Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins

M Stracy, J Schweizer, DJ Sherratt, AN Kapanidis… - Molecular cell, 2021 - cell.com
Despite their diverse biochemical characteristics and functions, all DNA-binding proteins
share the ability to accurately locate their target sites among the vast excess of non-target …

Choosing the right label for single-molecule tracking in live bacteria: side-by-side comparison of photoactivatable fluorescent protein and Halo tag dyes

N Banaz, J Mäkelä, S Uphoff - Journal of physics D: Applied …, 2018 - iopscience.iop.org
Visualizing and quantifying molecular motion and interactions inside living cells provides
crucial insight into the mechanisms underlying cell function. This has been achieved by …

Recurrent mismatch binding by MutS mobile clamps on DNA localizes repair complexes nearby

P Hao, SJ LeBlanc, BC Case… - Proceedings of the …, 2020 - National Acad Sciences
DNA mismatch repair (MMR), the guardian of the genome, commences when MutS identifies
a mismatch and recruits MutL to nick the error-containing strand, allowing excision and DNA …

Novel organophosphorus aminopyrimidines as unique structural DNA-targeting membrane active inhibitors towards drug-resistant methicillin-resistant …

D Li, RRY Bheemanaboina, N Battini… - …, 2018 - pubs.rsc.org
A series of novel unique structural organophosphorus aminopyrimidines were developed as
potential DNA-targeting membrane active inhibitors through an efficient one-pot procedure …

[HTML][HTML] Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes

HL Klein, KKH Ang, MR Arkin, EC Beckwitt… - Microbial Cell, 2019 - ncbi.nlm.nih.gov
Genomes are constantly in flux, undergoing changes due to recombination, repair and
mutagenesis. In vivo, many of such changes are studies using reporters for specific types of …

Single-molecule studies of helicases and translocases in prokaryotic genome-maintenance pathways

KS Whinn, AM van Oijen, H Ghodke - DNA repair, 2021 - Elsevier
Helicases involved in genomic maintenance are a class of nucleic-acid dependent ATPases
that convert the energy of ATP hydrolysis into physical work to execute irreversible steps in …

Dimerization of iLID optogenetic proteins observed using 3D single-molecule tracking in live E. coli

AM Achimovich, T Yan, A Gahlmann - Biophysical Journal, 2023 - cell.com
Abstract 3D single-molecule tracking microscopy has enabled measurements of protein
diffusion in living cells, offering information about protein dynamics and cellular …

Super-resolution microscopy and tracking of DNA-binding proteins in bacterial cells

CJ Cassaro, S Uphoff - Chromosome Architecture: Methods and Protocols, 2022 - Springer
The ability to detect individual fluorescent molecules inside living cells has enabled a range
of powerful microscopy techniques that resolve biological processes on the molecular scale …

Identification of multiple kinetic populations of DNA-binding proteins in live cells

HN Ho, D Zalami, J Köhler, AM van Oijen, H Ghodke - Biophysical journal, 2019 - cell.com
Understanding how multiprotein complexes function in cells requires detailed quantitative
understanding of their association and dissociation kinetics. Analysis of the heterogeneity of …

Single-Molecule Fluorescence Imaging of DNA Replication Stalling at Sites of Nucleoprotein Complexes

KS Whinn, N Sharma, AM van Oijen… - Single Molecule Analysis …, 2023 - Springer
DNA replication in cells occurs on crowded and often damaged template DNA, forming
potentially deleterious roadblocks to the progressing replication fork. Numerous tools have …