Affiliation: New England Biolabs
- Self-generated DNA termini relax the specificity of SgrAI restriction endonucleaseJurate Bitinaite
New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915, USA
Proc Natl Acad Sci U S A 99:1164-9. 2002..Based on our work and previous reports, a pathway of DNA binding and cleavage by the SgrAI restriction endonuclease is proposed...
- USER friendly DNA engineering and cloning method by uracil excisionJurate Bitinaite
New England Biolabs, Inc, Ipswich, MA 01938, USA
Nucleic Acids Res 35:1992-2002. 2007..By varying the design of the PCR primers, the protocol is easily adapted to perform one or more simultaneous DNA manipulations such as directional cloning, site-specific mutagenesis, sequence insertion or deletion and sequence assembly...
- Biochemical characterization of recombinant β-glucosyltransferase and analysis of global 5-hydroxymethylcytosine in unique genomesJolyon Terragni
New England Biolabs, Inc, Ipswich, Massachusetts 01938, United States
Biochemistry 51:1009-19. 2012..A comparison between cancer and healthy tissue genomes suggested a lower percentage of 5-hmC in cancer, which may reflect the global hypomethylation of 5-mC observed during oncogenesis...
- A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genesRichard J Roberts
New England Biolabs, Beverly, MA 01915, USA
Nucleic Acids Res 31:1805-12. 2003..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 genomes...
- Biochemical characterization of a Naegleria TET-like oxygenase and its application in single molecule sequencing of 5-methylcytosineJune E Pais
Research Department, New England Biolabs, Ipswich, MA 01938 and
Proc Natl Acad Sci U S A 112:4316-21. 2015..Finally, we demonstrate that NgTET1 can be readily used as a tool in (5m)C sequencing technologies such as single molecule, real-time sequencing to map (5m)C in bacterial genomes at base resolution. ..
- Kinetic analysis of the coordinated interaction of SgrAI restriction endonuclease with different DNA targetsKamini Hingorani-Varma
New England Biolabs Inc, Beverly, Massachusetts 01915, USA
J Biol Chem 278:40392-9. 2003..The free subunits of SgrAI have the flexibility to bind different target sites and, consequently, assemble into various catalytically active complexes, which differ in their catalytic efficiencies...
- Evaluation of UDP-GlcN derivatives for selective labeling of 5-(hydroxymethyl)cytosineNan Dai
New England Biolabs, Inc 240 County Road, Ipswich, MA 01938 USA
Chembiochem 14:2144-52. 2013..Alternative substrates for β-GT and correlated glycosyltransferases might prove useful for the study of the function and dynamics of 5-hmC and other modified nucleotides, as well as for multiplex analysis. ..
- Gene synthesis by assembly of deoxyuridine-containing oligonucleotidesRomualdas Vaisvila
New England Biolabs, Inc, Ipswich, MA, USA
Methods Mol Biol 978:165-71. 2013..The method consists of (1) synthesis of building blocks up to 500 bp; (2) assembly of genes up to 3 kb; (3) error correction reassembly; and (4) assembly of operons up to 15 kb if needed...
- DNA cloning and engineering by uracil excisionJurate Bitinaite
New England Biolabs, Ipswich, Massachusetts, USA
Curr Protoc Mol Biol . 2009..The use of a commercially available cloning vector and the preparation of custom vectors are also presented...
- Tissue-specific distribution and dynamic changes of 5-hydroxymethylcytosine in mammalian genomesShannon Morey Kinney
New England Biolabs, Inc, Ipswich, Massachusetts 01938, USA
J Biol Chem 286:24685-93. 2011..Finally, using a quantitative PCR approach, we established that a portion of VANGL1 and EGFR gene body methylation in human tissue DNA samples is indeed hydroxymethylation...
- The structure of SgrAI bound to DNA; recognition of an 8 base pair targetPete W Dunten
Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA 94025, USA
Nucleic Acids Res 36:5405-16. 2008..Recognition of the outer GC base pairs occurs through a single contact to the G from an arginine side chain located in a region unique to SgrAI...
- Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanismHemant K Joshi
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
J Biol Chem 281:23852-69. 2006..Analysis of these structures and the effect of Ca2+ binding on the protein-DNA interface illuminates the origin of the altered specificity by the mutation Q138F in the HincII enzyme...
- DNA distortion and specificity in a sequence-specific endonucleaseAndrea C Babic
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
J Mol Biol 383:186-204. 2008..The various complexes are fit into a model describing the different conformations of the DNA-bound enzyme and show how DNA conformational energetics determine DNA-cleavage rates by the Q138F HincII enzyme...