A. M. van Oijen

Fast Evolution of SOS-Independent Multi-Drug Resistance in Bacteria

This study shows that Escherichia coli lacking RecA rapidly develops beta-lactam resistance through an SOS-independent mechanism involving oxidative stress and DNA repair defects.

Spatiotemporal dynamics of single-stranded DNA intermediates in Escherichia coli

The paper uses fluorescence microscopy to study the spatiotemporal dynamics of single-stranded DNA in live E. coli cells, revealing patterns associated with DNA repair and replication.

Single-molecule visualization of stalled replication-fork rescue by the Escherichia coli Rep helicase

This study visualizes how the Escherichia coli Rep helicase rescues stalled replication forks by removing roadblocks, showing replication restart is the rate-limiting step.

Rapid single-molecule characterisation of nucleic-acid enzymes

This paper introduces a single-molecule assay to rapidly characterize DNA metabolism enzymes by measuring fluorescence intensity changes during DNA synthesis, unwinding, or digestion.

Defects in DNA double-strand break repair re-sensitise antibiotic-resistant Escherichia coli tomultiple bactericidal antibiotics

The paper identifies DNA double-strand break repair defects in antibiotic-resistant E. coli as a strategy to re-sensitize bacteria to multiple bactericidal antibiotics.

The E. coli helicase does not use ATP during replication.

The paper shows that the E. coli DnaB helicase does not use ATP during DNA replication, with polymerase-driven nucleotide incorporation providing the energy instead.

Mechanism of transcription modulation by the transcription-repair coupling factor

This study investigates how the bacterial TRCF Mfd modulates transcription by converting elongation complexes into catalytically poised states and then irreversibly terminating transcription through ATP hydrolysis.

Highly-parallel microfluidics-based force spectroscopy on single cytoskeletal motors

This paper introduces a microfluidics-based method to rapidly measure force-dependent motility parameters of kinesin-1 motors with improved throughput.

An α-cyanostilbene derivative for the enhanced detection and imaging of amyloid fibril aggregates

This paper introduces ASCP, a fluorescent probe with enhanced sensitivity and specificity for detecting amyloid fibrils and oligomeric intermediates compared to ThT.

Single-molecule live-cell imaging reveals parallel pathways of prokaryotic nucleotide excision repair

The paper uses live-cell imaging to compare UvrA kinetics in TCR-deficient and wild-type E. coli, showing UvrB governs UvrA residence times and UV-induced changes align with Mfd interactions.

Cooperative Chikungunya virus membrane fusion and its sub-stoichiometric inhibition by CHK-152 antibody

This study investigates how the CHK-152 antibody inhibits Chikungunya virus fusion by shielding virions and altering kinetic competition at lower pH.

A mechanism for the extension and unfolding of parallel telomeric G-quadruplexes by human telomerase at single-molecule resolution

This study uses single-molecule techniques to show that telomerase can extend and unfold parallel telomeric G-quadruplexes, revealing it acts as a resolvase.

Single-molecule fluorescence-based approach reveals novel mechanistic insights into small heat shock protein chaperone function

This study uses single-molecule fluorescence to reveal a two-step mechanism by which human Bc (HSPB5) interacts with misfolded proteins to prevent aggregation.

Identifying multiple kinetic populations of DNA binding proteins in live cells using single-molecule fluorescence imaging

This study analyzes the limitations of time-lapse single-molecule fluorescence imaging in measuring kinetic sub-populations of DNA-binding proteins and provides guidelines for reliable data collection and interpretation.

Modulation of DNA polymerase IV activity by UmuD and RecA* observed by single-molecule time-lapse microscopy

The paper shows UmuD and RecA modulate DNA polymerase IV binding to DNA substrates, with UmuD inhibiting and RecA promoting association, particularly in DNA-damaged cells.

Tunability of DNA polymerase stability during eukaryotic DNA replication

The paper shows how DNA polymerase stability and exchange dynamics in the yeast replisome are tuned by local concentrations, enabling efficient replication and adaptation to genomic challenges.

Single-molecule imaging reveals molecular coupling between transcription and DNA repair in live cells

The paper uses single-molecule imaging to study how transcription and DNA repair interact in live cells, showing that UvrB loading is tightly coupled to Mfd dissociation during repair.

Recycling of single-stranded DNA-binding protein by the bacterial replisome.

This study visualizes how the E. coli replisome recruits and recycles single-stranded DNA-binding protein using two mechanisms, showing their physiological relevance.

A Primase-Induced Conformational Switch Controls the Stability of the Bacterial Replisome

This study identifies a primase-induced conformational switch that enhances the stability of the bacterial replisome by strengthening the interaction between the polymerase holoenzyme and the replicative helicase.

Nuclease dead Cas9 is a programmable roadblock for DNA replication

The paper uses a modified Cas9 protein to create a programmable roadblock for studying DNA replication fork arrest in vitro and in vivo.

Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response

This study uses a fluorescent probe to track RecA dynamics in live E. coli, showing it is stored during normal metabolism and rapidly mobilizes to form SOS-signaling complexes upon DNA damage.