Single molecule studies of molecular motor driven viral DNA packaging

Friday, February 24, 2017 -
2:00pm to 3:00pm
The FUNG Auditorium
Douglas E. Smith


Department of Physics

University of California, San Diego

Single molecule studies of molecular motor driven viral DNA packaging


Many dsDNA viruses employ an ATP powered motor during assembly to package their genomes into preassembled capsid shells. Remarkably, these motors generate >20´ higher force than the skeletal muscle myosin motor. Understanding this process requires the elucidation of both the motor mechanism and complex physics governing tight DNA packaging, which is energetically unfavorable. We use optical tweezers to directly measure the packaging of single DNA molecules into single virus capsids. Our recent studies have shown that the confined DNA undergoes nonequilibrium (glassy) dynamics with a very long relaxation time, causing slowing and pausing of the motor and heterogeneous dynamics. Contrary to theoretical predictions, we find that attractive DNA‐self interactions mediated by polyamine cations are inhibitory to packaging. Our studies suggest that in this condition the DNA undergoes a nonequilibrium jamming transition analogous to that occurring in many colloidal and granular materials. Paradoxically, repulsive DNA-self interactions facilitate faster packaging. We found that packaging rate is regulated not only by load force on the motor but also by a novel allosteric mechanism wherein ATP binding and motor pausing is regulated in response to changes in the density and conformation of the packaged DNA. We have also used site-directed mutagenesis to gain insights on the motor mechanism and which regions of the motor protein are involved in force generation, ATP binding, and catalysis of ATP hydrolysis.


BA, Physics, University of Chicago; PhD, Applied Physics, Stanford University, 1999 (Advisor: Prof. Steve Chu); Postdoc, Biophysics, UC Berkeley, 1999-2001. Research areas: Viral DNA Packaging, Molecular Motors, Chromatin assembly, Protein-mediated DNA looping, DNA unzipping, knot formation. Techniques: Optical tweezers, fluorescence microscopy, molecular biology/biochemistry. Awards:  BWF Career Award in Biomedical Science, Searle Scholar, Beckman Young Investigator, Sloan Fellowship. Research funded by NIH and NSF.