[HTML][HTML] Dynamics in Cre-loxP site-specific recombination

MP Foster, MJ Benedek, TD Billings… - Current opinion in …, 2024 - Elsevier
Cre recombinase is a phage-derived enzyme that has found utility for precise manipulation
of DNA sequences. Cre recognizes and recombines pairs of loxP sequences characterized …

Predicting DNA structure using a deep learning method

J Li, TP Chiu, R Rohs - Nature communications, 2024 - nature.com
Understanding the mechanisms of protein-DNA binding is critical in comprehending gene
regulation. Three-dimensional DNA structure, also described as DNA shape, plays a key …

Deciphering the mechanical properties of B‐DNA duplex

H Dohnalová, F Lankaš - Wiley Interdisciplinary Reviews …, 2022 - Wiley Online Library
Abstract Structure and deformability of the DNA double helix play a key role in protein and
small ligand binding, in genome regulation via loo**, or in nanotechnology applications …

The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations

HL Dong, C Zhang, L Dai, Y Zhang… - Nucleic acids …, 2024 - academic.oup.com
The subtle differences in the chemical structures of double-stranded (ds) RNA and DNA lead
to significant variations in their biological roles and medical implications, largely due to their …

Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure

K Yamaura, N Takemata, M Kariya, A Osaka… - Nature …, 2025 - nature.com
In eukaryotes, structural maintenance of chromosomes (SMC) complexes form topologically
associating domains (TADs) by extruding DNA loops and being stalled by roadblock …

How acidic amino acid residues facilitate DNA target site selection

KA Hossain, M Kogut, J Słabońska, S Sappati… - Proceedings of the …, 2023 - pnas.org
Despite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly
participate in the base readout, with a strong preference for cytosine. In fact, in the solved …

The convergent xenogeneic silencer MucR predisposes α-proteobacteria to integrate AT-rich symbiosis genes

WT Shi, B Zhang, ML Li, KH Liu, J Jiao… - Nucleic Acids …, 2022 - academic.oup.com
Bacterial adaptation is largely shaped by horizontal gene transfer, xenogeneic silencing
mediated by lineage-specific DNA bridgers (H-NS, Lsr2, MvaT and Rok), and various anti …

Shape and size tunability of sheets of interlocked ring copolymers

J Luengo-Márquez, S Assenza, C Micheletti - Soft Matter, 2024 - pubs.rsc.org
Mechanically bonded membranes of interlocked ring polymers are a significant
generalization of conventional elastic sheets, where connectivity is provided by covalent …

Melting and bubble formation in a double-stranded DNA: microscopic aspects of early base-pair opening events and the role of water

S Mondal, S Mukherjee, B Bagchi - The Journal of Physical …, 2024 - ACS Publications
Despite its rigid structure, DNA is a remarkably flexible molecule. Flexibility is essential for
biological functions (such as transcription and gene repair), which require large-amplitude …

Computational modeling of DNA 3D structures: From dynamics and mechanics to folding

ZC Mu, YL Tan, J Liu, BG Zhang, YZ Shi - Molecules, 2023 - mdpi.com
DNA carries the genetic information required for the synthesis of RNA and proteins and
plays an important role in many processes of biological development. Understanding the …