Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers

F Kriegel, N Ermann, J Lipfert - Journal of structural biology, 2017 - Elsevier
Nucleic acids are central to the storage and transmission of genetic information. Mechanical
properties, along with their sequence, both enable and fundamentally constrain the …

Rotating magnetic particles for lab-on-chip applications–a comprehensive review

CP Moerland, LJ Van IJzendoorn, MWJ Prins - Lab on a Chip, 2019 - pubs.rsc.org
Magnetic particles are widely used in lab-on-chip and biosensing applications, because
they have a high surface-to-volume ratio, they can be actuated with magnetic fields and …

Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes

MD Szczelkun, MS Tikhomirova… - Proceedings of the …, 2014 - National Acad Sciences
Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated
(Cas) systems protect bacteria and archaea from infection by viruses and plasmids. Central …

Molecular structure, DNA binding mode, photophysical properties and recommendations for use of SYBR Gold

PJ Kolbeck, W Vanderlinden… - Nucleic acids …, 2021 - academic.oup.com
SYBR Gold is a commonly used and particularly bright fluorescent DNA stain, however, its
chemical structure is unknown and its binding mode to DNA remains controversial. Here, we …

Mechanisms of small molecule–DNA interactions probed by single-molecule force spectroscopy

AA Almaqwashi, T Paramanathan… - Nucleic acids …, 2016 - academic.oup.com
There is a wide range of applications for non-covalent DNA binding ligands, and
optimization of such interactions requires detailed understanding of the binding …

Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments

PJ Kolbeck, M Tišma, BT Analikwu… - Nucleic acids …, 2024 - academic.oup.com
DNA stores our genetic information and is ubiquitous in applications, where it interacts with
binding partners ranging from small molecules to large macromolecular complexes. Binding …

[HTML][HTML] An optimized software framework for real-time, high-throughput tracking of spherical beads

JP Cnossen, D Dulin, NH Dekker - Review of Scientific Instruments, 2014 - pubs.aip.org
Numerous biophysical techniques such as magnetic tweezers, flow stretching assays, or
tethered particle motion assays rely on the tracking of spherical beads to obtain quantitative …

The temperature dependence of the helical twist of DNA

F Kriegel, C Matek, T Dršata, K Kulenkampff… - Nucleic acids …, 2018 - academic.oup.com
DNA is the carrier of all cellular genetic information and increasingly used in
nanotechnology. Quantitative understanding and optimization of its functions requires …

Chromatin rigidity provides mechanical and genome protection

AD Stephens - … Research/Fundamental and Molecular Mechanisms of …, 2020 - Elsevier
The nucleus is the organelle in the cell that contains the genome and its associate proteins
which is collectively called chromatin. New work has shown that chromatin and its …

Torque spectroscopy for the study of rotary motion in biological systems

J Lipfert, MM van Oene, M Lee, F Pedaci… - Chemical …, 2015 - ACS Publications
To understand the mechanistic basis of cellular function, immense efforts are undertaken to
investigate the many different molecules that constitute a cell, aiming to probe both …