Helicases and DNA Translocases
Reviews:
“Non-hexameric DNA Helicases and Translocases: Mechanisms and Regulation”, T. M. Lohman, E. J. Tomko and C. G. Wu, Nat Rev Mol Cell Biol (2008) 9, 391-401. [PDF]
“DNA Helicases: Dimeric Enzyme Action” T. M. Lohman (2004) Encyclopedia of Biological Chemistry, W. J. Lennarz and M. D. Lane, eds. Elsevier Science. [PDF]
“DNA Helicases, Motors that Move Along Nucleic Acids: Lessons from the SF1 Helicase Superfamily”, T. M. Lohman, J. Hsieh, N. K. Maluf, W. Cheng, A. L. Lucius, C. J. Fischer, K. M.Brendza, S. Korolev & G. Waksman (2003). The Enzymes, vol XXIII, “ATP and Molecular Motors”, ed. F. Tamanoi and D. D. Hackney (Academic Press), pp. 303-369. [PDF]
“Staying on Track: Common Features of DNA Helicases and Microtubule Motors”, T. M. Lohman, K. Thorn and R. D. Vale, Cell (1998) 93 9-12. [PDF]
“Mechanisms of Helicase-Catalyzed DNA Unwinding”, T. M. Lohman and K.P. Bjornson, Annual Review of Biochemistry (1996) 65, 169-214. [PDF]
“Helicase-catalyzed DNA Unwinding: Energy Coupling by DNA Motor Proteins”, K. J. M. Moore and T. M. Lohman, Biophys. J. (1995) 68, 180s-185s.
“Helicase-catalyzed DNA Unwinding”, T. M. Lohman, J. Biological Chemistry (1993) 268, 2269-2272. [PDF]
“E.coli DNA Helicases: Mechanisms of DNA Unwinding”, T. M. Lohman, Molecular Microbiology (1992) 6, 5-14.
Selected Publications:
"Processive DNA Unwinding by RecBCD Helicase in the Absence of Canonical Motor Translocation", Simon, M., Sokoloski, J., Hao, L., Weiland, E. and Lohman, T.M. J Molecular Biology, (2016) (E-pub ahead of print.)
"Defining Single Molecular Forces Required for Notch Activation Using Nano Yoyo", Chowdhury, F., Li, I., Ngo, T., Leslie, B., Kim, B., Sokoloski, J.E., Weiland, E., Wang, X., Chemla, Y., Lohman, T.M. and Ha, T. Nano Letters, (2016) 16, 3892-3897. [Abstract]
"Chemo-mechanical Pushing of Proteins Along Single-Stranded DNA", Sokoloski, J., Kozlov, A.G., Galletto, R. and Lohman, T.M. PNAS, USA, (2016) 113, 6194-6199. [Abstract]
"Is a Fully Wrapped SSB-DNA Complex Essential for E. coli Survival?", Waldman, V., Weiland, E., Kozlov, A.G. and Lohman, T.M. Nucleic Acids Research, (2016) 44, 4317-4329. [Abstract]
"Structural Dynamics of E. coli Single-Stranded DNA Binding Protein Reveal DNA Wrapping and Unwrapping Pathways.", Suksombat, S., Khafizov, R., Kozlov, A.G., Lohman, T.M., and Chemla, Y.R. eLife, (2015) doi.org/10.7554/eLife.08193. [Abstract]
"Protein Structure. Direct Observation of Structure-function Relationship in a Nucleic Acid-processing Enzyme.", Comstock, M.J., Whitely, K.D., Jia, H., Sokoloski, J., Lohman, T.M., Ha, T. and Chemla, Y. Science, (2015) 348 352-354. [Abstract]
"Active Displacement of RecA Filaments by UvrD Translocase Activity", Petrova, V., Chen, S., Molzberger, E., Tomko, E., Chitteni-Pattu, S., Jia, H., Ordabayev, Y., Lohman, T.M. and Cox, M. Nucleic Acids Res., (2015) 43, 4133-4139. [Abstract]
"Intrinsically Disordered C-terminal Tails of E. coli Single Stranded DNA Binding Protein Regulate Cooperative Binding to Single Stranded DNA", Kozlov, A.G., Weiland, E., Mittal, A., Waldman, V., Antony, E., Fazio, N., Pappu, R.V. and Lohman, T.M. J Mol Biol (2015) 427, 763-774 . [Abstract] [Article]
“Diffusion of Human Replication Protein A Along Single Stranded DNA”, Nguyen, B., Sokoloski, J.E., Galletto, R., Elson, E.L., Wold, M.S. and Lohman, T.M. J Mol Biol, (2014) 426:3246-3261. [Abstract]
“Srs2 Prevents Rad51 Filament Formation by Repetitive Motion on DNA”, Qiu, Y., Antony, E., Doganay, S., Koh, H., Lohman, T. M. and Myong, S. Nature Communications, (2013) 4:228. [Abstract]
“Direct Imaging of Single UvrD Helicase Dynamics on Long Single-Stranded DNA”, Lee, K.S., Balci, H., Jia, H., Lohman, T.M. and Ha, T. Nature Communications (2013) 4:1878. [Abstract]
“Asymmetric Regulation of Bipolar Single-stranded DNA Translocation by the Two Motors withinE. coli RecBCD Helicase”, Xie, F., Wu, C.G., Weiland, E. and Lohman, T.M. J Biol Chem (2013) 288, 1055-1064. [Abstract]
“The Primary and Secondary Translocase Activities within E. coli RecBC Helicase are Tightly Coupled to ATP Hydrolysis by the RecB Motor”, Wu, C.G., Xie, F. and Lohman, T.M. J Mol Biol (2013) 423, 303-314. [Abstract]
“Fluorescence Methods to Study DNA Translocation and Unwinding Kinetics by Nucleic Acid Motors”, Fischer, C.J., Tomko, E.J., Wu, C.G. and Lohman, T.M. Methods Mol Biol 875, 85-104 (2012). [Abstract]
“Single Stranded DNA Translocation of E. coli UvrD Monomer is Tightly Coupled to ATP Hydrolysis”, Tomko, E.J., Fischer, C.J. and Lohman, T.M. J Mol Biol (2012) 418, 32-46. [Abstract]
“Single-Molecule Nanopositioning: Structural Transitions of a Helicase-DNA Complex During ATP Hydrolysis”, Balci, H., Arslan, S., Myong, S., Lohman, T.M. and Ha, T. Biophys J 101. 976-984 (2011). [PDF]
“Self-assembly of E. coli MutL and its Complexes with DNA”, Niedziela-Majka, A., Maluf, N.K., Antony, E. and Lohman, T.M. Biochemistry 50, 7868-7880 (2011). [PDF]
“Rotations of the 2B Sub-domain of E. coli UvrD Helicase/Translocase Coupled to Nucleotide and DNA Binding.”, Jia, H., Korolev, S., Niedziela-Majka, A., Maluf, N.K., Gauss, G.H., Myong, S., Ha, T., Waksman, G. and Lohman, T.M. J Mol Biol 411, 633-648 (2011). [PDF]
“5′-Single-stranded/duplex DNA Junctions are Loading Sites for E. coli UvrD Translocase”, Tomko, E.J., Jia, H., Park, J., Maluf, N.K., Ha, T. and Lohman, T.M. EMBO J (2010) 29, 3826-3839 [PDF]
“Non-hexameric SF1 DNA Helicases and Translocases”, Antony, E. and Lohman, T.M.Encyclopedia of Biological Chemistry (2nd Edition) W.J. Lennarz and M.D. Lane, eds. (2010)
“Escherichia coli RecBC Helicase has Two Translocase Activities Controlled by a Single ATPase Motor”, Wu, C.G., Bradford, C. and Lohman, T.M. Nat Struct Mol Biol (2010) (E-pub ahead of print.) [PDF]
“PcrA Helicase Dismantles RecA Filaments by Reeling in DNA in Uniform Steps”, Park, J., Myong, S., Niedziela-Majka, A., Lee, K.S., Yu, J., Lohman, T.M. and Ha, T. Cell (2010) 142, 544-555 [PDF]
“Clipping Along”, Lohman, T.M. J Mol Biol (2010) 399, 663-664. [PDF]
“Ensemble Methods for Monitoring Enzyme Translocation Along Single Stranded Nucleic Acids”, E.J. Tomko, Fischer, C.J. and T.M. Lohman Methods (2010) 51, 269-276. [PDF]
“Regulation of Single Stranded DNA Binding by the C-terminal of E. coli SSB Protein”, A.G. Kozlov, M.M. Cox and T.M. Lohman J Biol Chem (2010) 285, 17246-17252. [PDF]
“Binding Specificity of E. coli SSB Protein for the Chi Subunit of DNA Pol III Holoenzyme and PriA Helicase”, A.G. Kozlov, M.J. Jezewska, W. Bujalowski and T.M. Lohman Biochemistry (2010)49, 3555-3566. [PDF]
“Kinetics of Motor Protein Translocation on Single-Stranded DNA”, C.J. Fischer, L. Wooten, E.J. Tomko and T.M. Lohman Methods Mol Biol (2010) 587, 45-56. [PDF]
“Srs2 Disassembles Rad51 Filaments by a Protein-Protein Interaction Triggering ATP Turnover and Dissociation of Rad51 from DNA”, E. Antony, E.J. Tomko, Q. Xiao, L. Krejci, T.M. Lohman and T. Ellenberger, Mol Cell (2009) 35, 105-115. [PDF]
“Influence of DNA End Structure on the Mechanism of Initiation of DNA Unwinding by the Escherichia coli RecBCD and RecBC Helicases”, C. J. Wu and T. M. Lohman, J Mol Biol (2008)382, 312-326. [PDF]
“Kinetic Control of Mg(2+)-dependent Melting of Duplex DNA Ends by Escherichia coli RecBC”, C. J. Wong and T. M. Lohman, J Mol Biol (2008) 378, 759-775. [PDF]
“B. stearothermophilus PcrA Monomer is a Single Stranded DNA Translocase but not a Processive Helicase in vitro”. A. Niedziela-Majka, M. A. Chesnik, E. J. Tomko & T. M. Lohman (2007) J. Biological Chemistry 282, 27076-27085. [PDF]
“A Nonuniform Stepping Mechanism for E. coli UvrD Monomer Translocation Along Single-stranded DNA” Tomko, E.J., Fischer, C.J., Niedziela-Majka, A. and Lohman, T.M., Mol Cell (2007)26 335-347. [PDF] [Supplement]
“Probing 3′-ssDNA Loop Formation in E. coli RecBCD/RecBC-DNA Complexes Using Non-natural DNA: A Model for “chi” Recognition Complexes.”, Wong, C.J., Rice, R.L., Baker, N.A., Ju, T. and Lohman, T.M., J Mol Biol (2006) 362, 26-43. [PDF]
“Repetitive Shuttling of a Motor Protein on DNA,” S. Myong, I. Rasnik, C. Joo, T. M. Lohman and T. Ha. Nature (2005) 437, 1321-1325. [PDF]
“Energetics of DNA End Binding by E.coli RecBC and RecBCD Helicases Indicate Loop Formation in the 3′-Single-stranded DNA Tail ” J. C. Wong, A. L. Lucius and T. M. Lohman. J MolBiol (2005) 352, 765-782. [PDF]
“Autoinhibition of Escherichia coli Rep Monomer Helicase Activity by its 2B Subdomain” K.M.Brendza, W. Cheng, C.J. Fischer, M.A. Chesnick, A. Niedziela-Majka and T.M. Lohman. PNAS(2005) 102, 10076-10081. [PDF]
“DNA Helicases: Dimeric Enzyme Action” T.M. Lohman. Encyclopedia of Biological Chemistry(2004), W.J. Lennarz and M.D. Lane, eds. Elsevier Science.
“ATP-dependent Translocation of Proteins Along Single-stranded DNA: Models and Methods of Analysis of Pre-steady State Kinetics.” C. J. Fischer and T. M. Lohman. J Mol Biol (2004) 344, 1265-1286. [PDF]
“Mechanism of ATP-dependent Translocation of E. coli UvrD Monomers Along Single-stranded DNA.” C. J. Fischer, N. K. Maluf and T. M. Lohman. J Mol Biol (2004) 344, 1287-1309. [PDF]
“Effects of Temperature and ATP on the Kinetic mechanism and Kinetic Step-size for E. ColiRecBCD Helicase-catalyzed DNA Unwinding.”, A. L. Lucius and T. M. Lohman. J Mol Biol (2004)339, 751-771. [PDF]
“Fluorescence Stopped-flow Studies of Single Turnover Kinetics of E. coli RecBCD Helicase-catalyzed DNA Unwinding”, A.L. Lucius, J. C. Wong and T. M. Lohman. J Mol Biol (2004) 339, 731-750. [PDF]
“Probing Single-stranded DNA Conformational Flexibility Using Fluorescence Spectroscopy”, M. C. Murphy, I. Rasnik, W. Cheng, T. M. Lohman, and T. Ha. Biophys. J. (2004) 86, 2530-2537. [PDF]
“DNA-binding Orientation and Domain Conformation of the E. coli rep Helicase Monomer Bound to a Partial Duplex Junction: Single-molecule Studies of Fluorescently Labeled Enzymes”, I.Rasnik, S. Myong, T. M. Lohman, T. Ha J Mol Biol (2004) 336, 395-408. [PDF]
“General Methods for Analysis of Sequential “n-step Kinetic Mechanisms: Application to Single Turnover Kinetics of Helicase-catalyzed DNA Unwinding”, A. L. Lucius, N. K. Maluf, C. J. Fischer, T. M. Lohman Biophys. J. (2003) 84, 2224-2239. [PDF]
“Kinetic Mechanism for Formation of the Active, Dimeric UvrD Helicase-DNA Complex”, N. K.Maluf, J. A. Ali, T. M. Lohman, J. Biol. Chem. (2003) 278, 31930-31940. [PDF]
“A Dimer of E. coli UvrD is the Active From of the Helicase in vitro“, N. K. Maluf, C. J. Fischer, T. M. Lohman, J. Mol. Biol. (2003) 325, 913-935. [PDF]
“Self Association Equilbria of E. coli UvrD Helicase Studied by Analytical Ultracentrifugation”, N. K. Maluf, T. M. Lohman, J. Mol. Biol. (2003) 325, 889-912. [PDF]
“DNA Helicases, Motors That Move Along Nucleic Acids: Lessons for the SF1 Helicase Superfamily”, T. M. Lohman, J. Hsieh, N.K. Maluf, W. Cheng, A.L. Lucius, C.J. Fischer, K.M. Brendza, S. Korolev and G. Waksman The Enzymes (2003) vol XXIII, “ATP and Molecular Motors”, ed. F. Tamanoi and D.D. Hackney (Academic Press), 303-369.
“Initiation and Re-initiation of DNA Unwinding by the Escherichia coli Rep helicase.”, T. Ha, I.Rasnik, W. Cheng, H. P. Babcock, G. H. Gauss, T. M. Lohman and S. Chu, Nature (2002) 419, 638-641. [PDF] [Supplemental]
“DNA Unwinding Step-size of E. coli RecBCD Helicase Determined from Single Turnover Chemical Quenched-flow Kinetic Studies.”, A. L. Lucius, A. Vindigni, R. Gregorian, J. A. Ali, A. F. Taylor, G. R. Smith and T. M. Lohman J. Mol. Biol. (2002) 324, 409-428. [PDF]
“The 2B domain of E. coli Rep Helicase is not Required for Duplex DNA Unwinding Activity”, W. Cheng, K. M. Brendza, G. H. Gauss, S. Korolev, G. Waksman and T. M. Lohman, Proceedings of the National Academy of Sciences (USA). (2002) 99, 16006-16011. [PDF] [Supplemental]
“E. coli Rep Oligomers are Required to Initiate DNA Unwinding in vitro“, W. Cheng, J. Hsieh, K. M. Brendza, T. M. Lohman, J. Mol. Biol. (2001) 310, 327-350. [PDF]
“An Oligomeric Form of E. coli UvrD is Required for Optimal Helicase Activity”, J. A. Ali, N. K.Maluf and T. M. Lohman, J. Mol. Biol. (1999) 293, 815-834. [PDF]
“A Two-site Kinetic Mechanism for ATP Binding and Hydrolysis by E. coli Rep Helicase Dimer Bound to a Single Stranded Oligodeoxynucleotide”, J. Hsieh, K. J. M. Moore and T. M. Lohman, J. Mol. Biol. (1999) 288, 255-274. [PDF]
“Kinetic Mechanism for the Sequential binding of Two Single-stranded Oligodeoxynucleotides to the E. coli Rep Helicase Dimer”, K. P. Bjornson, J. Hsieh, M. Amaratunga and T. M. Lohman,Biochemistry (1998) 37, 891-899. [PDF]
“Comparisons Between the Structures of HCV and Rep Helicases Reveal Structural Similarities Between SF1 and SF2 Superfamilies of Helicases”, S. Korolev, N. Yao, T. M. Lohman, P. C. Weber and G. Waksman, Protein Science (1998) 7, 605-610. [PDF]
“Major Domain Swivelling Revealed by the Crystal Structures of Binary and Ternary Complexes ofE. coli Rep Helicase Bound to Single Stranded DNA and ADP”, S. Korolev, J. Hsieh, G. H. Gauss, T. M. Lohman and G. Waksman, Cell (1997) 90, 635-647. [PDF]
“A Two-site Mechanism for ATP Hydrolysis by the Asymmetric Rep Dimer (P2S) as Revealed by Site-specific Inhibition with ADP-AIF4“, I. Wong and T. M. Lohman, Biochemistry (1997) 36, 3115-3125. [PDF]
“Kinetic Measurement of the Step-size of DNA Unwinding by E. coli UvrD Helicase”, J. A. Ali and T. M. Lohman, Science (1997) 275, 377-380. [PDF]
“ATP Hydrolysis Stimulates Binding and Release of Single Stranded DNA from Alternating Subunits of the Dimeric E. coli Rep Helicase: Implications for ATP-driven Helicase Translocation”, K. P. Bjornson, I. Wong and T. M. Lohman, J. Molecular Biology (1996) 263, 411-422. [PDF]
“ATPase Activity of Escherichia coli Rep Helicase Crosslinked to Single Stranded DNA: Implications for ATP-driven Helicase Translocation”, I. Wong and T. M. Lohman, P.N.A.S., U.S.A.(1996) 93, 10051-10056. [PDF]
“ATPase Activity of Escherichia coli Rep Helicase is Dramatically Dependent on its DNA-Ligationand Protein Oligomeric States”, I. Wong, K. J. M. Moore, K. P. Bjornson, J. Hsieh and T. M. Lohman, Biochemistry (1996) 35, 5726-5734. [PDF]
“Kinetic Mechanism of DNA Binding and DNA-Induced Dimerization of the Escherichia coli Rep Helicase”, K. P. Bjornson, K. J. M. Moore, and T. M. Lohman, Biochemistry (1996) 35, 2268-2282. [PDF]
“Linkage of Protein Assembly to Protein-DNA Binding”, I. Wong and T. M. Lohman, Methods inEnzymology, G. K. Ackers and M. Johnson, eds., (1995) 259, 95-127.
“Kinetic Mechanism of Adenine Nucleotide Binding to and Hydrolysis by the E. coli Rep Monomer. I. Use of Fluorescent Nucleotide Analogues”, K. J. M. Moore and T. M. Lohman,Biochemistry (1994) 33,14550-14564. [PDF]
“Kinetic Mechanism of Adenine Nucleotide Binding to the E. coli Rep Monomer. II. Application of a Kinetic Competition Approach”, K. J. M. Moore and T. M. Lohman, Biochemistry (1994) 33, 14565-14578. [PDF]
“Single-turnover Kinetics of Helicase-catalyzed DNA Unwinding Monitored Continuously by Fluorescence Energy Transfer”, K. P. Bjornson, M. Amaratunga, K. J. M. Moore and T. M. Lohman, Biochemistry (1994) 33, 14306-14316. [PDF]
“Hetero-dimer Formation Between Escherichia coli Rep and UvrD Proteins”, I. Wong, M.Amaratunga and T. M. Lohman J. Biol. Chem. (1993) 268, 20386-20391. [PDF]
“E.coli Rep Helicase Unwinds DNA by an Active Mechanism”, M. Amaratunga and T. M. Lohman,Biochemistry (1993) 32, 6815-6820. [PDF]
“A Double-filter Method for Nitrocellulose Filter Binding:Application to Protein-Nucleic Acid Interactions”, I. Wong and T. M. Lohman, Proc. Natl. Acad. Sci., U.S.A. (1993) 90, 5428-5432.
“Kinetics of E. coli Helicase II-catalyzed Unwinding of Fully Duplex and Nicked-circular DNA”, G. T. Runyon and T. M. Lohman, Biochemistry (1993) 32,4128-4138. [PDF]
“Overexpression, Purification, DNA Binding and Dimerization of the E. coli uvrD Gene Product (Helicase II)”, G. T. Runyon, I. Wong and T. M. Lohman, Biochemistry (1993) 32, 602-612. [PDF]
“Allosteric Effects of Nucleotide Cofactors on E. coli Rep Helicase-DNA Binding”, I. Wong and T. M. Lohman, Science (1992) 256, 350-355.
“DNA-induced Dimerization of the E. coli Rep Helicase: Allosteric Effects of Single Stranded and Duplex DNA”, I. Wong, K. L. Chao, W. Bujalowski and T. M. Lohman, J. Biological Chemistry(1992) 267, 7596-7610. [PDF]
“DNA-induced Dimerization of the Escherichia coli Rep Helicase”, K. Chao and T. M. Lohman, J. Molecular Biology (1991) 221, 1165-1181.
“E.coli Helicase II (UvrD) Protein Initiates DNA Unwinding at Nicks and Blunt-ends”, G.T. Runyon, D. G. Bear and T. M. Lohman, Proc. Natl. Acad. Sci., U.S.A. (1990) 87, 6383-6387.
“DNA and Nucleotide-Induced Conformational Changes in the E. coli Rep and Helicase II (UvrD) Proteins”, K. Chao and T. M. Lohman, J. Biological Chemistry (1990) 265, 1067-1076. [PDF]
“E. coli Helicase II (UvrD) Protein Can Completely Unwind Fully Duplex Linear and Nicked-Circular DNA”, G. T. Runyon and T. M. Lohman, J. Biological Chemistry (1989) 264, 17502-17512. [PDF]
“Large-scale Purification and Characterization of the E. coli rep Gene Product”, T. M. Lohman, K.Chao, S. Sage, J. M. Green and G. T. Runyon, J. Biological Chemistry (1989) 264, 10139-10147. [PDF]
SSB Proteins
Reviews
"Single Molecule Views of Protein Movement on Single-stranded DNA", T. Ha, A. G. Kozlov, and T. M. Lohman, Annual Review of Biophysics (2012) 41, 295-319. [PDF]
"SSB as an Organizer/Mobilizer of Genome Maintenance Complexes", R. D. Shereda, A. G. Kozlov, T. M. Lohman, M. M. Cox and J. L. Keck, CRC
Critical Reviews in Biochemistry and Molecular Biology (2008) 43, 289-318. [PDF]
"E. coli Single Stranded DNA Binding Protein: Multiple Binding Modes and Cooperativities", T. M. Lohman and M. E. Ferrari, Annual Review of Biochemistry (1994) 63, 527-570. [PDF]
"E. coli Single
"E. coli SSB Protein: Multiple Binding Modes and Cooperativities", T. M. Lohman and W. Bujalowski, The Biology of Nonspecific DNA-Protein Interactions, ed. A. Revzin. CRC Press (1990), 131-168.
Selected Publications:
"Ultrafast Redistribution of E. coli SSB Along Long Single-Stranded DNA via Intersegment Transfer" Lee, K.S., Marciel, A.B., Kozlov, A.G., Schroeder, C.M., Lohman, T.M. and Ha, T., J. Mol. Biol. 426, 2413-2421 (2014) [Abstract] [PDF]
"Multiple C-terminal Tails Within a Single E. coli SSB Homotetramer Coordinate DNA Replication and Repair" Antony, E., Weiland, E., Yuan, Q., Manhart, C. M., Nguyen, B., Kozlov, A. G., McHenry, C. S. and Lohman, T. M.,.J. Mol. Biol. 425, 4802-4819 (2013) [Abstract] [PDF]
"SSB-DNA Binding Monitored by Fluorescence Intensity and Anisotropy." Kozlov, A.G., Galletto, R. and Lohman, T.M., Methods Mol Biol. 922, 55-83 (2012) [Abstract]
"SSB Binding to ssDNA Using Isothermal Titration Calorimetry" Kozlov, A.G. and Lohman, T.M., Methods Mol Biol. 922, 37-54 (2012)[Abstract]
"Plasmodium falciparum SSB Tetramer Wraps Single Stranded DNA with Similar Topology but Opposite Polarity to E. coli SSB." Antony, E., Korolev, S., Weiland, E.A. and Lohman, T.M. J Mol Biol 420, 269-283 (2012) [PDF]
"Plasmodium falciparum SSB Tetramer Binds Single Stranded DNA only in a Fully Wrapped Mode." Antony, E., Kozlov, A.G., Nguyen, B. and Lohman, T.M. J Mol Biol 420, 284-295 (2012) [PDF]
"SSB Functions as a Sliding Platform that Migrates on DNA via Reptation." Zhou, R., Kozlov, A.G., Roy, R., Zhang, J., Korolev, S., Lohman, T.M. and Ha, T. Cell 146, 222-232(2011) [PDF]
"E. coli SSB Tetramer Binds the First and Second Molecules of (dT)(35) with Heat Capacities of Opposite Sign." Kozlov, A.G. and Lohman, T.M., Biophys Chem 159, 48-57 (2011) [PDF]
"Binding of the Dimeric Deinococcus radiodurans SSB Protein to Single-stranded DNA." Roy, R., Kozlov, A.G., Eggington, J.M., Cox, M.M. and Lohman, T.M., Biochemistry 49, 8266-8275. (2010) [PDF]
"SSB protein Diffusion on Single-stranded DNA Stimulates RecA Filament Formation." Roy, R., Kozlov, A.G., Lohman, T.M. and Ha, T., Nature (2009) 461, 1092-1097. [PDF] | "Slip Sliding on DNA" George, N.P. and Keck, J.L. Nature (2009) 461, 1067-1068. [PDF]
"Dynamic Structural Rearrangements between DNA Binding Modes of E. coli SSB Protein." Roy, R., Kozlov, A.G., Lohman, T.M. and Ha, T., J Mol Biol (2007) 369, 1244-1257. [PDF]
"Polar Destabilization of DNA Duplexes with Single-stranded Overhangs by the Deinococcus radiodurans SSB Protein." Eggington, J.M., Kozlov, A.G., Cox, M.M. and Lohman, T.M., Biochemistry (2006) 45 14490-14502. [PDF]
"Saccharomyces cerevisiae Replication Protein A Binds to Single-stranded DNA in Multiple Salt-dependent Modes." Kumaran, S., Kozlov, A.G. and Lohman, T.M., Biochemistry (2006) 45 11958-11973. [PDF]
"Microsecond Dynamics of Protein-DNA Interactions: Direct Observation of the Wrapping/Unwrapping Kinetics of Single-stranded DNA Around the E. coli SSB tetramer.", Kuznetsov, S.V., Kozlov, A.G., Lohman, T.M. and Ansari, A., J Mol Biol (2006) 359, 55-65. [PDF]
"Effects of Monovalent Anions on a Temperature-dependent Heat Capacity Change for Escherichia coli SSB Tetramer.", Kozlov, A.G. and Lohman, T.M., Biochemistry (2006) 45, 5190-5205. [PDF]
"The C-terminal Domain of Full-length E. coli SSB is Disordered Even When Bound to DNA.", Savvides, S.N., Raghunathan, S., Futterer, K., Kozlov, A.G., Lohman, T.M. and Waksman, G., Protein Science (2004) 13, 1942-1947. [PDF]
"Kinetic Mechanism of Direct Transfer of E. coli SSB Tetramers between Single-stranded DNA Molecules.", A.G. Kozlov and T. M. Lohman, Biochemistry (2002) 41, 11611-11627. [PDF]
"Stopped-flow Studies of the Kinetics of Single Stranded DNA Binding and Wrapping around the E. coli SSB Tetramer", A. G. Kozlov and T. M. Lohman, Biochemistry (2002) 41, 6032-44. [PDF]
"Structure of the DNA Binding Domain of E.coli SSB Bound to ssDNA", S. Raghunathan, A. Kozlov, T. M. Lohman and G. Waksman, Nature Structural Biology (2000) 7, 648-652. [PDF]
"Large Contributions of Coupled Protonation Equilibria to the Observed Enthalpy and Heat Changes for ssDNA Binding to E. coli SSB Protein", A. G. Kozlov and T. M. Lohman, Proteins: Structure, Function and Genetics (2000) Supplement 4, 8-22. [PDF]
"Adenine Base Unstacking Dominates the Observed Enthalpy and Heat Capacity Changes for E. coli SSB tetramer Binding to Single Stranded Oligoadenylates", A.G. Kozlov and T. M. Lohman, Biochemistry (1999) 38, 10691-10698. [PDF]
"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", W. Zhang, H. Ni, M.W. Capp, C.F. Anderson, T.M. Lohman and M.T. Record, Jr., Biophysical J. (1999) 76, 1008-1017. [PDF]
"Calorimetric Studies of E. coli SSB Protein Single-stranded DNA interactions. Effects of Monovalent Salts on binding Enthalpy", A.G. Korolev and T.M. Lohman, J. Mol. Biol. (1998) 278, 999-1014. [PDF]
"Crystal Structure of the Homo-tetrameric Single Stranded DNA Binding Domain of E. coli Single Stranded DNA Binding Protein Determined by Multiwavelength X-ray Diffraction on the Selenomethionyl Protein at 2.9 Angstrom Resolution", S. Raghunathan, C.S. Ricard, T.M. Lohman and G. Waksman, P.N.A.S., U.S.A. (1997) 94, 6652-6657. [PDF]
"A Mutation in E. coli SSB Protein (W54S) Alters Intra-tetramer Negative Cooperativity and Inter-tetramer Positive Cooperativity for Single Stranded DNA Binding", M. E. Ferrari, J. Fang, and T. M. Lohman, Biophysical Chemistry (1997), 64, 235-251.
"A Highly Salt-dependent Enthalpy Change for E. coli SSB Protein-Nucleic Acid Binding Due to Ion-Protein Interactions", T.M. Lohman, L.B. Overman, M.E. Ferrari and A.G. Kozlov, Biochemistry (1996) 35, 5272-5279. [PDF]
"Apparent Heat Capacity Change Accompanying a Non-specific Protein-DNA Interaction. E. coli SSB Tetramer Binding to Oligodeoxyadenylates", M.E. Ferrari and T.M. Lohman, Biochemistry (1994) 33, 12896-12910. [PDF]
"Cooperative Binding of Escherichia coli SSB Tetramers to Single Stranded DNA in the (SSB)35 Binding Mode", M.E. Ferrari, W. Bujalowski and T.M. Lohman, J. Mol. Biol. (1994) 236, 106-123. [PDF]
"Effects of Base Composition on the Negative Cooperativity and Binding Mode Transitions of E. coli SSB-Single Stranded DNA Complexes", T.M. Lohman and W. Bujalowski, Biochemistry (1994) 33, 6167-6176. [PDF]
"Linkage of pH, Anion and Cation Effects in Protein-Nucleic Acid Equilibria. E. coli SSB Protein-Single Stranded Nucleic Acid Interactions", L.B. Overman and T.M. Lohman, J. Mol. Biol. (1994) 236, 165-178. [PDF]
"Cooperative Binding of Polyamines Induces the Transitions Between E. coli SSB Protein-DNA Binding Modes", T-F. Wei, W. Bujalowski and T.M. Lohman, Biochemistry (1992) 31, 6166-6174.
"Monomers of the Escherichia coli SSB-1 Mutant Protein Bind Single Stranded DNA", W. Bujalowski and T.M. Lohman, J. Molecular Biology (1991) 217, 63-74.
"Monomer-tetramer Equilibrium of the SSB-1 Mutant Single Strand Binding Protein", W. Bujalowski and T.M. Lohman, J. Biological Chemistry (1991) 266, 1616-1626. [PDF]
"E. coli SSB protein: Multiple Binding Modes and Cooperativities", T.M. Lohman and W. Bujalowski, The Biology of Nonspecific DNA-Protein Interactions, ed. A. Revzin. CRC Press (1990), 131-168.
"Negative Cooperativity in E. coli Single Strand Binding Protein – Oligonucleotide Interactions. I. Evidence and a Quantitative Model", W. Bujalowski and T. M. Lohman, J. Molecular Biology (1989) 207, 249-268.
"Negative Cooperativity in E. coli Single Strand Binding Protein-Oligonucleotide Interactions. II. Salt, temperature and oligonucleotide length effects", W. Bujalowski and T.M. Lohman, J. Molecular Biology (1989) 207, 269-288.
"On the Cooperative Binding of Large Ligands to a One-dimensional Homogeneous Lattice: The Generalized Three-State Lattice Model", W. Bujalowski, T.M. Lohman and C.F. Anderson, Biopolymers (1989) 28, 1637-1643.
"Negative Cooperativity within Individual Tetramers of E. coli SSB Protein is Responsible for the Transition Between the (SSB)35 and (SSB)56 DNA Binding Modes", T.M. Lohman and W. Bujalowski, Biochemistry (1988) 27, 2260-2265. [PDF]
"Equilibrium Binding of E. coli Single Strand Binding Protein to Single Stranded Nucleic Acids in the (SSB)65 Binding Mode. Cation and Anion Effects and Polynucleotide Specificity", L.B. Overman, W. Bujalowski and T.M. Lohman, Biochemistry (1988) 27, 456-471.
"Binding Mode Transitions of E. coli Single Strand Binding Protein-Single Stranded DNA Complexes. Cation, Anion, pH and Binding Density Effects ", W. Bujalowski, L.B. Overman and T.M. Lohman, J. Biological Chemistry (1988) 263, 4629-4640. [PDF]
"Limited Cooperativity in Protein-Nucleic Acid Interactions. A Thermodynamic Model for the Interactions of E. coli Single Strand Binding Protein with Single Stranded Nucleic Acids in the "Beaded", (SSB)65 Mode", W. Bujalowski and T.M. Lohman, J. Molecular Biology (1987) 195, 897-907.
"A General Method of Analysis of Ligand-Macromolecule Equilibria Using a Spectroscopic Signal from the Ligand to Monitor Binding. Application
to E. coli SSB Protein-Nucleic Acid Interactions", W. Bujalowski and T.M. Lohman, Biochemistry (1987) 26, 3099-3106.
"E. coli Single Strand Binding Protein Forms Multiple, Distinct Complexes with Single Stranded DNA", W. Bujalowski and T. M. Lohman, Biochemistry (1986) 25, 7799-7802. [PDF]
"Salt Dependent Changes in the DNA Binding Cooperativity of E. coli Single
"Large Scale Overproduction and Rapid Purification of the E. coli ssb Gene Product. Expression of the ssb Gene Under PL Control", T.M. Lohman, J.M. Green and R.S. Beyer, Biochemistry (1986) 25, 21-25. [PDF]
"Two Binding Modes in E. coli Single Strand Binding Protein (SSB-Single Stranded DNA Complexes: Modulation by NaCl Concentration", T.M. Lohman and L.B. Overman, J. Biological Chemistry (1985) 260, 3594-3603. [PDF]
"A Model for the Irreversible Dissociation Kinetics of Cooperatively Bound Protein-Nucleic Acid Complexes", T.M. Lohman, Biopolymers22, 1697-1713.
"Kinetics and Mechanism of the Association on of the Bacteriophage T4 Gene 32 (Helix Destabilizing) Protein with Single Stranded Nucleic Acids.
Evidence for Protein Translocation", T.M. Lohman and S.C. Kowalczykowski, Journal of Molecular Biology (1981) 152, 67-109.
"The Kinetics and Mechanism of Dissociation of Cooperatively Bound T4 Gene32 Protein-Single Stranded Nucleic Acid Complexes. I. Irreversible
Dissociation Induced by NaCl Concentration Jumps", T.M. Lohman, Biochemistry (1984) 23, 4656-4665.
"The Kinetics and Mechanism of Dissociation of Cooperatively BoundT4 Gene 32 Protein-Single Stranded Nucleic Acid Complexes. II. Changes in Mechanism as a Function of [NaCl] and other Solution Variables", T.M. Lohman, Biochemistry (1984) 23, 4665-4675.
Thermodynamics and Kinetics of Charged Ligand-Nucleic Acid Interactions and Nucleic Acid Conformational Transitions
Reviews:
"Thermodynamics of Ligand-Nucleic Acid Interactions", T.M. Lohman and D.P. Mascotti, Methods in Enzymology (1992) 212, 400-424, J. E. Dahlberg and D. M. J. Lilley, eds.
"Non-specific Ligand-DNA Equilibrium Binding Parameters Determined by Fluorescence Methods", T.M. Lohman and D.P. Mascotti, Methods in Enzymology (1992) 212, 424-458, J. E. Dahlberg and J. Lilley, eds.
"Thermodynamic Methods for the Model-Independent Determination of Equilibrium Binding Isotherms for Protein-DNA Interactions, Using Spectroscopic Approaches to Monitor Binding", T.M. Lohman and W. Bujalowski, Methods in Enzymology (1991) 208, 258-290, R.T. Sauer, ed.
"Kinetics of Protein-Nucleic Acid Interactions: Use of Salt Effects to Probe Mechanisms of Interaction", T.M. Lohman, CRC Critical Reviews in Biochemistry (1986) 19, 191-245.
"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", M.T. Record, Jr., C.F. Anderson and T.M. Lohman, Quarterly Reviews of Biophysics (1978) 11, 103-178.
Selected Publications:
“Probing Single Stranded DNA Conformational Flexibility Using Fluorescence Spectroscopy”, M.C. Murphy, I. Rasnik, W. Cheng, T.M. Lohman & T. Ha (2004) Biophysical Journal 86, 2530-2537.
"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", W. Zhang, H. Ni, M.W. Capp, C.F. Anderson, T.M. Lohman, M.T. Record, Jr., Biophysical J. (1999) 76, 1008-1017.
"Thermodynamics of Oligoarginines Binding to RNA and DNA", D.P. Mascotti and T.M. Lohman, Biochemistry (1997) 36, 7272-7279.[PDF]
"Large Electrostatic Differences in the Binding Energetics of a Cationic Peptide toOligomeric and Polymeric DNA", W. Zhang, J.P. Bond, C.F. Anderson, T.M. Lohman and M.T. Record, Jr., P.N.A.S., U.S.A.,(1996) 93, 2511-2516. [PDF]
"Thermodynamics of Charged Oligopeptide-Heparin Interactions", D.P. Mascotti and T.M. Lohman, Biochemistry (1995) 34, 2908-2915. [PDF]
"Thermodynamics of Single Stranded RNA and DNA Interactions with Oligolysines Containing Tryptophan. Effects of Base Composition", D.P. Mascotti and T.M. Lohman, Biochemistry (1993) 32, 10568-10579. [PDF]
"Thermodynamics of Single Stranded RNA Binding to Oligolysines Containing Tryptophan", D. P. Mascotti and T.M. Lohman, Biochemistry (1992) 31, 8932-8946. [PDF]
"Thermodynamic Extent of Counterion Release Upon Binding Oligolysines to Single Stranded Nucleic Acids", D. P. Mascotti and T. M. Lohman, Proc. Natl. Acad. Sci., U.S.A. (1990) 87, 3142-3146.
"Use of Difference Boundary Sedimentation Velocity to Investigate Non-specific Protein-Nucleic Acid Interactions", T. M. Lohman, C. G. Wensley, J. Cina, R. R. Burgess and M. T. Record, Jr., Biochemistry (1980) 19, 3516-3522.
"Pentalysine-DNA Interactions: A Model for the General Effects of Ion Concentrations on the Interactions of Proteins with Nucleic Acids", T. M. Lohman, P. L. de Haseth and M. T. Record, Jr., Biochemistry (1980) 19, 3522-3530.
"Nonspecfic Interactions of E. coli RNA Polymerase with Native and Denatured DNA: Differences in the Binding Behavior of Core and Holoenzyme" P. L. de Haseth, T. M. Lohman, R. R. Burgess and M. T. Record, Jr., Biochemistry (1978) 17, 1612-1622.
"An Analysis of Ion Concentration Effects on the Kinetics of Protein-Nucleic Acid Interactions: Application to lac Repressor-Operator Interactions", T. M. Lohman, P. L. de Haseth and M. T. Record, Jr., Biophysical Chemistry (1978) 8, 281-294.
"A Semi-empirical Extension of Polyelectrolyte Theory to the Treatment of Oligo-electrolytes", M. T. Record, Jr. and T. M. Lohman, Biopolymers (1978) 17, 159-166.
"Interpretation of Monovalent and Divalent Ion Effects on the Binding of lac-Repressor to Operator", M. T. Record, Jr., P. L. de Haseth and T. M. Lohman, Biochemistry (1977) 16, 4791-4796.
"The Nonspecific Binding of lac-Repressor to DNA. An Association Reaction Driven by Counterion Release", P. L. de Haseth, T. M. Lohman and M.T. Record, Jr., Biochemistry (1977) 16, 4783-4790.
"Ion Effects on Ligand-Nucleic Acid Interactions", M. T. Record, Jr., T. M. Lohman and P. de Haseth, Journal of Molecular Biology (1976) 107, 145-158.
"Ion Effects on Ligand-Nucleic Acid Interactions", M. T. Record, Jr., T. M. Lohman and P. de Haseth, Journal of Molecular Biology (1976) 107, 145-158.
"Deactivation of Electronically Excited Thallium, Tl(6p2P3/2), in Collisions with Small Molecules", P. D. Foo, T. Lohman, J. Podolske and J. R. Wiesenfeld, Journal of Physical Chemistry (1975) 79, 414-418.