Publications
Synergistic Coordination of Chromatin Torsional Mechanics and Topoisomerase Activity
The material properties of eukaryotic chromatin fibers partition supercoiling ahead of progressing replication forks, illustrating that chromatin provides a buffer against torsional stress and that its unique mechanical properties help to facilitate replication and minimize genome instability. © 2019 Elsevier Inc. DNA replication in eukaryotes generates DNA supercoiling, which may intertwine (braid) daughter chromatin fibers to form precatenanes, posing topological challenges during chromosome segregation. The mechanisms that limit precatenane formation remain unclear.
High Trap Stiffness Microcylinders for Nanophotonic Trapping
Nanophotonic waveguides have enabled on-chip optical trap arrays for high-throughput manipulation and measurements. However, the realization of the full potential of these devices requires trapping enhancement for applications that need large trapping force. Here, we demonstrate a solution via fabrication of high refractive index cylindrical trapping particles.
Transcription factor regulation of RNA polymerase’s torque generation capacity
During transcription, RNA polymerase (RNAP) supercoils DNA as it translocates. The resulting torsional stress in DNA can accumulate and, in the absence of regulatory mechanisms, becomes a barrier to RNAP elongation, causing RNAP stalling, backtracking, and transcriptional arrest. Here we investigate whether and how a transcription factor may regulate both torque-induced Escherichia coli RNAP stalling and the torque generation capacity of RNAP.
High-Performance Image-Based Measurements of Biological Forces and Interactions in a Dual Optical Trap
Optical traps enable the nanoscale manipulation of individual biomolecules while measuring molecular forces and lengths. This ability relies on the sensitive detection of optically trapped particles, typically accomplished using laser-based interferometric methods. Recently, image-based particle tracking techniques have garnered increased interest as a potential alternative to laser-based detection; however, successful integration of image-based methods into optical trapping instruments for biophysical applications and force measurements has remained elusive.
Optical Tweezers: A Force to Be Reckoned With
The 2018 Nobel Prize in Physics has been awarded jointly to Arthur Ashkin for the discovery and development of optical tweezers and their applications to biological systems and to Gérard Mourou and Donna Strickland for the invention of laser chirped pulse amplification. Here we focus on Arthur Ashkin and how his revolutionary work opened a window into the world of molecular mechanics and spurred the rise of single-molecule biophysics.
Molecular Highways—Navigating Collisions of DNA Motor Proteins
Fundamental biological processes require concurrent sharing of DNA by numerous motor proteins and complexes. Thus, collision, congestion, and roadblocks are inescapable on these busy “molecular highways.†The consequences of these traffic problems are diverse, resulting in complex cellular mechanisms to resolve threats to genome stability and ensure cellular viability. Here, we review the different types of events and the diverse consequences that an RNA polymerase may encounter during transcription.
Helicase promotes replication re-initiation from an RNA transcript
To ensure accurate DNA replication, a replisome must effectively overcome numerous obstacles on its DNA substrate. After encountering an obstacle, a progressing replisome often aborts DNA synthesis but continues to unwind. However, little is known about how DNA synthesis is resumed downstream of an obstacle. Here, we examine the consequences of a non-replicating replisome collision with a co-directional RNA polymerase (RNAP). Using single-molecule and ensemble methods, we find that T7 helicase interacts strongly with a non-replicating T7 DNA polymerase (DNAP) at a replication fork.
Erratum: Mfd Dynamically Regulates Transcription via a Release and Catch-Up Mechanism (Cell (2018) 172(1-2) (344–357.e15)(S0092867417313648)(10.1016/j.cell.2017.11.017))
(Cell 172, 344–357.e1–e7; January 11, 2018) Our paper reported a mechanism where E. coli transcription-coupled repair factor Mfd utilizes DNA translocation to dynamically regulate transcription. We have identified three minor errors in the manuscript.
Mfd Dynamically Regulates Transcription via a Release and Catch-Up Mechanism
The bacterial Mfd ATPase is increasingly recognized as a general transcription factor that participates in the resolution of transcription conflicts with other processes/roadblocks. This function stems from Mfd's ability to preferentially act on stalled RNA polymerases (RNAPs). However, the mechanism underlying this preference and the subsequent coordination between Mfd and RNAP have remained elusive. Here, using a novel real-time translocase assay, we unexpectedly discovered that Mfd translocates autonomously on DNA.
Nanophotonic trapping: precise manipulation and measurement of biomolecular arrays
Optical trapping is a powerful and widely used laboratory technique in the biological and materials sciences that enables rapid manipulation and measurement at the nanometer scale. However, expanding the analytical throughput of this technique beyond the serial capabilities of established single-trap microscope-based optical tweezers remains a current goal in the field.