REBASE—a database for DNA restriction and modification: enzymes, genes and genomes
TLDR
REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems that contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data.Abstract:
REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems. It contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data. All genomes that are completely sequenced are analyzed for RM system components, and with the advent of PacBio sequencing, the recognition sequences of DNA methyltransferases (MTases) are appearing rapidly. Thus, Type I and Type III systems can now be characterized in terms of recognition specificity merely by DNA sequencing. The contents of REBASE may be browsed from the web http://rebase.neb.com and selected compilations can be downloaded by FTP (ftp.neb.com). Monthly updates are also available via email.read more
Citations
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Journal ArticleDOI
Single-Molecule DNA Methylation Quantification Using Electro-optical Sensing in Solid-State Nanopores
Tal Gilboa,Chen Torfstein,Matyas Juhasz,Assaf Grunwald,Yuval Ebenstein,Elmar Weinhold,Amit Meller,Amit Meller +7 more
TL;DR: A labeling and single-molecule quantification method for multiple unmethylated cytosine-guanine dinucleotides (CpGs) and may permit sequence-specific, direct targeting of clinically relevant hypomethylated sites in the genome.
Journal ArticleDOI
The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection
TL;DR: The 2015 Nucleic Acids Research Database Issue contains 172 papers that include descriptions of 56 new molecular biology databases, and updates on 115 databases whose descriptions have been previously published in NAR or other journals.
Journal ArticleDOI
Phase-variable methylation and epigenetic regulation by type I restriction–modification systems
Megan De Ste Croix,Irene Vacca,Min Jung Kwun,Joseph D. Ralph,Stephen D. Bentley,Richard D. Haigh,Nicholas J. Croucher,Marco R. Oggioni +7 more
TL;DR: The ability of these RM systems to allow bacteria to reversibly switch between different physiological states, combined with the existence of such loci across many species of medical and industrial importance, highlights the potential of phase-variable DNA methylation to act as a global regulatory mechanism in bacteria.
Journal ArticleDOI
Cleavage of phosphorothioated DNA and methylated DNA by the type IV restriction endonuclease ScoMcrA.
Guang Liu,Hong-Yu Ou,Tao Wang,Li Li,Huarong Tan,Xiufen Zhou,Kumar Rajakumar,Zixin Deng,Xinyi He +8 more
TL;DR: This is the first report of in vitro endonuclease activity of a McrA homologue and also the first demonstration of an enzyme that specifically cleaves S-modified DNA.
Journal ArticleDOI
Construction of a stable replicating shuttle vector for Caldicellulosiruptor species: use for extending genetic methodologies to other members of this genus.
Daehwan Chung,Daehwan Chung,Minseok Cha,Minseok Cha,Joel Farkas,Joel Farkas,Janet Westpheling,Janet Westpheling +7 more
TL;DR: The construction of a replicating shuttle vector for Caldicellulosiruptor species based on pBAS2, the smaller of two native C. bescii plasmids, is reported, which was successful for transformation of C. hydrothermalis, an attractive species for many applications.
References
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