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pUC19 digested with HphI
HphI recognises GGTGA and cuts circular pUC19 (GenBank L09137.2, 2,686 bp) at 7 sites, so a complete digest gives 7 fragments.
Fragments
Fragment
Length (bp)
From base
To base
1
9
25
33
2
1,509
34
1,542
3
227
1,543
1,769
4
416
1,770
2,185
5
206
2,186
2,391
6
35
2,392
2,426
7
284
2,427
24
The fragments add up to 2,686 bp, the length of the record.
Cut sites
Site
Recognition site: first base on the top strand
Site reads on
Cuts after base (top strand)
1
12
top strand
24
2
21
top strand
33
3
1,550
bottom strand
1,542
4
1,777
bottom strand
1,769
5
2,173
top strand
2,185
6
2,399
bottom strand
2,391
7
2,414
top strand
2,426
Positions are in the numbering of GenBank L09137.2. 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 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) digested with HphI
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
HphI: GGTGA, cut GGTGANNNNNNN_N^N, leaving a 1-base 3′ overhang whose bases are not fixed by the recognition site.
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/puc19.1.json (GenBank L09137.2, SHA-256 8a205af08518dae1b0045c7b098986dca18824ef654e75233603602ab89cad04) 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.