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. 2003 Jul 1;31(13):3688-91.
doi: 10.1093/nar/gkg526.

NEBcutter: A program to cleave DNA with restriction enzymes

Tamas Vincze  1 , Janos Posfai, Richard J Roberts
Affiliations

NEBcutter: A program to cleave DNA with restriction enzymes

Tamas Vincze et al. Nucleic Acids Res. .

Abstract

NEBcutter, version 1.0, is a program available via a web server (http://tools.neb.com/NEBcutter) that will accept an input DNA sequence and produce a comprehensive report of the restriction enzymes that will cleave the sequence. It produces a variety of outputs including restriction enzyme maps, theoretical digests and links into the restriction enzyme database, REBASE (http://www.neb.com/rebase). Importantly, its table of recognition sites is updated daily from REBASE and it marks all sites that are potentially affected by DNA methylation (Dam, Dcm, etc.). Many options exist to choose the enzymes used for digestion, including all known specificities, subsets of those that are commercially available or sets of enzymes that produce compatible termini.

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Figures

Figure 1
Figure 1
The linear display of a digest of the plasmid pBR322. Note that the two main ORFs are flanked by sites (MseI and PflMI; BspHI and EarI) that could be used to excise them from the complete plasmid sequence. In this display only enzymes that cleave the sequence once are shown. Options for further digestion and display are available through the buttons at the bottom of the display.
Figure 2
Figure 2
Zoomed display of a short region from pBR322. Note that bases highlighted in red and blue form parts of restriction enzyme recognition sites. The red ones are unambiguous, whereas the blue ones are degenerate bases. Thus BsiEI recognizes the sequence CGRYCG. The outer CG residues are invariant, while the inner bases are degenerate and, in the specific sequence shown, are GT. Bases shown in black do not form part of any restriction enzyme recognition site. This display can be useful to find restriction enzymes able to distinguish SNP alleles.
Figure 3
Figure 3
A theoretical digest showing the effects of overlapping Dcm methylation on the MscI sites (recognition sequence: TGGCCA) present in the sequence if the bacteriophage lambda had been grown in an E.coli strain expressing the Dcm methyltransferase (recognition sequence: CCWGG). Fragments that are affected by Dcm methylation are shown in red. The virtual gel is based on interpolation of a cubic spline curve generated from experimental data produced with fragments of known size.
See this image and copyright information in PMC

References

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