A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes

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 naming the putative genes found by sequence analysis of microbial genome

New clues in the allosteric activation of DNA cleavage by SgrAI: structures of SgrAI bound to cleaved primary-site DNA and uncleaved secondary-site DNA

The structures of SgrAI bound to secondary-site DNA and Ca2+ or Mg2+, as well as bound to cleaved primary-site DNA and Mg2+, are presented and show similar overall conformations interpreted as the low-activity form of the enzyme. A third Mg2+ ion-binding site is found in the structure with cleaved primary-site DNA, as predicted by the two-metal-ion mechanism

Outline of the chloramphenicol (Cat) gene mutagenesis and assembly experiment

<p><b>Copyright information:</b></p><p>Taken from "USER™ friendly DNA engineering and cloning method by uracil excision"</p><p></p><p>Nucleic Acids Research 2007;35(6):1992-2002.</p><p>Published online 6 Mar 2007</p><p>PMCID:PMC1874603.</p><p>© 2007 The Author(s)</p> () PCR primer design strategy. Lines with the arrowheads symbolize priming sequences in the PCR primers. Left and Right cloning primers contain 5′ extensions compatible with the single-stranded extensions on the linearized pNEB206A vector. The overlapping primers P1/P2 and P3/P4 are selected in the vicinity of the targeted mutations. Asterisks designate the point mismatches in the primers compared to the template sequence. Overlapping primers are complementary to each other within the boxed sequences. The 3′ dT of the boxed sequence in the primer sequences is replaced by dU. () Schematic representation of six PCR products amplified using the indicated primers. Cycling conditions are described in Materials and Methods. The label, Cat926 etc. shows the PCR fragment size in bp. The ends of the PCR products are flanked by the compatible overlapping sequences with a single dU residue at the junction. () Four assembly reactions were carried out using the indicated PCR fragments to assemble a full-length Cat gene carrying the indicated phenotype into pNEB206A