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[HTML][HTML] Dynamics in Cre-loxP site-specific recombination
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 …
of DNA sequences. Cre recognizes and recombines pairs of loxP sequences characterized …
Predicting DNA structure using a deep learning method
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 …
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 …
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 …
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 …
associating domains (TADs) by extruding DNA loops and being stalled by roadblock …
How acidic amino acid residues facilitate DNA target site selection
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 …
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
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 …
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
Mechanically bonded membranes of interlocked ring polymers are a significant
generalization of conventional elastic sheets, where connectivity is provided by covalent …
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
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 …
biological functions (such as transcription and gene repair), which require large-amplitude …
Computational modeling of DNA 3D structures: From dynamics and mechanics to folding
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 …
plays an important role in many processes of biological development. Understanding the …