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pBR322 digested with NaeI
NaeI recognises GCCGGC and cuts circular pBR322 (GenBank J01749.1, 4,361 bp) at 4 sites, so a complete digest gives 4 fragments.
NgoMIV recognises the same site and gives the same fragment lengths; its ends are listed below.
Fragments
Fragment
Length (bp)
From base
To base
1
368
404
771
2
160
772
931
3
354
932
1,285
4
3,479
1,286
403
The fragments add up to 4,361 bp, the length of the record.
Cut sites
Site
Recognition site: first base on the top strand
Cuts after base (top strand)
1
401
403
2
769
771
3
929
931
4
1,283
1,285
Positions are in the numbering of GenBank J01749.1. A cut after base n leaves base n at the end of one fragment and the next base at the start of the next. A fragment that runs past the record's last base continues from its first. A vendor's map, or your own stock, may differ from this record.
The cut sites and fragment ends above are NaeI's. An enzyme below that cuts at a different base of the same site has its positions shifted by the same amount at every site; the lengths do not change.
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
pBR322 (J01749.1) digested with NaeI
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.
Ends
NaeI: GCCGGC, cut GCC^_GGC, leaving blunt ends.
NgoMIV: GCCGGC, cut G^CCGG_C, leaving a 4-base 5′ overhang (CCGG).
Methylation
Every one of these sites is cut in unmethylated DNA and in DNA from a dam and dcm methylating host, by the recorded dam and dcm sensitivities. Only dam and dcm are considered; CpG, EcoKI and other modifications are not modelled.
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.
The workspace draws a schematic gel of these fragments, not a prediction of where bands will run. Fragments under 100 bp are listed here but not drawn there, and fragments within 5 percent of each other are drawn as one band.
How this page was made
Computed when the site was built by the Drybench Plasmid engine, version 1.0.0, from /data/plasmid-map/examples/pbr322.1.json (GenBank J01749.1, SHA-256 536042a7485bdabdf49c4d21a306213a098d77d19bdba57a1c6adc76ce2b8372) and enzyme table version 1, /data/plasmid-map/enzymes.8829d35c83.json (2026-10-06). Every cut position and fragment length on this page was compared with Biopython 1.88 (REBASE release 404, recorded 2026-10-06); a disagreement stops the build.