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NotI restriction site and cut
NotI recognises GCGGCCGC and cuts GC^GGCC_GC, leaving a 4-base 5′ overhang (GGCC).
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.
Sites in pUC19, pBR322, pBluescript II SK(+), pBluescript II KS(+), pGEM-3Z, pACYC184, pEGFP-N1 and pGEX-4T-1
Vector
Sites
Cut under dam and dcm methylation
Cuts after base (top strand)
pUC19 (L09137.2, 2,686 bp)
0
0
none
pBR322 (J01749.1, 4,361 bp)
0
0
none
pBluescript II SK(+) (X52328.1, 2,961 bp)
1 (unique site)
1
738
pBluescript II KS(+) (X52327.1, 2,961 bp)
1 (unique site)
1
670
pGEM-3Z (X65304.3, 2,743 bp)
0
0
none
pACYC184 (X06403.1, 4,245 bp)
0
0
none
pEGFP-N1 (U55762.1, 4,733 bp)
1 (unique site)
1
1,401
pGEX-4T-1 (U13853.1, 4,969 bp)
1 (unique site)
1
960
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
pBluescript II SK(+) (X52328.1) with NotI 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
No base that dam or dcm methylates can fall within NotI's site, so neither changes where it cuts.
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
No other enzyme in the table recognises this site.
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), /data/plasmid-map/examples/pbr322.1.json (GenBank J01749.1, SHA-256 536042a7485bdabdf49c4d21a306213a098d77d19bdba57a1c6adc76ce2b8372), /data/plasmid-map/examples/pbluescript-sk.1.json (GenBank X52328.1, SHA-256 b332229320366853c638f602edbd368bdc515b1846fc1ab95600813c1e0a2514), /data/plasmid-map/examples/pbluescript-ks.1.json (GenBank X52327.1, SHA-256 cac12f3e67407fd0653b1c5e88d3a95ca86f13602a3b3045f4fae6b048c2da15), /data/plasmid-map/examples/pgem-3z.1.json (GenBank X65304.3, SHA-256 4f560f61d69429fe294d5d5218159d1e5c69a7025ce66fc439c680ef7ffb6b9a), /data/plasmid-map/examples/pacyc184.1.json (GenBank X06403.1, SHA-256 f9484eb2ae4c5d157b08c3c19af0933984ed1605753d8d73897728d914eee021), /data/plasmid-map/examples/pegfp-n1.1.json (GenBank U55762.1, SHA-256 63918e4dcae6eed7f21a2d430f8b24a7172acc9a174e307d933550034189efde) and /data/plasmid-map/examples/pgex-4t-1.1.json (GenBank U13853.1, SHA-256 7c27086ba934e96953ebd29bdcf2b5da67bcbcf2c0148bbb8dd4350aa8f59e38). The site, cut and ends, and every cut position on this page, were compared with Biopython 1.88 (REBASE release 404, recorded 2026-11-07); a disagreement stops the build.
Link to and cite this page
Link to this page
https://www.drybench.com/plasmid/enzymes/noti
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Cite this page
Drybench. NotI restriction site and cut. Drybench Plasmid0.19.0; enzyme table version 1, checked against Biopython 1.88 (REBASE release 404). https://www.drybench.com/plasmid/enzymes/noti. Accessed [date].
The versions and the date tell a reader which numbers you saw; a later table or engine version may change them. How to cite