First-passage problems in DNA replication: effects of template tension on stepping and exonuclease activities of a DNA polymerase motor

Understanding the Target Search by Multiple Transcription Factors on Nucleosomal DNA

The association of multiple Transcription Factors (TFs) in the cis-regulatory region is imperative for developmental changes in eukaryotes. The underlying process is exceedingly complex, and it is not at all clear what orchestrates the overall search process by multiple TFs. In this study, by developing a theoretical model based on a discrete-state stochastic approach, we investigated the target search mechanism of multiple TFs on nucleosomal DNA. Experimental kinetic rate constants of different TFs are taken as input to estimate the Mean-First-Passage time to recognize the binding motifs by two TFs on a dynamic nucleosome model. The theory systematically analyzes when the TFs search their binding motifs hierarchically and when simultaneously by proceeding via the formation of a protein-protein complex. Our results, validated by extensive Monte Carlo simulations, elucidate the molecular basis of the complex target search phenomenon of multiple TFs on nucleosomal DNA.

Template-specific fidelity of DNA replication with high-order neighbor effects: A first-passage approach

DNA replication fidelity is a critical issue in molecular biology. Biochemical experiments have provided key insights on the mechanism of fidelity control by DNA polymerases in the past decades, whereas systematic theoretical studies on this issue began only recently. Because of the underlying difficulties of mathematical treatment, comprehensive surveys on the template-specific replication kinetics are still rare. Here we propose a first-passage approach to address this problem, in particular the positional fidelity, for complicated processes with high-order neighbor effects. Under biologically relevant conditions, we derived approximate analytical expressions of the positional fidelity which show intuitively how some key kinetic pathways are coordinated to guarantee the high fidelity, as well as the high velocity, of the replication processes. It is also shown that the fidelity at any template position is dominantly determined by the nearest-neighbor template sequences, which is consistent with the idea that replication mutations are randomly distributed in the genome.