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ScrFI restriction site and cut
ScrFI recognises CCNGG and cuts CC^N_GG, leaving a 1-base 5′ overhang (N).
In this notation, read on the top strand from five prime to three prime, ^ marks where the top strand is cut and _ where the bottom strand is cut. N stands for any base; Ns before or after the site are flanking bases, not part of it. The site uses IUPAC codes: N is any base.
Counts are for the GenBank record named, as a circle, in that record's numbering. The third column counts the sites cut in DNA with dam and dcm methylation (the Drybench Plasmid default); any other site is blocked, or its outcome is not known. The positions list every recognition site, cut or not. A vendor's map, or your own stock, may differ from this record.
The same question is open below in Drybench Plasmid. Change the enzymes, the host's methylation or the vector there; nothing you do here is saved unless you save it.
Reference dataset active
pUC19 (L09137.2) with ScrFI shown
Opening what was sent…
Not medical advice. For research and education only, and not medical advice: this app designs restriction, Golden Gate and Gibson products from the sequences you supply; a designed product is not evidence that the reaction occurred, and nothing here predicts whether a reaction works, how well, or whether the product is expressed.
Dam and dcm methylation
The source below records these outcomes for ScrFI on methylated forms of its site:
Methylated form (bracketed base modified)
Outcome
[m5C]CNGG
Cut
C[m5C]NGG
Not cut
Drybench Plasmid treats an entry marked slow or variable as not known, uses one marked slow only when hemimethylated as recorded, since dam and dcm methylate both strands, and treats a methylated form not listed here as not known. Forms are printed as the source prints them, on either strand.
Source: McClelland M, Nelson M, Raschke E. Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res 1994;22:3640-3659 (doi 10.1093/nar/22.17.3640), Table I, read 6 October 2026.
Only dam and dcm are considered, from one source. CpG, EcoKI and other modifications are not modelled.
Other enzymes with the same site
Neoschizomers in the table (same site, a different cut, so different ends): StyD4I.
How this page was made
Computed when the site was built by the Drybench Plasmid engine, version 1.0.0, from enzyme table version 1, /data/plasmid-map/enzymes.8829d35c83.json (2026-10-06), and the records /data/plasmid-map/examples/puc19.1.json (GenBank L09137.2, SHA-256 8a205af08518dae1b0045c7b098986dca18824ef654e75233603602ab89cad04) and /data/plasmid-map/examples/pbr322.1.json (GenBank J01749.1, SHA-256 536042a7485bdabdf49c4d21a306213a098d77d19bdba57a1c6adc76ce2b8372). The site, cut and ends, and every cut position on this page, were compared with Biopython 1.88 (REBASE release 404, recorded 2026-10-06); a disagreement stops the build.