Prof. Douglas E. Smith Profile

Prof. Douglas E. Smith

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Publications (19)

Proceedings Article | 4 August 2021 Poster

Solution exchange techniques applied to optical tweezers studies of viral DNA packaging

Brandon Rawson, Mariam Ordyan, Douglas Smith

Proceedings Volume 11798, 117982G (2021) https://doi.org/10.1117/12.2595468

KEYWORDS: Packaging, Optical tweezers, Microfluidics, Acquisition tracking and pointing, Molecules, Diffusion

Proceedings Article | 4 August 2021 Poster

Determining trap compliances, microsphere size variations, and response linearities in single DNA molecule elasticity measurements with optical tweezers

Mounir Fizari, Youbin Mo, Kristina Koharchik, Douglas Smith

Proceedings Volume 11798, 117982F (2021) https://doi.org/10.1117/12.2595172

KEYWORDS: Packaging, Viruses, Optical tweezers, Optical testing, Magnesium, Ions, Acquisition tracking and pointing

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Proceedings Article | 1 August 2021 Presentation

Function of a viral genome packaging motor from bacteriophage T4 is insensitive to DNA sequence

Douglas Smith, Youbin Mo, Nick Keller, Damian delToro, Neeti Ananthaswamy, Venigalla Rao, Stephen Harvey

Proceedings Volume 11798, 1179803 (2021) https://doi.org/10.1117/12.2595386

KEYWORDS: Packaging, Viruses, Stochastic processes, Optical tweezers, Optical testing, Modulation

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Proceedings Article | 20 August 2020 Presentation

Restricted mobility of DNA packaged in phage phi29 viral proheads assessed by single-molecule optical tweezers measurements of DNA exit

Mounir Fizari, Nicholas Keller, Douglas Smith

Proceedings Volume 11463, 1146303 (2020) https://doi.org/10.1117/12.2570185

KEYWORDS: Optical tweezers, Optical testing, Packaging, Viruses, Acquisition tracking and pointing, Luminescence

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Proceedings Article | 12 September 2013 Paper

Evidence for non-equilibrium dynamics in viral DNA packaging from optical tweezers measurements

Zachary Berndsen, Nicholas Keller, Douglas Smith

Proceedings Volume 8810, 881033 (2013) https://doi.org/10.1117/12.2027187

KEYWORDS: Packaging, Polymers, Optical tweezers, Molecules, Optical testing, Viruses, Physics, Proteins, Resistance, Acquisition tracking and pointing

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Proceedings Article | 12 September 2013 Paper

Testing a structural model for viral DNA packaging motor function by optical tweezers measurements, site directed mutagenesis, and molecular dynamics calculations

Nicholas Keller, Amy Migliori, Gaurav Arya, Venigalla Rao, Douglas Smith

Proceedings Volume 8810, 881032 (2013) https://doi.org/10.1117/12.2027158

KEYWORDS: Packaging, Optical tweezers, X-rays, Optical testing, Proteins, Crystallography, Interfaces, Acquisition tracking and pointing, Viruses, Molecules

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Proceedings Article | 12 September 2013 Paper

Direct measurement of formation of loops in DNA by a human tumor suppressor protein

Amy Migliori, Samuel Kung, Danielle Wang, Douglas Smith

Proceedings Volume 8810, 881030 (2013) https://doi.org/10.1117/12.2027153

KEYWORDS: Proteins, Optical tweezers, Tumors, Systems modeling, Cancer, Optical testing, Mechanics, Cell death, Collagen, Nickel

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Proceedings Article | 10 October 2012 Paper

Experimental and computational studies on the DNA translocation mechanism of the T4 viral packaging motor

Amy Migliori, Gaurav Arya, Douglas Smith

Proceedings Volume 8458, 84582N (2012) https://doi.org/10.1117/12.930390

KEYWORDS: Packaging, Ions, Proteins, Optical tweezers, Molecules, Acquisition tracking and pointing, X-rays, Crystals, Velocity measurements, Sun

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Bacteriophage T4 is a double stranded DNA virus that infects E.coli by injecting the viral genome through the cellular wall of a host cell. The T4 genome must be ejected from the viral capsid with sufficient force to ensure infection. To generate high ejection forces, the genome is packaged to high density within the viral capsid. A DNA translocation motor, in which the protein gp17 hydrolyzes ATP and binds to the DNA, is responsible for translocating the genome into the capsid during viral maturation of T4. This motor generates forces in excess of 60 pN and packages DNA at rates exceeding 2000 base pairs/second (bp/s)¹. Understanding these small yet powerful motors is important, as they have many potential applications. Though much is known about the activity of these motors from bulk and single molecule biophysical techniques, little is known about their detailed molecular mechanism. Recently, two structures of gp17 have been obtained: a high-resolution X-ray crystallographic structure showing a monomeric compacted form of the enzyme, and a cryo-electron microscopic structure of the extended form of gp17 in complex with actively packaging prohead complexes. Comparison of these two structures indicates several key differences, and a model has been proposed to explain the translocation action of the motor². Key to this model are a set of residues forming ion pairs across two domains of the gp17 molecule that are proposed to be involved in force generation by causing the collapse of the extended form of gp17. Using a dual optical trap to measure the rates of DNA packaging and the generated forces, we present preliminary mutational data showing that these several of these ion pairs are important to motor function. We have also performed preliminary free energy calculations on the extended and collapsed state of gp17, to confirm that these interdomain ion pairs have large contributions to the change in free energy that occurs upon the collapse of gp17 during the proposed ratcheting mechanism.

Proceedings Article | 10 October 2012 Paper

Mechanism of termination of bacteriophage DNA packaging investigated with optical tweezers

Damian delToro, Douglas Smith

Proceedings Volume 8458, 84582O (2012) https://doi.org/10.1117/12.930425

KEYWORDS: Packaging, Optical tweezers, Acquisition tracking and pointing, Viruses, Proteins, Switches, Particles, Sensors, Molecules, Physics

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Proceedings Article | 10 October 2012 Paper

Single-molecule studies of the effect of spermidine on DNA mechanics and viral DNA packaging

Nicholas Keller, Douglas Smith

Proceedings Volume 8458, 845818 (2012) https://doi.org/10.1117/12.930381

KEYWORDS: Packaging, Molecules, Optical tweezers, Ions, Mechanics, In vitro testing, Acquisition tracking and pointing, Viruses, Sodium, Optical testing

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Proceedings Article | 29 August 2008 Paper

Mechanism of a viral DNA packaging motor studied by characterization of biochemical mutants via optical tweezers measurements

James Tsay, Jean Sippy, Michael Feiss, Douglas Smith

Proceedings Volume 7038, 703806 (2008) https://doi.org/10.1117/12.797139

KEYWORDS: Packaging, Optical tweezers, Optical testing, Acquisition tracking and pointing, Velocity measurements, Proteins, Molecules, Magnesium, Physics, Lanthanum

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Proceedings Article | 10 September 2007 Paper

Studies of viral DNA packaging motors with optical tweezers: a comparison of motor function in bacteriophages phi29, lambda, and T4

Douglas Smith, Derek Fuller, Dorian Raymer, Peter Rickgauer, Shelley Grimes, Paul Jardine, Dwight Anderson, Carlos Catalano, Vishal Kottadiel, Venigalla Rao

Proceedings Volume 6644, 664404 (2007) https://doi.org/10.1117/12.739629

KEYWORDS: Packaging, Optical tweezers, Proteins, Viruses, Molecules, Acquisition tracking and pointing, Systems modeling, Velocity measurements, Molecular biology, Molecular assembly

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Proceedings Article | 5 September 2007 Paper

Direct measurement of the intermolecular forces confining a single entangled DNA molecule

Rae Robertson, Douglas Smith

Proceedings Volume 6644, 66440C (2007) https://doi.org/10.1117/12.739632

KEYWORDS: Molecules, Polymers, Optical tweezers, Data modeling, Motion models, Time metrology, Linear filtering, Data integration, Solids, Physics

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Proceedings Article | 4 October 2006 Paper

Dependence of bacteriophage ø29 DNA packaging on ionic conditions studied by optical tweezers manipulation of single DNA molecules

Derek Fuller, John Rickgauer, Shelley Grimes, Paul Jardine, Dwight Anderson, Douglas Smith

Proceedings Volume 6326, 632622 (2006) https://doi.org/10.1117/12.682097

KEYWORDS: Packaging, Optical tweezers, Magnesium, Sodium, Molecules, Modulation, Proteins, Diamond, Cobalt, Ions

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Proceedings Article | 14 September 2006 Paper

DNA looping and cleavage by restriction enzymes studied by manipulation of single DNA molecules with optical tweezers

Douglas Smith, Gregory Gemmen, Rachel Millin

Proceedings Volume 6326, 632625 (2006) https://doi.org/10.1117/12.681504

KEYWORDS: Molecules, Proteins, Optical tweezers, Calcium, Magnesium, Mechanics, Electron microscopy, Optical testing, Data modeling, Particles

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Proceedings Article | 11 September 2006 Paper

Calibration and performance of dual-beam force-measuring optical tweezers

John Rickgauer, Derek Fuller, Douglas Smith

Proceedings Volume 6326, 632624 (2006) https://doi.org/10.1117/12.681509

KEYWORDS: Calibration, Molecules, Optical tweezers, Metrology, Biophysics, Computer simulations, Standards development, Biological research, Sensors, Signal detection

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Proceedings Article | 11 September 2006 Paper

Initiation of bacteriophage ø29 DNA packaging studied by optical tweezers manipulation of single DNA molecules

John Peter Rickgauer, Derek Fuller, Bo Hu, Shelley Grimes, Paul Jardine, Dwight Anderson, Douglas Smith

Proceedings Volume 6326, 632623 (2006) https://doi.org/10.1117/12.682101

KEYWORDS: Packaging, Proteins, Molecules, Optical tweezers, Viruses, Connectors, Molecular assembly, Electron microscopy, Optical testing, Acousto-optics

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Proceedings Article | 27 August 2005 Paper

A general method for manipulating DNA sequences from any organism with optical tweezers

Derek Fuller, Gregory Gemmen, John Peter Rickgauer, Aurelie DuPont, Rachel Millin, Pierre Recouvreux, Allen Schweitzer, Douglas Smith

Proceedings Volume 5930, 593013 (2005) https://doi.org/10.1117/12.618068

KEYWORDS: Optical tweezers, Molecules, Organisms, Proteins, Data modeling, Microfluidics, Optical testing, Time metrology, Blood, Manufacturing

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Proceedings Article | 19 August 2005 Paper

Using optical tweezers to study protein-DNA interactions

Douglas Smith, Gregory Gemmen, Rachel Millin, John Rickgauer, Allan Schweitzer, Derek Fuller

Proceedings Volume 5930, 593012 (2005) https://doi.org/10.1117/12.618038

KEYWORDS: Optical tweezers, Molecules, Proteins, Polymers, Resistance, Molecular interactions, Magnesium, Mechanics, Modulation, Distance measurement

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Showing 5 of 19 publications

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