coli to Osmotic Stress: the Biophysical Basis of Osmoprotection by Glycine Betaine.? Biochemistry 42(43); 12596-12609 (2003).

139. J. Hong, M. W. Capp, C. F. Anderson and M. T. Record,Jr.  ?Preferential Interactions in Aqueous Solutions of Urea and KCl.? Biophys. Chem., 105, 517-532 (2003).

138. D. J. Felitsky and M. T. Record, Jr. ?Thermal and Urea-Induced Unfolding of the Marginally-Stable Lac Repressor DNA-Binding Domain:  A Model System for Analysis of Solute Effects on Protein Processes?. Biochemistry 42, 2202-2217 (2003).

137. C. F. Anderson, D. J. Felitsky, J. Hong, and M. T. Record Jr.  ?Generalized Derivation of an Exact Relationship Linking Different Coefficients that Characterize Thermodynamic Effects of Preferential Interactions.?  Biophys. Chem., 101-102, 497-511 (2002).

136. Ruth M. Saecker, Oleg V. Tsodikov, Kristi L. McQuade, Peter E. Schlax, Jr., Michael W. Capp and M. Thomas Record, Jr. ?Kinetic Studies and Structural Models of the Association of E. coli sigma70 RNA Polymerase with the lambdaPR Promoter: Large Scale Conformational Changes in Forming the Kinetically-Significant Intermediates?. Journal of Molecular Biology, 319, 649-671 (2002).

135. R. M. Saecker and M. T. Record, Jr. ?Protein Surface Salt Bridges and Paths for DNA Wrapping.? Current Opinion in Structural Biology, 12, 311-319 (2002).

134. O. V. Tsodikov, M. T. Record, Jr. and Y. V. Sergeev. "A Novel Computer Program for Fast Exact Calculation of Accessible and Molecular Surface Areas and Average Surface Curvature". J. Comput. Chem., 23, 600-609 (2002).

133. I. A. Shkel, O. V. Tsodikov and M. T. Record, Jr. ?Asymptotic Solution of the Cylindrical Poisson-Boltzmann Equation at Low Salt Concentration: Analytic Expressions for Surface Potential and Preferential Interaction Coefficient.? Proc. Natl. Acad. Sci, USA, 99(5), 2597-2602 (2002).

132. C. F. Anderson, E. S. Courtenay, M. Thomas Record, Jr. "Thermodynamic Expressions Relating Different Types of Preferential Interaction Coefficients in Solutions Containing Two Solute Components". J. Phys. Chem B, 106(2), 418-433 (2002).

131. E. Courtenay, M. W. Capp., and M. T. Record, Jr. "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". Protein Science, 10, 2485-2497 (2001).

130. O. V. Tsodikov, J. A. Holbrook, I. A. Shkel and M. T. Record, Jr. "Analytical Binding Isotherms Describing Competitive Interactions of a Protein Ligand with Specific and Nonspecific Sites on a DNA Oligomer". Biophys. J., 81, 1960-1969 (2001).

129. J. A. Holbrook, O. V. Tsodikov, R. M. Saecker and M. T. Record, Jr. "Specific and Nonspecific Interactions of Integration Host Factor with DNA: Thermodynamic Evidence for Disruption of Multiple IHF Surface Salt Bridges Coupled to DNA Binding. " J. Mol. Biol., 310(2), 379-401 (2001).

128. E. Courtenay, M. W. Capp., R. M. Saecker and M. T. Record, Jr. "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 Genetics 41(S4),72-85 (2000).

127. I. A. Shkel, O. Tsodikov and M. T. Record, Jr. "Complete Asymptotic Solution of Cylindrical and Spherical Poisson-Boltzmann Equations at Experimental Salt Concentrations." J. Phys. Chem. B. 104, 5161-5170 (2000).

126. E. S. Courtenay, M. W. Capp, C. F. Anderson and M. Thomas Record, Jr. "Vapor Pressure Osmometry Studies of Osmolyte-Protein Interactions: Implications for the Action of Osmoprotectants in vivo and for the Interpretation of "Osmotic Stress" Experiments in vitro." Biochemistry, 39(15), 4455-4471 (2000).

125. D. S. Cayley, H. J. Guttman and M. Thomas Record, Jr. "Biophysical Characterization of Changes in Amounts and Activity of Escherichia coli Cell and Compartment Water and Turgor Pressure in Response to Osmotic Stress. Biophys. J. 78, 1748-1764 (2000).

124. O. V. Tsodikov, R. M. Saecker, S. E. Melcher, M. M. Levandoski, D. E. Frank, M. W. Capp and M. T. Record, Jr. "Wrapping of Flanking Nonoperator DNA in Lac Repressor-Operator Complexes: Implications for DNA Looping." J. Mol. Biol. 294, 639-655 (1999).

123. J. A. Holbrook, M. W. Capp, R. M. Saecker and M. T. Record, Jr. "Enthalpy and Heat Capacity Changes for Formation of an Oligomer DNA Duplex: Interpretation in Terms of Coupled Processes of Formation and Association of Single-Stranded Helices." Biochemistry, 38, 8409-8422 (1999).

122. H. Ni, C. F. Anderson, and M. T. Record, Jr. "Quantifying the Thermodynamic Consequences of Cation (M2+, M+) Accumulation and Anion (X-) Exclusion in Mixed Salt Solutions of Polyanionic DNA Using Monte Carlo and Poisson-Boltzmann Calculations of Ion-Polyion Preferential Interaction Coefficients." J. Phys. Chem. 103, 3489-3504 (1999).

121. O. V. Tsodikov and M. T. Record Jr. "General Method of Analysis of Kinetic Equations for Multistep Reversible Mechanisms in the Single-Exponential Regime: Application to Kinetics of Open Complex Formation between Esigma70 RNA Polymerase and lambdaPR Promoter DNA." Biophysical J. 76, 1320-1329 (1999).

120. W. Zhang, H. Ni, M. W. Capp, C. F. Anderson, T. M. Lohman and M. T. Record, Jr. "The Importance of Coulombic End Effects: Experimental Characterization of the Effects of Oligonucleotide Flanking Charges on the Strength and Salt-Dependence of Oligocation (L8+) Binding to Single-Stranded DNA Oligomers." Biophysical J. 76, 1008-1017 (1999).

119. O. V. Tsodikov, M. L. Craig, R. M. Saecker, M. T. Record, Jr. "Quantitative Analysis of Multiple-Hit Footprinting Studies to Characterize DNA Conformational Changes in Protein-DNA Complexes: Application to DNA Opening by Es70 RNA Polymerase." J. Mol. Biol. 283, 757-769 (1998).

118. M. L. Craig, O. V. Tsodikov, K. L. McQuade, P. E. Schlax, Jr., M. W. Capp, R. M. Saecker, and M. T. Record, Jr. "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." J. Mol. Biol. 283, 741-756 (1998).

117. P. L. de Haseth, M. L. Zupancic, and M. T. Record, Jr. "RNA Polymerase-Promoter Interaction: the Comings and Goings of RNA Polymerase." J. Bacteriol., 180, 3019-3025 (1998).

116. M. T. Record, Jr., E. S. Courtenay, D. S. Cayley, and H. J. Guttman. "Biophysical Compensation Mechanisms Buffering E. coli Protein-Nucleic Acid Interactions Against Changing Environments." TiBS 23, 190-194 (1998).

115. M. T. Record, Jr., E. S. Courtenay, D. S. Cayley, and H. J. Guttman. "Responses of E. coli to Osmotic Stress: Large Changes in Amounts of Cytoplasmic Solutes and Water." TiBS 23, 143-149 (1998).

114. M. T. Record, Jr., W. Zhang and C. F. Anderson. "Analysis of Effects of Salts and Uncharged Solutes on Protein and Nucleic Acid Equilibria and Processes: A Practical Guide to Recognizing and Interpreting Polyelectrolyte Effects, Hofmeister Effects, and Osmotic Effects of Salts." Advances in Protein Chemistry, 51, 281-353 (1998).

113. S. Padmanabhan, W. Zhang, M. W. Capp, C. F. Anderson and M. T. Record Jr. "Binding of Cationic (+4) Alanine and Glycine Containing Oligopeptides to Double-Stranded DNA: Thermodynamic Analysis of Effects of Coulombic Interactions and alpha-Helix Induction." Biochemistry, 36, 5193-5206 (1997).

112. D. E. Frank, R. M. Saecker, J. P. Bond, M. W. Capp, O. V. Tsodikov, S. E. Melcher, M. M. Levandoski and M. T. Record, Jr. "Thermodynamics of the Interactions of Lac Repressor with Variants of the Symmetric Lac Operator: Effects of Converting a Consensus Site to a Nonspecific Site." J. Mol. Biol., 267, 1186-1206 (1997).

111. W. Zhang, M. W. Capp, J. P. Bond, C. F. Anderson and M. T. Record, Jr. "Thermodynamic Characterization of Interactions of Native Bovine Serum Albumin with Highly Excluded (Glycine Betaine) and Moderately Accumulated (Urea) Solutes by a Novel Application of Vapor Pressure Osmometry." Biochemistry, 35, 10506-10516 (1996).

110. M. M. Levandoski, O. V. Tsodikov, D. Frank, S. Melcher, R. M. Saecker and M. T. Record, Jr. "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." J. Mol. Biol., 260, 697-717 (1996).

109. V. M. Stein, L. A. Wright, C. F. Anderson and M. T. Record, Jr. "Quadrupolar NMR Studies of Cation-DNA Interactions." Encyclopedia of Nuclear Magnetic Resonance (D. M. Grant and R. K. Harris, eds.) John Wiley & Sons, Vol. 3, pp. 1717-1725 (1996).

108. M. T. Record, Jr., W. S. Reznikoff, M. L. Craig, K. L. McQuade and P. J. Schlax. "Escherichia coli RNA Polymerase (Esigma70), Promoters, and the Kinetics of the Steps of Transcription Initiation." Second Edition of Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2, 792-821 (1996).

107. M. W. Capp, D. S. Cayley, W. Zhang, H. J. Guttman, S. E. Melcher, R. M. Saecker, C. F. Anderson and M. T. Record, Jr. "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." J. Mol. Biol., 258, 25-36 (1996).

106. W. Zhang, J. P. Bond, C. F. Anderson, T. M. Lohman and M. T. Record, Jr. "Large Electrostatic Differences in the Binding Energetics of a Cationic Peptide to Oligomeric and Polymeric DNA." Proc. Natl. Acad. Sci. USA, 93, 2511-2516 (1996).

105. M. L. Craig, W-C. Suh and M. T. Record, Jr. "HO• and DNase I Probing of Esigma70 RNA Polymerase-lambdaPR Promoter Open Complexes: Mg2+ Binding and Its Structural Consequences at the Transcription Start Site." Biochemistry, 34, 15624-15632 (1995).

104. Y. M. Ayala, A. Vindigni, M. Nayal, R., Spolar, R. S., M. T. Record, Jr., and E. DiCera. "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." J. Mol. Biol., 253, 787-798 (1995).

103. C. F. Anderson and M. T. Record, Jr. "Salt-Nucleic Acid Interactions." Annual Review of Physical Chemistry, 46, 657-700 (1995).

102. V. M. Stein, J. P. Bond, M. W. Capp, C. F. Anderson and M. T. Record, Jr. "Importance of Coulombic End Effects on Cation Accumulation Near Oligoelectrolyte B-DNA: A Demonstration using 23Na NMR." Biophysical J. 68, 1063-1072 (1995).

101. H. J. Guttman, S. Cayley, M. Li, C. F. Anderson and M. T. Record, Jr. "K+-Ribosome Interactions Determine the Large Enhancements of 39K NMR Transverse Relaxation Rates in the Cytoplasm of Escherichia coli K-12." Biochemistry (1995) 34:393-1404 (1995).

100. H. J. Guttman, C. F. Anderson and M. T. Record, Jr. "Analyses of Thermodynamic Data for Concentrated Hemoglobin Solutions Using Scaled Particle Theory: Implications for a Simple Two State Model of Water in Thermodynamic Analyses of Crowding In Vitro and In Vivo." Biophysical J. (1995) 68:835-846 (1995).

99. M. C. Olmsted, J. P. Bond, C. F. Anderson and M. T. Record, Jr. "GCMC Molecular and Thermodynamic Predictions of Ion Effects on Binding of an Oligocation (L8+) to the Center of DNA Oligomers." Biophysical J. 68, 634-647 (1995).

98. P. E. Schlax, Jr., M. W. Capp, and M. T. Record, Jr. "Preparative-Scale Purification of DNA Restriction Fragments by Continuous-Flow Gel Electrophoresis." BioTechniques, 18, 94-100 (1995).

97. P. J. Schlax, M. W. Capp and M. T. Record, Jr. "Inhibition of Transcription Initiation by Lac Repressor." J. Mol. Biol. 245, 331-350 (1995) .

96. M. T. Record, Jr. and C. F. Anderson. "Interpretation of Preferential Interaction Coefficients of Nonelectrolytes and of Electrolyte Ions in Terms of a Two Domain Model." Biophysical J. 68, 786-794 (1995).

95. J. P. Bond, C. F. Anderson and M. T. Record, Jr. "Conformational Transitions of Duplex and Triplex Nucleic Acid Helices: Thermodynamic Analysis of Effects of Salt Concentration on Stability Using Preferential Interaction Coefficients." Biophysical J. 67, 825-836 (1994).

94. L. Rao, W. Ross, J. A. Appleman, T. Gaal, S. Leirmo, P. J. Schlax, M. T. Record, Jr. and R. L. Gourse. "Factor Independent Activation of rrnB P1: An "Extended" Promoter with an Upstream Element that Dramatically Increases Promoter Strength." J. Mol. Biol. 235, 1421-1435 (1994).

93. R. S. Spolar and M. T. Record, Jr. "Coupling of Local Folding to Site-Specific Binding of Proteins to DNA. Science 263, 777-784 (1994).

92. J. P. Bond, C. F. Anderson and M. T. Record, Jr. "DNA-Ion Interactions: Monte Carlo Methodology and Comparison with Poisson-Boltzmann Calculations of Molecular and Thermodynamic Properties," Polymer Preprints 34, 932-933 (1993).

91. C. F. Anderson and M. T. Record, Jr. "The Salt-Dependence of Oligoion-Polyion Binding: A Thermodynamic Description Based on Preferential Interaction Coefficients. J. Phys. Chem. 97, 7116-7126 (1993).

90. S. M. Law, G. R. Bellomy, P. J. Schlax and M. T. Record, Jr. "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." J. Mol. Biol., 230, 161-173 (1993).

89. W.-C. Suh, W. Ross and M. T. Record, Jr. "Two Open Complexes and a Requirement for Mg2+ to Open the lambdaPR Transcription Start Site." Science, 259, 358-361 (1993).

88. J.-H. Ha, M. W. Capp, M. D. Hohenwalter, M. Baskerville and M. T. Record, Jr. "Thermodynamic Stoichiometries of Participation of Water, Cations and Anions in Specific and Nonspecific Binding of lac Repressor to DNA: Possible Thermodynamic Origins of the "Glutamate Effect" on Protein-DNA Interactions." J. Mol. Biol. 228, 252-264 (1992).

87. W. C. Suh, S. Leirmo and M. T. Record, Jr. "Roles of Mg2+ in the Mechanism of Formation and Dissociation of Open Complexes Between E. coli RNA Polymerase and the lambdaPR Promoter: Kinetic Evidence for a Second Open Complex Requiring Mg2+." Biochemistry 31, 7815-7825 (1992).

86. A. J. Dombroski, W. A. Walter, M. T. Record, Jr., D. A. Siegele and C. A. Gross. "Polypeptides Containing Highly Conserved Regions of Transcription Initiation Factor sigma70 Exhibit Specificity of Binding to Promoter DNA." Cell 70, 501-512 (1992).

85. R. S. Spolar, J. R. Livingstone and M. T. Record, Jr. "Use of Liquid Hydrocarbon and Amide Transfer Data to Estimate Contributions to Thermodynamic Functions of Protein Folding from the Removal of Nonpolar and Polar Surface from Water." Biochemistry 31, 3947-3955 (1992).

84. S. Cayley, B. A. Lewis and M. T. Record, Jr. "Origins of the Osmoprotective Properties of Betaine and Proline in Escherichia Coli K-12." J. Bacteriol. 174, 1586-1595 (1992).

83. M. C. Olmsted, C. F. Anderson and M. T. Record, Jr. "Importance of Oligoelectrolyte End Effects for the Thermodynamics of Conformational Transitions of Nucleic Acid Oligomers: A Grand Canonical Monte Carlo Analysis." Biopolymers 31, 1593-1604 (1991).

82. S. Cayley, B. A. Lewis, H. J. Guttman and M. T. Record, Jr. "Characterization of the Cytoplasm of Escherichia Coli K-12 as a Function of External Osmolarity: Implications for Protein-DNA Interactions In Vivo." J. Mol. Biol. 222, 281-300 (1991).

81. S. Padmanabhan, V. M. Brushaber, C. F. Anderson and M. T. Record, Jr. "Relative Affinities of Divalent Polyamines and of their N-methylated Analogs for Helical DNA Determined by 23Na NMR." Biochemistry 30, 7550-7559 (1991).

80. M. T. Record, Jr., J.-H. Ha and M. Fisher. "Use of Equilibrium and Kinetic Measurements to Determine the Thermodynamic Origins of Stability and Specificity and Mechanism of Formation of Site Specific Complexes Between Proteins and Helical DNA" in Methods in Enzymology, 208, 291-343 (1991).

79. J. R. Livingstone, R. S. Spolar and M. T. Record Jr. "The Contribution to the Thermodynamics of Protein Folding from the Reduction in Water-Accessible Nonpolar Surface Area." Biochemistry, 30, 4237-4244 (1991).

78. B. A. Lewis, S. Cayley, S. Padmanabhan, V. M. Kolb, V. Brushaber, C. F. Anderson and M. T. Record, Jr. "Natural Abundance 14N and 13C NMR of Glycine Betaine and Trehalose As Probes of the Cytoplasm of Escherichia coli K12." J. Mag. Reson. 90, 612-617 (1990).

77. B. A. Beutel and M. T. Record, Jr. "E. coli Promoter Regions Contain Nonrandom Sequences which Correlate to Spacer Length." Nucl. Acids Res. 18, 3597-3603 (1990).

76. G. R. Bellomy and M. T. Record, Jr. "Stable DNA Loops in Vivo and In Vitro: Roles in Gene Regulation at a Distance and in Biophysical Characterization of DNA" in Progress in Nucleic Acid Research and Molecular Biology (W. Cohn and K. Moldave, eds.) Academic Press, Vol. 39, pp. 81-128 (1990).

75. C. F. Anderson and M. T. Record, Jr. "Ion Distributions Around DNA and Cylindrical Polyions: Theoretical Descriptions and Physical Implications." Ann. Rev. Biophys. Biophys. Chem. 19 , pp. 423-465 (1990).

74. M. T. Record, Jr., M. Olmsted and C. F. Anderson. "Theoretical Studies of the Thermodynamic Consequences of Interactions of Ions with Polymeric and Oligomeric DNA: The Preferential Interaction Coefficient and Its Application of the Thermodynamic Analysis of Electrolyte Effects on Conformational Stability and Ligand Binding" in Theoretical Biochemistry and Molecular Biophysics (D.L. Beveridge and R. Lavery, eds.), pp. 285-307 (1990).

73. M. T. Record, Jr. and R. S. Spolar. "Some Thermodynamic Principles of Nonspecific and Site-Specific Protein-DNA Interactions," in Nonspecific DNA-Protein Interactions (Arnold Revzin ed.) CRC Press, pp. 33-69 (1990).

72. S. Leirmo and M. T. Record, Jr. "Structural, Thermodynamic and Kinetic Studies of the Interaction of Esigma70 RNA Polymerase with Promoter DNA" in Nucleic Acids and Molecular Biology, Vol. 4, (D.M.J. Lilley and F. Eckstein, eds.) Springer-Verlag, pp. 123-151 (1990).

71. S. Padmanabhan, M. Paulsen, C. F. Anderson and M. T. Record, Jr. "Cation-DNA Interactions: NMR and Theoretical Studies of Ion Distributions and Dynamics," in Monovalent Cations in Biological Systems, Chap. 14 (C. Pasternak, ed.) CRC Press, pp. 321-338 (1990).

70. G. R. Bellomy and M. T. Record, Jr. "Studies of DNA Loops Involved in Repression of the lac Promoter: Implications for the Physical Properties of DNA in Vivo, " in Structural and Organizational Aspects of Metabolic Regulation: UCLA Symposia on Molecular and Cellular Biology, New Series, Volume 133 (P. Srere, M. E. Jones and C. Matthews, eds.) Alan R. Liss, Inc., New York, N.Y., pp. 307-319 (1990).

69. M. Olmsted, C. F. Anderson and M. T. Record, Jr. "Monte Carlo Description of Oligoelectrolyte Properties of DNA Oligomers: Range of the End Effect and the Approach of Molecular and Thermodynamic Properties to the Polyelectrolyte Limits." Proc. Natl. Acad. Sci. U.S.A. 86, 7766-7770 (1989).

68. R. S. Spolar, J.-H. Ha and M. T. Record, Jr. "The Hydrophobic Effect in Protein Folding and Other Noncovalent Processes Involving Proteins." Proc. Natl. Acad. Sci. U.S.A. 86, 8382-385 (1989).

67. J.-H. Ha, R. S. Spolar and M. T. Record, Jr. "Role of the Hydrophobic Effect in Stability of Site-Specific Protein-DNA Complexes." J. Mol. Biol. 209, 801-816 (1989).

66. D. W. Cowing, J. Mecsas, M. T. Record, Jr. and C. A. Gross. "Intermediates in the Formation of the Open Complex by RNA Polymerase Holoenzyme Containing the Sigma Factor sigma32 at the groE Promoter." J. Mol. Biol. 210, 521-530 (1989).

65. S. Cayley, B. A. Lewis and M. T. Record, Jr. "Accumulation of 3-[N Morpholino]propane-sulfonate by Osmotically Stressed Escherichia coli K12." J. Bacteriol. 171, 3597-3602 (1989).

64. S. B. Jovanovich, M. T. Record, Jr. and R. R. Burgess. "In an Escherichia coli Coupled Transcription-translation System, Expression of the Osmoregulated Gene proU is Stimulated at Elevated Potassium Concentrations and by an Extract from Cells Grown at High Osmolality. J. Biol. Chem. 264, 7821-7825 (1989).

63. S. J. Mazur and M. T. Record, Jr. "Association Kinetics of Site-Specific Protein-DNA Interactions: Roles of Nonspecific DNA Sites and of the Molecular Location of the Specific Site." Biopolymers 28, 929-953 (1989). Erratum, Biopolymers 29, 1329 (1990).

62. G. R. Bellomy and M. T. Record, Jr. "A Method for Horizontal Polyacrylamide Slab Gel Electrophoresis." BioTechniques 7, 16-21 (1989).

61. M. D. Paulsen, C. F. Anderson and M. T. Record, Jr. "Counterion Exchange Reactions on DNA: Monte Carlo and Poisson-Boltzmann Analysis." Biopolymers 27, 1249-1265 (1988).

60. G. Bellomy, M. C. Mossing and M. T. Record, Jr. "Physical Properties of DNA In Vivo as Probed by the Length Dependence of the lac Operator Looping Process." Biochemistry 27, 3900-3906 (1988).

59. S. Padmanabhan, B. Richey, C. F. Anderson and M. T. Record, Jr. "The Interaction of an N-methylated Polyamine Analog, Hexamethonium (+2), with NaDNA: Quantitative 14N and 23Na NMR Relaxation Rate Studies of Cation Exchange Process." Biochemistry 27, 4367-4376 (1988).

58. S. B. Jovanovich, M. Martinell, M. T. Record, Jr. and R. R. Burgess. "Rapid Response to Osmotic Shock by Osmoregulated Genes in Escherichia coli and Salmonella typhimurium." J. Bacteriol., 170, 534-539 (1988).

57. M. T. Record, Jr. and B. Richey. "Physical Chemical Analysis of Biopolymer Self-Assembly Interactions," in ACS Sourcebook for Physical Chemistry Instructors (T. Lippincott, ed.) American Chemical Society, pp. 145-159 (1988).

56. M. T. Record, Jr. "Biophysical Principles of Specificity and Stability of Protein-DNA Interactions: Application to RNA Polymerase (Esigma70)-Promoter Interactions," in Unusual DNA Structures (R. D. Wells and S. C. Harvey, eds.) Springer-Verlag, pp. 237-251 (1988).

55. M. D. Paulsen, B. Richey, C. F. Anderson and M. T. Record, Jr. "The Salt-Dependence of the Preferential Interaction Coefficient in DNA Solutions as Determined by Grand Canonical Monte Carlo Simulations." Chem. Phys. Lett. 139, 448-452 (1987). Erratum, Chem. Phys. Let. 143, 115 (1988).
54. W. H. Braunlin, C. F. Anderson and M. T. Record, Jr. "Competitive Interactions of Co(NH3)63+ and Na+ with Helical B-DNA Probed by 59Co and 23Na NMR." Biochemistry 26, 7724-7731 (1987).

53. S. Leirmo, C. Harrison, D. S. Cayley, R. R. Burgess and M. T. Record, Jr. "Replacement of KCl by K Glutamate Dramatically Enhances Protein-DNA Interactions In Vitro." Biochemistry 26, 2095-2101 (1987).

52. B. Richey, S. Cayley, M. Mossing, C. Kolka, C. F. Anderson, T. C. Farrar and M. T. Record, Jr. "Variability of The Intracellular Ionic Environment of E. coli: Differences Between In Vitro and In Vivo Effects of Ion Concentrations on Protein-DNA Interactions and Gene Expression," J. Biol. Chem., 15, 7157-7164 (1987).

51. M. T. Record, Jr. and M. C. Mossing. "Physical Chemical Origins of Stability, Specificity and Control of Protein-DNA Interactions," in RNA Polymerase and Regulation of Transcription (W. Reznikoff et al., eds.) Elsevier Science Publishing Co., N. Y. pp 61-83 (1987).

50. P. Mills, M. Paulsen, C. F. Anderson and M. T. Record, Jr. "Monte Carlo Simulations of Counterion Accumulation Near Helical DNA." Chem. Phys. Lett. 129, 155-158 (1986).

49. P. Mills, C. F. Anderson and M. T. Record, Jr. "Grand Canonical Monte Carlo Calculations of Thermodynamic Coefficients for a Primitive Model of DNA-Salt Solutions." J. Phys. Chem. 90, 6541-6548 (1986).

48. M. Mossing and M. T. Record, Jr. "Upstream Operators Enhance Repression of the Lac Promoter." Science, 223, 889-892 (1986).

47. S. J. Mazur and M. T. Record, Jr. "Kinetics of Nonspecific Binding Reactions of Proteins with DNA Flexible Coils: Site-based and Molecule-based Association Rate Constants." Biopolymers, 25, 985-1008 (1986).
46. W. R. Braunlin, C. F. Anderson and M. T. Record, Jr. "23Nalphalpha-NMR Investigations of Counterion Exchange Reactions of Helical DNA." Biopolymers, 25, 205-214 (1986).

45. J.-H. Roe and M. T. Record, Jr. "Regulation of the Kinetics of the Interaction of E. coli RNA Polymerase with the lambdaPR Promoter by Salt Concentration." Biochemistry, 24, 4721-4726 (1985).

44. M. T. Record, Jr., C. F. Anderson, P. Mills, M. Mossing and J.-H. Roe. "Ions as Regulators of Protein-Nucleic Acid Interactions In Vitro and In Vivo." Adv. Biophys, 20, 109-135 (1985).

43. M. C. Mossing and M. T. Record, Jr. "Thermodynamic Origins of Specificity in the Lac Repressor-Operator Interaction: Adaptability in the Recognition of Mutant Operator Sites." J. Mol. Biol., 186, 295-305 (1985).

42. J.-H. Roe, R. R. Burgess and M. T. Record, Jr. "Temperature Dependence of the Rate Constants of the E. coli RNA Polymerase-lPR Promoter Interaction: Assignment of the Kinetic Steps Corresponding to Protein Conformational Change and DNA Opening." J. Mol. Biol., 184, 441-453 (1985).

41. P. Mills, C. F. Anderson and M. T. Record, Jr. "Monte Carlo Studies of Counterion-DNA Interactions. Comparison of the Radial Distribution of Counterions with Predictions of Other Polyelectrolyte Theories." J. Phys. Chem., 89, 3984-3994 (1985).

40. J.-H. Roe, R. R. Burgess and M. T. Record, Jr., "Kinetics and Mechanism of the Interaction of E. coli RNA Polymerase with the lambdaPR Promoter," J. Mol. Biol., 176, 495-521 (1984).

39. L. Nordenskiold, D. K. Chang, C. F. Anderson and M. T. Record, Jr. "23Na NMR Relaxation Study of the Effects of Conformation and Base Composition on the Interactions of Counterions with Double-Helical DNA." Biochemistry, 23, 4309-4317 (1984).

38. M. L. Bleam, C. F. Anderson and M. T. Record, Jr. "23Na NMR Studies of Cation-DNA Interactions." Biochemistry, 22, 5418-5425 (1983).

37. P. Melancon, R. R. Burgess and M. T. Record, Jr. "Direct Evidence for the Preferential Interaction of E. coli RNA Polymerase with the Ends of DNA Restriction Fragments. Biochemistry, 22, 5169-5176 (1983).

36. C. F. Anderson and M. T. Record, Jr. "The Thermodynamic Effects of Polyelectrolyte-Electrolyte Interactions," in Structure and Dynamics: Nucleic Acids and Proteins (E. Clementi and R. Sarma, Eds.) Adenine Press, N.Y. pp. 301-319 (1983).

35. S. L. Shaner, P. Melancon, K. S. Lee, R. R. Burgess and M. T. Record, Jr. "Ion Effects on the Aggregation and DNA Binding Reactions of E. coli RNA Polymerase," Cold Spring Harbor Symposium of Quantitative Biology 47, 463-472 (1983).

34. C. F. Anderson and M. T. Record, Jr. "Polyelectrolyte Theories and Their Applications to DNA." Annual Review of Physical Chemistry, 33, 191-222 (1982).

33. S. L. Shaner, D. M. Piatt, C. G. Wensley, H. Yu, R. R. Burgess and M. T. Record, Jr. "Aggregation Equilibria of E. coli RNA Polymerase: Evidence for Anion-Linked Conformational Transitions in the Protomers of Core and Holo-enzyme." Biochemistry, 21, 5539-5551 (1982).

32. P. Melancon, R. R. Burgess and M. T. Record, Jr. "Nitrocellulose Filter Binding Studies of the Interactions E. coliof RNA Polymerase Holoenzyme with Deoxyribonucleic Acid Restriction Fragments: Evidence for Multiple Classes of Nonpromoter Interactions, Some of Which Display Promoter-like Properties." Biochemistry, 21, 4318-4331 (1982).

31. W. H. Braunlin, T. J. Strick and M. T. Record, Jr. "Equilibrium Dialysis Studies of Polyamine Binding to DNA. Biopolymers, 21, 1301-1314 (1982).

30. D. M. Rose, P. A. Tovo, R. G. Bryant, M. L. Bleam, M. T. Record, Jr. "25Mg NMR Applications to Problems in Biophysical Chemistry." Biochemical Structure Determination by NMR, A. A. Bothner-By, J. D. Glickson and B. D. Sykes, ed., Marcel Dekker, N. Y. pp. 53-63 (1982).

29. B. K. Klein, C. F. Anderson and M. T, Record, Jr. "Comparison of Poisson-Boltzmann and Condensation Model Expressions for the Colligative Properties of Cylindrical Polyions." Biopolymers, 20, 2263-80 (1981).

28. H. S. Strauss, R. S. Boston, M. T. Record, Jr. and R. R. Burgess. "Variables Affecting the Selectivity and Efficiency of Retention of DNA Fragments by E. coli RNA Polymerase in the Nitrocellulose Filter Binding Assay." Gene, 13, 75-87 (1981).

27. M. T. Record, Jr., S. J. Mazur, P. Melancon, J.-H. Roe, S. L. Shaner and L. Unger. "Double Helical DNA: Conformations, Physical Properties, and Interactions with Ligands." Ann. Rev. Biochem., 50, 997-1024 (1981).

26. D. M. Rose, M. L. Bleam, M. T. Record, Jr. and R. J. Bryant. "25Mg NMR in DNA Solutions: Dominance of Site Binding Effects." Proc. Natl. Acad. Sci. USA 77, 6289-6292 (1980).

25. M. L. Bleam, C. F. Anderson and M. T. Record, Jr. "Relative Binding Affinities of Monovalent Cations for Double-Stranded DNA." Proc. Natl. Acad. Sci. USA 77, 3085-3089 (1980).

24. C. F. Anderson and M. T. Record, Jr. "The Relationship Between the Poisson-Boltzmann Model and the Condensation Hypothesis: An Analysis Based on the Low Salt Form of the Donnan Coefficient." Biophys. Chem. 11, 353-360 (1980).

23. T. M. Lohman, P. L. deHaseth and M. T. Record, Jr. "Pentalysine-Deoxyribonucleic Acid Interactions: A Model for the General Effects of Ion Concentrations on the Interactions of Proteins with Nucleic Acids." Biochemistry 19, 3522-3530 (1980).

22. T. M. Lohman, C. G. Wensley, J. Cina, R. R. Burgess and M. T. Record, Jr. "Use of Difference Boundary Sedimentation Velocity to Investigate Non-specific Protein Nucleic Acid Interactions." Biochemistry 19, 3516-3522 (1980).

21. H. S. Strauss, R. R. Burgess and M. T. Record, Jr. "Binding of Escherichia coli Ribonucleic Acid Polymerase Holoenzyme to a Bacteriophage T7 Promoter- Containing Fragment: Evaluation of Promoter Binding Constants as a Function of Solution Conditions." Biochemistry 19, 3504-3515 (1980).

20. H. S. Strauss, R. R. Burgess and M. T. Record, Jr. "Binding of Escherichia coli Ribonucleic Acid Polymerase Holoenzyme to a Bacteriophage T7 Promoter-Containing Fragment: Selectivity Exists over a Wide Range of Solution Conditions." Biochemistry 19, 3496-3504 (1980).

19. M. T. Record, Jr., C. F. Anderson and T. M. Lohman. "Thermodynamic Analysis of Ion Effects on the Binding and Conformational Equilibria of Proteins and Nucleic Acids: The Roles of Ion Association or Release, Screening, and Ion Effects on Water Activity," Quart. Rev. Biophysics 11, 102-178 (1978).

18. T. M. Lohman, P. L. deHaseth and M. T. Record, Jr. "Analysis of Ion Concentration Effects on the Kinetics of Protein-Nucleic Acid Interactions. Application to Lac Repressor-Operator Interactions." Biophysical Chemistry 8, 281-294 (1978).

17. P. L. deHaseth, T. M. Lohman, R. R. Burgess and M. T. Record, Jr. "Nonspecific Interactions of Escherichia coli RNA Polymerase with Native and Denatured DNA: Differences in the Binding Behavior of Core and Holoenzyme," Biochemistry 17, 1612-1622 (1978).

16. C. F. Anderson, M. T. Record, Jr. and P. A. Hart. "Sodium-23 NMR Studies of Cation-DNA Interactions." Biophysical Chemistry 7, 301-316 (1978).

15. M. T. Record, Jr. and T. M. Lohman. "A Semiempirical Extension of Polyelectrolyte Theory to the Treatment of Oligoelectrolytes: Application to Oligonucleotide Helix-Coil Transitions." Biopolymers 17, 159-166 (1978).

14. M. T. Record, Jr., P. L. deHaseth and T. M. Lohman, "Interpretation of Monovalent and Divalent Cation Effects on the Lac Repressor-Operator Interaction," Biochemistry 16, 4791-4796 (1977).

13. P. L. deHaseth, T. M. Lohman and M. T. Record, Jr. "Nonspecific Interaction of Lac Repressor with DNA: An Association Reaction Driven by Counterion Release." Biochemistry 16, 4783-4790 (1977).

12. P. L. deHaseth, C. A. Gross, R. R. Burgess and M. T. Record, Jr. "Measurement of Binding Constants for Protein-DNA Interactions by DNA Cellulose Chromatography." Biochemistry 16, 4777-4783 (1977).

11. M. T. Record, Jr., T. M. Lohman and P. L. deHaseth. "Ion Effects on Ligand-Nucleic Acid Interactions." J. Mol. Biol. 107, 145-158 (1976).

10. M. T. Record, Jr., C. P. Woodbury and T. M. Lohman. "Na+ Effects on Transitions of DNA and Polynucleotides of Variable Linear Charge Density." Biopolymers 15, 893-915 (1976).

9. C. G. Wensley and M. T. Record, Jr. "Intermediates in the Strand-Separation Transition of T7 DNA." Biopolymers 15, 717-728 (1976).

8. M. T. Record, Jr. "Effects of Na+ and Mg++ Ions on the Helix-Coil Transition of DNA." Biopolymers 14, 2137-2158 (1975).

7. C. P. Woodbury and M. T. Record, Jr. "A Range of G+C Independent Denaturation Solvents for DNA." Biopolymers 14, 2417-2420 (1975).

6. M. T. Record, Jr., C. P. Woodbury and R. B. Inman. "Characterization of Rodlike DNA Fragments," Biopolymers 14, 393-408 (1975).

5. M. Kallay and M. T. Record, Jr. "The Strand-Separation Transition of T7 DNA." Biopolymers 13, 825-841 (1974).

4. E. L. Elson and M. T. Record, Jr. "The Strand-Separation Transition of T2 Bacteriophage DNA." Biopolymers 13, 797-824 (1974).

3. M. T. Record, Jr. and B. H. Zimm. "Kinetics of the Helix-Coil Transition in DNA." Biopolymers 11, 1435-1484 (1972).

2. M. T. Record, Jr. "Electrostatic Effects on Polynucleotide Transitions. II. Behavior of Titrated Systems." Biopolymers 5, 993-1008 (1967).