Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures
Abstract Web 3DNA (w3DNA) 2.0 is a significantly enhanced version of the widely used
w3DNA server for the analysis, visualization, and modeling of 3D nucleic-acid-containing …
w3DNA server for the analysis, visualization, and modeling of 3D nucleic-acid-containing …
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 looping, or in nanotechnology applications …
small ligand binding, in genome regulation via looping, or in nanotechnology applications …
[HTML][HTML] Beyond the double helix: DNA structural diversity and the PDB
S Neidle - Journal of Biological Chemistry, 2021 - ASBMB
The determination of the double helical structure of DNA in 1953 remains the landmark
event in the development of modern biological and biomedical science. This structure has …
event in the development of modern biological and biomedical science. This structure has …
OxDNA. org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures
E Poppleton, R Romero, A Mallya… - Nucleic acids …, 2021 - academic.oup.com
OxDNA and oxRNA are popular coarse-grained models used by the DNA/RNA
nanotechnology community to prototype, analyze and rationalize designed DNA and RNA …
nanotechnology community to prototype, analyze and rationalize designed DNA and RNA …
Structure, folding and flexibility of co-transcriptional RNA origami
RNA origami is a method for designing RNA nanostructures that can self-assemble through
co-transcriptional folding with applications in nanomedicine and synthetic biology. However …
co-transcriptional folding with applications in nanomedicine and synthetic biology. However …
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
M Pasi, JH Maddocks, D Beveridge… - Nucleic acids …, 2014 - academic.oup.com
We present the results of microsecond molecular dynamics simulations carried out by the
ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct …
ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct …
MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion
INTRODUCTION Rett syndrome is a severe neurodevelopmental disorder that is mainly
caused by mutations in the methyl-CpG-binding protein 2 gene (MeCP2). Initially, MeCP2 …
caused by mutations in the methyl-CpG-binding protein 2 gene (MeCP2). Initially, MeCP2 …
[HTML][HTML] Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA
L Yin, K Shi, H Aihara - Nature Structural & Molecular Biology, 2023 - nature.com
The interbacterial deaminase toxin DddA catalyzes cytosine-to-uracil conversion in double-
stranded (ds) DNA and enables CRISPR-free mitochondrial base editing, but the molecular …
stranded (ds) DNA and enables CRISPR-free mitochondrial base editing, but the molecular …
[PDF][PDF] Structural basis of transposon end recognition explains central features of Tn7 transposition systems
Z Kaczmarska, M Czarnocki-Cieciura… - Molecular cell, 2022 - cell.com
Tn7 is a bacterial transposon with relatives containing element-encoded CRISPR-Cas
systems mediating RNA-guided transposon insertion. Here, we present the 2.7 Å …
systems mediating RNA-guided transposon insertion. Here, we present the 2.7 Å …
The structural impact of DNA mismatches
The structure and dynamics of all the transversion and transition mismatches in three
different DNA environments have been characterized by molecular dynamics simulations …
different DNA environments have been characterized by molecular dynamics simulations …