DNA looping in prokaryotes: experimental and theoretical approaches

A Cournac, J Plumbridge - Journal of bacteriology, 2013 - Am Soc Microbiol
Transcriptional regulation is at the heart of biological functions such as adaptation to a
changing environment or to new carbon sources. One of the mechanisms which has been …

Copy‐out—Paste‐in Transposition of IS911: A Major Transposition Pathway

M Chandler, O Fayet, P Rousseau, BT Hoang… - Mobile DNA …, 2015 - Wiley Online Library
The bacterial insertion sequence, IS911, is a member of the large IS3family. It transposes
using a mechanism known as Copy‐out–Paste‐in. This is a major transposition pathway as …

Concentration and length dependence of DNA looping in transcriptional regulation

L Han, HG Garcia, S Blumberg, KB Towles… - PloS one, 2009 - journals.plos.org
In many cases, transcriptional regulation involves the binding of transcription factors at sites
on the DNA that are not immediately adjacent to the promoter of interest. This action at a …

Interconvertible Lac repressor–DNA loops revealed by single-molecule experiments

OK Wong, M Guthold, DA Erie, J Gelles - PLoS biology, 2008 - journals.plos.org
At many promoters, transcription is regulated by simultaneous binding of a protein to
multiple sites on DNA, but the structures and dynamics of such transcription factor-mediated …

Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices

M Schickinger, M Zacharias… - Proceedings of the …, 2018 - National Acad Sciences
We describe a tethered multifluorophore motion assay based on DNA origami for revealing
bimolecular reaction kinetics on the single-molecule level. Molecular binding partners may …

Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level

C Monico, M Capitanio, G Belcastro, F Vanzi… - International journal of …, 2013 - mdpi.com
The maintenance of intact genetic information, as well as the deployment of transcription for
specific sets of genes, critically rely on a family of proteins interacting with DNA and …

High-throughput single-molecule analysis of DNA–protein interactions by tethered particle motion

T Plenat, C Tardin, P Rousseau… - Nucleic acids …, 2012 - academic.oup.com
Tethered particle motion (TPM) monitors the variations in the effective length of a single DNA
molecule by tracking the Brownian motion of a bead tethered to a support by the DNA …

Prokaryotic Argonaute from Archaeoglobus fulgidus interacts with DNA as a homodimer

E Golovinas, D Rutkauskas, E Manakova… - Scientific reports, 2021 - nature.com
Argonaute (Ago) proteins are found in all three domains of life. The best-characterized group
is eukaryotic Argonautes (eAgos), which are the core of RNA interference. The best …

Tethered particle motion: an easy technique for probing DNA topology and interactions with transcription factors

DT Kovari, Y Yan, L Finzi, D Dunlap - Single Molecule Analysis: Methods …, 2018 - Springer
Abstract Tethered Particle Motion (TPM) is a versatile in vitro technique for monitoring the
conformations a linear macromolecule, such as DNA, can exhibit. The technique involves …

Atomic force microscopy of the EcoKI Type I DNA restriction enzyme bound to DNA shows enzyme dimerization and DNA looping

KJ Neaves, LP Cooper, JH White… - Nucleic acids …, 2009 - academic.oup.com
Atomic force microscopy (AFM) allows the study of single protein–DNA interactions such as
those observed with the Type I Restriction–Modification systems. The mechanisms …