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
Crystal Structure and Directed Evolution of Specificity of NlaIV Restriction Endonuclease.
Honorata Czapinska,Wojciech Siwek,Roman H. Szczepanowski,Janusz M. Bujnicki,Janusz M. Bujnicki,Matthias Bochtler,Krzysztof Skowronek +6 more
TL;DR: A directed evolution approach to the engineering of a dimeric, blunt end cutting restriction enzyme NlaIV (GGN/NCC), which obtained variants cleaved target sites with an up to 100-fold kcat/KM preference for AT or TA (GGW/WCC) over GC or CG (GGS/SCC) in the central dinucleotide step.
Journal ArticleDOI
Characterization of Vsr endonucleases from Neisseria meningitidis
TL;DR: It is demonstrated that the VSP repair system may have a wider significance and broader substrate specificity than DNA lesions that only result from 5-methylcytosine deamination, and for the first time, this work reports on the mutagenic potential of the meningococcal C5-methyltransferases.
Journal ArticleDOI
The Architecture of Restriction Enzymes
TL;DR: A high resolution structure of a polymerized form of the SgrAI restriction enzyme is described, which shows that it forms a helical assembly with four enzyme molecules per turn of the helix.
Journal ArticleDOI
Cofactor analogue-induced chemical reactivation of endonuclease activity in a DNA cleavage/methylation deficient TspGWI N473A variant in the NPPY motif
TL;DR: A case study of a novel strategy for REase activity/specificity alteration by a single aa substitution, based on the bioinformatic analysis of active motif locations, combining the alteration of protein enzymatic properties, and the use of cofactor–analogue cleavage reconstitution and stimulation.
Journal ArticleDOI
Optimizing restriction site placement for synthetic genomes
Pablo Montes,Heraldo Memelli,Charles B. Ward,Joondong Kim,Joseph S. B. Mitchell,Steven Skiena +5 more
TL;DR: It is shown that the resulting problem is NP-Complete, the resulting modified genomes have several times more unique restriction sites and reduce the maximum gap between adjacent sites by three to nine-fold.
References
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