Novel DNA-binding fold and DNA-recognition mode discovered in restriction enzyme PabI

Novel protein fold discovered in the PabI family of restriction enzymes

Although structures of many DNA-binding proteins have been solved, they fall into a limited number of folds. Here, we describe an approach that led to the finding of a novel DNA-binding fold. Based on the behavior of Type II restriction-modification gene complexes as mobile elements, our earlier work identified a restriction enzyme, R.PabI, and its cognate modification enzyme in Pyrococcus abys...

The average spacing of restriction enzyme recognition sites in DNA.

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. Several hundred of these “restriction” enzymes are known and they are a very common tool both for analysis and manipul...

Characterization of Avian Pasteurella multocida Isolates by Protein Profiles and Restriction Enzyme Analysis of Chromosomal DNA

Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis

Decades of intensive experimental studies of the recognition of DNA sequences by proteins have provided us with a view of a diverse and complicated world in which few to no features are shared between individual DNA-binding protein families. The originally conceived direct readout of DNA residue sequences by amino acid side chains offers very limited capacity for sequence recognition, while the...

DNA cloning without restriction enzyme and ligase.

One common problem in using the traditional DNA cloning procedure is that suitable natural restriction sites are often unavailable for a given task. Creating new restriction sites is often time consuming. Here, I describe a simple technique of producing "customized cohesive ends" by a combination of PCR primer design and lambda exonuclease digestion. These complementary cohesive ends can form h...