M. Depken

Quantitative parameters of bacterial RNA polymerase open-complex formation, stabilization and disruption on a consensus promoter

The paper quantifies the kinetics of bacterial RNA polymerase open-complex formation, stabilization, and disruption on a consensus promoter using single-molecule magnetic tweezers.

The nucleotide addition cycle of the SARS-CoV-2 polymerase

This study describes the mechanochemical behavior of the SARS-CoV-2 polymerase using magnetic tweezers, revealing three catalytic conformations and a thermal ratchet mechanism for nucleotide incorporation.

Accounting for RNA polymerase heterogeneity reveals state switching and two distinct long-lived backtrack states escaping through cleavage

The paper uses high-throughput magnetic tweezers to study E. coli RNA polymerase dynamics, identifying two long-lived backtrack pause states and showing RNA cleavage governs recovery from deep backtracks.

Inhibition of SARS-CoV-2 polymerase by nucleotide analogs: a single moleculeperspective

This study investigates how nucleotide analogs like Remdesivir affect SARS-CoV-2 polymerase activity using single-molecule techniques, revealing backtracking rather than termination and evasion of ddhCTP.

Skipping and sliding to optimize target search on protein-bound DNA and RNA

The paper shows that skipping and sliding motions allow searchers to maintain search speed on crowded nucleic-acid substrates, as demonstrated by analyzing human and bacterial Argonaute proteins.

A mechanistic model improves off-target predictions and reveals the physical basis of SpCas9 fidelity

This paper develops a mechanistic model to predict SpCas9 off-target activity and explains its structural basis for fidelity.

Temperature controlled high-throughput magnetic tweezers show striking difference in activation energies of replicating viral RNA-dependent RNA polymerases.

This study uses temperature-controlled magnetic tweezers to compare replication kinetics of RdRps from three RNA viruses, finding temperature-dependent activation differences.

Argonaute bypasses cellular obstacles without hindrance during target search

This study shows Argonaute proteins efficiently search for targets by gliding over secondary structures and bypassing protein barriers through lateral diffusion and intersegmental jumps.

Kinetic analysis methods applied to single motor protein trajectories

The paper introduces two new statistical methods to analyze single motor protein trajectories and extract kinetic parameters from both simulated and experimental data.

Pausing controls branching between productive and non-productive pathways during initial transcription

The paper investigates how RNA polymerase pausing controls transcriptional pathways in bacteria, showing that paused RNA synthesis directs RNAP to productive or abortive pathways.

Crowding-induced transcriptional bursts dictate nucleosome and polymerase density profiles along genes

The paper shows that crowding-induced polymerase interactions create pelotons, explaining nucleosome and polymerase density profiles and transcriptional bursts.