Douglas E Smith - Publications

Affiliations: 
University of California, San Diego, La Jolla, CA 
Area:
Biophysics, Polymer Physics

33 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Ordyan M, Alam I, Mahalingam M, Rao VB, Smith DE. Nucleotide-dependent DNA gripping and an end-clamp mechanism regulate the bacteriophage T4 viral packaging motor. Nature Communications. 9: 5434. PMID 30575768 DOI: 10.1038/s41467-018-07834-2  0.76
2018 Ortiz D, delToro D, Ordyan M, Pajak J, Sippy J, Catala A, Oh CS, Vu A, Arya G, Feiss M, Smith DE, Catalano CE. Evidence that a catalytic glutamate and an 'Arginine Toggle' act in concert to mediate ATP hydrolysis and mechanochemical coupling in a viral DNA packaging motor. Nucleic Acids Research. PMID 30541105 DOI: 10.1093/nar/gky1217  1
2018 Keller N, delToro DJ, Smith DE. Single-Molecule Measurements of Motor-Driven Viral DNA Packaging in Bacteriophages Phi29, Lambda, and T4 with Optical Tweezers. Methods in Molecular Biology (Clifton, N.J.). 1805: 393-422. PMID 29971729 DOI: 10.1007/978-1-4939-8556-2_20  1
2018 delToro DJ, Smith DE. Measuring Unzipping and Rezipping of Single Long DNA Molecules with Optical Tweezers. Methods in Molecular Biology (Clifton, N.J.). 1805: 371-392. PMID 29971728 DOI: 10.1007/978-1-4939-8556-2_19  1
2017 Keller N, Berndsen ZT, Jardine PJ, Smith DE. Experimental comparison of forces resisting viral DNA packaging and driving DNA ejection. Physical Review. E. 95: 052408. PMID 28618627 DOI: 10.1103/PhysRevE.95.052408  1
2016 Keller N, Grimes S, Jardine PJ, Smith DE. Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging. Nature Physics. 12: 757-761. PMID 27540410 DOI: 10.1038/nphys3740  1
2016 delToro D, Ortiz D, Ordyan M, Sippy J, Oh CS, Keller N, Feiss M, Catalano CE, Smith D. Walker-A motif acts to coordinate ATP hydrolysis with motor output in viral DNA packaging. Journal of Molecular Biology. PMID 27139643 DOI: 10.1016/j.jmb.2016.04.029  1
2015 Berndsen ZT, Keller N, Smith DE. Continuous allosteric regulation of a viral packaging motor by a sensor that detects the density and conformation of packaged DNA. Biophysical Journal. 108: 315-24. PMID 25606680 DOI: 10.1016/j.bpj.2014.11.3469  1
2014 delToro D, Smith DE. Accurate measurement of force and displacement with optical tweezers using DNA molecules as metrology standards. Applied Physics Letters. 104: 143701. PMID 25316922 DOI: 10.1063/1.4871005  1
2014 Migliori AD, Smith DE, Arya G. Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor. Journal of Molecular Biology. 426: 4002-17. PMID 25311860 DOI: 10.1016/j.jmb.2014.09.023  1
2014 Keller N, delToro D, Grimes S, Jardine PJ, Smith DE. Repulsive DNA-DNA interactions accelerate viral DNA packaging in phage Phi29. Physical Review Letters. 112: 248101. PMID 24996111 DOI: 10.1103/PhysRevLett.112.248101  1
2014 Migliori AD, Keller N, Alam TI, Mahalingam M, Rao VB, Arya G, Smith DE. Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor. Nature Communications. 5: 4173. PMID 24937091 DOI: 10.1038/ncomms5173  1
2014 Berndsen ZT, Keller N, Grimes S, Jardine PJ, Smith DE. Nonequilibrium dynamics and ultraslow relaxation of confined DNA during viral packaging. Proceedings of the National Academy of Sciences of the United States of America. 111: 8345-50. PMID 24912187 DOI: 10.1073/pnas.1405109111  1
2012 Chemla YR, Smith DE. Single-molecule studies of viral DNA packaging. Advances in Experimental Medicine and Biology. 726: 549-84. PMID 22297530 DOI: 10.1007/978-1-4614-0980-9_24  1
2011 Torigoe SE, Urwin DL, Ishii H, Smith DE, Kadonaga JT. Identification of a rapidly formed nonnucleosomal histone-DNA intermediate that is converted into chromatin by ACF. Molecular Cell. 43: 638-48. PMID 21855802 DOI: 10.1016/j.molcel.2011.07.017  1
2010 Tsay JM, Sippy J, DelToro D, Andrews BT, Draper B, Rao V, Catalano CE, Feiss M, Smith DE. Mutations altering a structurally conserved loop-helix-loop region of a viral packaging motor change DNA translocation velocity and processivity. The Journal of Biological Chemistry. 285: 24282-9. PMID 20525695 DOI: 10.1074/jbc.M110.129395  1
2010 Meluzzi D, Smith DE, Arya G. Biophysics of knotting. Annual Review of Biophysics. 39: 349-66. PMID 20192771 DOI: 10.1146/annurev.biophys.093008.131412  1
2009 Tsay JM, Sippy J, Feiss M, Smith DE. The Q motif of a viral packaging motor governs its force generation and communicates ATP recognition to DNA interaction. Proceedings of the National Academy of Sciences of the United States of America. 106: 14355-60. PMID 19706522 DOI: 10.1073/pnas.0904364106  1
2008 Rickgauer JP, Fuller DN, Grimes S, Jardine PJ, Anderson DL, Smith DE. Portal motor velocity and internal force resisting viral DNA packaging in bacteriophage phi29. Biophysical Journal. 94: 159-67. PMID 17827233 DOI: 10.1529/biophysj.107.104612  1
2007 Fuller DN, Raymer DM, Kottadiel VI, Rao VB, Smith DE. Single phage T4 DNA packaging motors exhibit large force generation, high velocity, and dynamic variability. Proceedings of the National Academy of Sciences of the United States of America. 104: 16868-73. PMID 17942694 DOI: 10.1073/pnas.0704008104  1
2007 Robertson RM, Smith DE. Direct measurement of the intermolecular forces confining a single molecule in an entangled polymer solution. Physical Review Letters. 99: 126001. PMID 17930521 DOI: 10.1103/PhysRevLett.99.126001  1
2007 Fuller DN, Raymer DM, Rickgauer JP, Robertson RM, Catalano CE, Anderson DL, Grimes S, Smith DE. Measurements of single DNA molecule packaging dynamics in bacteriophage lambda reveal high forces, high motor processivity, and capsid transformations. Journal of Molecular Biology. 373: 1113-22. PMID 17919653 DOI: 10.1016/j.jmb.2007.09.011  1
2007 Raymer DM, Smith DE. Spontaneous knotting of an agitated string. Proceedings of the National Academy of Sciences of the United States of America. 104: 16432-7. PMID 17911269 DOI: 10.1073/pnas.0611320104  1
2007 Fuller DN, Rickgauer JP, Jardine PJ, Grimes S, Anderson DL, Smith DE. Ionic effects on viral DNA packaging and portal motor function in bacteriophage phi 29. Proceedings of the National Academy of Sciences of the United States of America. 104: 11245-50. PMID 17556543 DOI: 10.1073/pnas.0701323104  1
2007 Robertson RM, Smith DE. Strong effects of molecular topology on diffusion of entangled DNA molecules. Proceedings of the National Academy of Sciences of the United States of America. 104: 4824-7. PMID 17360350 DOI: 10.1073/pnas.0700137104  1
2007 Raymer DM, Smith DE. A simple system for staining protein and nucleic acid electrophoresis gels. Electrophoresis. 28: 746-8. PMID 17265540 DOI: 10.1002/elps.200600325  1
2006 Gemmen GJ, Millin R, Smith DE. Dynamics of single DNA looping and cleavage by Sau3AI and effect of tension applied to the DNA. Biophysical Journal. 91: 4154-65. PMID 16963513 DOI: 10.1529/biophysj.106.088518  1
2006 Rickgauer JP, Fuller DN, Smith DE. DNA as a metrology standard for length and force measurements with optical tweezers. Biophysical Journal. 91: 4253-7. PMID 16963512 DOI: 10.1529/biophysj.106.089524  1
2006 Gemmen GJ, Millin R, Smith DE. Tension-dependent DNA cleavage by restriction endonucleases: two-site enzymes are "switched off" at low force. Proceedings of the National Academy of Sciences of the United States of America. 103: 11555-60. PMID 16868081 DOI: 10.1073/pnas.0604463103  1
2006 Gemmen GJ, Millin R, Smith DE. DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force. Nucleic Acids Research. 34: 2864-77. PMID 16723432 DOI: 10.1093/nar/gkl382  1
2006 Robertson RM, Laib S, Smith DE. Diffusion of isolated DNA molecules: dependence on length and topology. Proceedings of the National Academy of Sciences of the United States of America. 103: 7310-4. PMID 16648255 DOI: 10.1073/pnas.0601903103  1
2006 Fuller DN, Gemmen GJ, Rickgauer JP, Dupont A, Millin R, Recouvreux P, Smith DE. A general method for manipulating DNA sequences from any organism with optical tweezers. Nucleic Acids Research. 34: e15. PMID 16452295 DOI: 10.1093/nar/gnj016  1
2005 Gemmen GJ, Sim R, Haushalter KA, Ke PC, Kadonaga JT, Smith DE. Forced unraveling of nucleosomes assembled on heterogeneous DNA using core histones, NAP-1, and ACF. Journal of Molecular Biology. 351: 89-99. PMID 16002089 DOI: 10.1016/j.jmb.2005.05.058  1
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