Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences [PDF]
PLoS ONE, 2019 Restriction enzymes recognize and bind to specific sequences on invading bacteriophage DNA. Like a key in a lock, these proteins require many contacts to specify the correct DNA sequence. Using information theory we develop an equation that defines the number of independent contacts, which is the dimensionality of the binding. We show that EcoRI, which
Thomas D Schneider, Vishnu Jejjala
arxiv +2 more sources
On the DNA cleavage mechanism of Type I restriction enzymes [PDF]
Nucleic Acids Research, 2005 Although the DNA cleavage mechanism of Type I restriction–modification enzymes has been extensively studied, the mode of cleavage remains elusive. In this work, DNA ends produced by EcoKI, EcoAI and EcoR124I, members of the Type IA, IB and IC families ...
Bickle, Thomas A. +4 more
core +9 more sources
Revised selection criteria for candidate restriction enzymes in genome walking. [PDF]
PLoS ONE, 2012 A new method to improve the efficiency of flanking sequence identification by genome walking was developed based on an expanded, sequential list of criteria for selecting candidate enzymes, plus several other optimization steps.
Ali Taheri +3 more
doaj +8 more sources
Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains [PDF]
Nucleic Acids Research, 2000 This study concerns chimeric restriction enzymes that are hybrids between a zinc finger DNA-binding domain and the non-specific DNA-cleavage domain from the natural restriction enzyme FOK:I.
Jarrett Smith
openalex +2 more sources
7-Deazaguanine modifications protect phage DNA from host restriction systems [PDF]
Nature Communications, 2019 Genome modifications are central components of the continuous arms race between viruses and their hosts. The archaeosine base (G+), which was thought to be found only in archaeal tRNAs, was recently detected in genomic DNA of Enterobacteria phage 9g and ...
Geoffrey Hutinet +18 more
semanticscholar +3 more sources
REBASE—a database for DNA restriction and modification: enzymes, genes and genomes [PDF]
Nucleic Acids Research, 2014 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 ...
R. Roberts +3 more
semanticscholar +6 more sources
The average spacing of restriction enzyme recognition sites in DNA [PDF]
Journal of Theoretical Biology, 1982 The discovery of naturally occurring enzymes which cleave DNA at sites specific to particular nucleotide sequences has had a great impact on molecular biology. The function of these enzymes in uivo is to protect bacterial cells from viral invasion by degradation of foreign DNA.
Gordon P. Moore, A. R. Moore
openalex +5 more sources
REBASE—a database for DNA restriction and modification: enzymes, genes and genomes [PDF]
Nucleic Acids Res., 2009 REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction–modification (R–M).
Richard J. Roberts +3 more
openalex +2 more sources
A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. [PDF]
Nucleic Acids Research, 2003 A nomenclature is described for restriction endonucleases, DNA methyltransferases, homing endonucleases and related genes and gene products. It provides explicit categories for the many different Type II enzymes now identified and provides a system for ...
R. Roberts +46 more
semanticscholar +9 more sources
Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation [PDF]
Nucleic Acids Research, 2006 Hypermethylation of CpG island (CGI) sequences is a nearly universal somatic genome alteration in cancer. Rapid and sensitive detection of DNA hypermethylation would aid in cancer diagnosis and risk stratification.
Srinivasan Yegnasubramanian +4 more
openalex +2 more sources