Nucleases: diversity of structure, function and mechanism

W Yang - Quarterly reviews of biophysics, 2011 - cambridge.org
Nucleases cleave the phosphodiester bonds of nucleic acids and may be endo or exo,
DNase or RNase, topoisomerases, recombinases, ribozymes, or RNA splicing enzymes. In …

Type II restriction endonucleases—a historical perspective and more

A Pingoud, GG Wilson, W Wende - Nucleic acids research, 2014 - academic.oup.com
This article continues the series of Surveys and Summaries on restriction endonucleases
(REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II'REases, the …

Sequence, structure and functional diversity of PD-(D/E) XK phosphodiesterase superfamily

K Steczkiewicz, A Muszewska, L Knizewski… - Nucleic acids …, 2012 - academic.oup.com
Proteins belonging to PD-(D/E) XK phosphodiesterases constitute a functionally diverse
superfamily with representatives involved in replication, restriction, DNA repair and tRNA …

Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R. DpnI

W Siwek, H Czapinska, M Bochtler… - Nucleic acids …, 2012 - academic.oup.com
DNA methylation-dependent restriction enzymes have many applications in genetic
engineering and in the analysis of the epigenetic state of eukaryotic genomes. Nevertheless …

Investigating the antimicrobial and anti-inflammatory activities of novel thiophene derivatives by in-vitro studies, molecular docking, spectral analysis, and quantum …

MAF Mohamed, N Roy, I Benjamin, SW Joo… - Journal of Molecular …, 2024 - Elsevier
The rise of antibiotic-resistant pathogens and the widespread occurrence of inflammatory
diseases have raised considerable global health concerns. Consequently, there is a critical …

Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands

KL Sanders, LE Catto, SRW Bellamy… - Nucleic acids …, 2009 - academic.oup.com
Many restriction endonucleases are dimers that act symmetrically at palindromic DNA
sequences, with each active site cutting one strand. In contrast, FokI acts asymmetrically at a …

Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity

F Chen, Z Yang, M Yan, JB Alvarado… - Nucleic acids …, 2011 - academic.oup.com
To explore the possibility of using restriction enzymes in a synthetic biology based on
artificially expanded genetic information systems (AEGIS), 24 type-II restriction …

Structural changes in DNA-binding proteins on complexation

S Poddar, D Chakravarty… - Nucleic Acids Research, 2018 - academic.oup.com
Abstract Characterization and prediction of the DNA-biding regions in proteins are essential
for our understanding of how proteins recognize/bind DNA. We analyze the unbound (U) …

Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation

M Kisiala, M Kowalska, M Pastor, HJ Korza… - Nucleic acids …, 2020 - academic.oup.com
Restriction endonucleases naturally target DNA duplexes. Systematic screening has
identified a small minority of these enzymes that can also cleave RNA/DNA heteroduplexes …

The dynamics of the monomeric restriction endonuclease BcnI during its interaction with DNA

G Kostiuk, J Dikić, FW Schwarz… - Nucleic acids …, 2017 - academic.oup.com
Endonucleases that generate DNA double strand breaks often employ two independent
subunits such that the active site from each subunit cuts either DNA strand. Restriction …