Replication stalling activates SSB for recruitment of DNA damage tolerance factors.

Translesion synthesis (TLS) polymerases bypass DNA lesions that block replicative polymerases, allowing cells to tolerate DNA damage encountered during replication. It is well known that most bacterial TLS polymerases must interact with the sliding-clamp processivity factor to carry out TLS, but recent work in has revealed that single-stranded DNA-binding protein (SSB) plays a key role in enriching the TLS polymerase Pol IV at stalled replication forks in the presence of DNA damage. It remains unclear how this interaction with SSB enriches Pol IV in a stalling-dependent manner given that SSB is always present at the replication fork.

Compartmentalization of the replication fork by single-stranded DNA-binding protein regulates translesion synthesis.

Processivity clamps tether DNA polymerases to DNA, allowing their access to the primer-template junction. In addition to DNA replication, DNA polymerases also participate in various genome maintenance activities, including translesion synthesis (TLS). However, owing to the error-prone nature of TLS polymerases, their association with clamps must be tightly regulated.

XLF acts as a flexible connector during non-homologous end joining.

Non-homologous end joining (NHEJ) is the predominant pathway that repairs DNA double-strand breaks in vertebrates. During NHEJ DNA ends are held together by a multi-protein synaptic complex until they are ligated. Here, we use egg extract to investigate the role of the intrinsically disordered C-terminal tail of the XRCC4-like factor (XLF), a critical factor in end synapsis.

Quantifying the Contribution of Habitats and Pathways to a Spatially Structured Population Facing Environmental Change.

The consequences of environmental disturbance and management are difficult to quantify for spatially structured populations because changes in one location carry through to other areas as a result of species movement. We develop a metric, , for measuring the contribution of a habitat or pathway to network-wide population growth rate in the face of environmental change. This metric is different from other contribution metrics, as it quantifies effects of modifying vital rates for habitats and pathways in perturbation experiments.

The Role of Noncognate Sites in the 1D Search Mechanism of EcoRI.

A one-dimensional (1D) search is an essential step in DNA target recognition. Theoretical studies have suggested that the sequence dependence of 1D diffusion can help resolve the competing demands of a fast search and high target affinity, a conflict known as the speed-selectivity paradox. The resolution requires that the diffusion energy landscape is correlated with the underlying specific binding energies.

Analyzing dwell times with the Generalized Method of Moments.

The Generalized Method of Moments (GMM) is a statistical method for the analysis of samples from random processes. First developed for the analysis of econometric data, the method is here formulated to extract hidden kinetic parameters from measurements of single molecule dwell times. Our method is based on the analysis of cumulants of the measured dwell times.