The other face of restriction: modification-dependent enzymes

The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine

(2012) Rasa Sukackaite et al.   NUCLEIC ACIDS RESEARCH

Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease

(2012) John R. Horton et al.   NUCLEIC ACIDS RESEARCH

Context-dependent conservation of DNA methyltransferases in bacteria

(2012) Aswin Sai Narain Seshasayee et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Kamil Steczkiewicz et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Wojciech Siwek et al.   NUCLEIC ACIDS RESEARCH

CDD: conserved domains and protein three-dimensional structure

(2012) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Transforming the Untransformable: Application of Direct Transformation To Manipulate Genetically Staphylococcus aureus and Staphylococcus epidermidis

(2012) I. R. Monk et al.   mBio

Success of a suicidal defense strategy against infection in a structured habitat

(2012) Masaki Fukuyo et al.   Scientific Reports

Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids

(2011) Lakshminarayan M. Iyer et al.   CELL CYCLE

Methylation-dependent DNA restriction in Bacillus anthracis

(2011) Ramakrishnan Sitaraman et al.   GENE

A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo

(2011) E. Rajakumara et al.   GENES & DEVELOPMENT

Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems

(2011) K. S. Makarova et al.   JOURNAL OF BACTERIOLOGY

Cleavage of a model DNA replication fork by a methyl-specific endonuclease

(2011) Ken Ishikawa et al.   NUCLEIC ACIDS RESEARCH

Evidence for an evolutionary antagonism between Mrr and Type III modification systems

(2011) M. Tesfazgi Mebrhatu et al.   NUCLEIC ACIDS RESEARCH

Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine

(2011) Hua Wang et al.   NUCLEIC ACIDS RESEARCH

MMDB: 3D structures and macromolecular interactions

(2011) T. Madej et al.   NUCLEIC ACIDS RESEARCH

A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300

(2011) Shuang-yong Xu et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

DNA phosphorothioation is widespread and quantized in bacterial genomes

(2011) L. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The MspJI family of modification-dependent restriction endonucleases for epigenetic studies

(2011) D. Cohen-Karni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA restriction-modification systems in the ethanologen, Zymomonas mobilis ZM4

(2010) Aidan L. Kerr et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Bacteriophage Mu Mom protein responsible for DNA modification is a new member of the acyltransferase superfamily

(2010) Katarzyna H. Kaminska et al.   CELL CYCLE

Conflicts Targeting Epigenetic Systems and Their Resolution by Cell Death: Novel Concepts for Methyl-Specific and Other Restriction Systems

(2010) K. Ishikawa et al.   DNA RESEARCH

Innovation in gene regulation: The case of chromatin computation

(2010) Sonja J. Prohaska et al.   JOURNAL OF THEORETICAL BIOLOGY

Characterization of Helicobacter pylori factors that control transformation frequency and integration length during inter-strain DNA recombination

(2010) Olivier Humbert et al.   MOLECULAR MICROBIOLOGY

Bacteriophage resistance mechanisms

(2010) Simon J. Labrie et al.   NATURE REVIEWS MICROBIOLOGY

A unique family of Mrr-like modification-dependent restriction endonucleases

(2010) Yu Zheng et al.   NUCLEIC ACIDS RESEARCH

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes

(2010) R. J. Roberts et al.   NUCLEIC ACIDS RESEARCH

Genome comparison and context analysis reveals putative mobile forms of restriction–modification systems and related rearrangements

(2010) Yoshikazu Furuta et al.   NUCLEIC ACIDS RESEARCH

Cofactor Requirement of HpyAV Restriction Endonuclease

(2010) Siu-Hong Chan et al.   PLoS One

Molecular coupling of DNA methylation and histone methylation

(2010) Hideharu Hashimoto et al.   Epigenomics

Cleavage of Phosphorothioated DNA and Methylated DNA by the Type IV Restriction Endonuclease ScoMcrA

(2010) Guang Liu et al.   PLoS Genetics

DNA phosphorothioation in Streptomyces lividans: mutational analysis of the dnd locus

(2009) Tiegang Xu et al.   BMC MICROBIOLOGY

Characterization of the methyl-specific restriction system ofStreptomyces coelicolorA3(2) and of the role played by laterally acquired nucleases

(2009) Gabriela González-Cerón et al.   FEMS MICROBIOLOGY LETTERS

DNA cleavage and methylation specificity of the single polypeptide restriction–modification enzyme LlaGI

(2009) Rachel M. Smith et al.   NUCLEIC ACIDS RESEARCH

Differential binding of Escherichia coli McrA protein to DNA sequences that contain the dinucleotide m5CpG

(2009) Elizabeth A. Mulligan et al.   NUCLEIC ACIDS RESEARCH

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

(2009) Richard J. Roberts et al.   NUCLEIC ACIDS RESEARCH

dndDB: A Database Focused on Phosphorothioation of the DNA Backbone

(2009) Hong-Yu Ou et al.   PLoS One

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE

Base J: Discovery, Biosynthesis, and Possible Functions

(2008) Piet Borst et al.   Annual Review of Microbiology

Mutational analysis and a structural model of methyl-directed restriction enzyme Mrr

(2008) Jerzy Orlowski et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Substrate specificity of new methyl-directed DNA endonuclease GlaI

(2008) Galina V Tarasova et al.   BMC MOLECULAR BIOLOGY

Clocks and switches: bacterial gene regulation by DNA adenine methylation

(2008) David A Low et al.   CURRENT OPINION IN MICROBIOLOGY

The Fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases

(2008) H. Wei et al.   NUCLEIC ACIDS RESEARCH

Cloning, purification and initial characterization of E. coli McrA, a putative 5-methylcytosine-specific nuclease

(2008) Elizabeth A. Mulligan et al.   PROTEIN EXPRESSION AND PURIFICATION

Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases

(2008) Eri Fukuda et al.   GENOME BIOLOGY

Restriction Endonuclease Inhibitor IPI* of Bacteriophage T4: A Novel Structure for a Dedicated Target

(2007) Dalin Rifat et al.   JOURNAL OF MOLECULAR BIOLOGY