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Home  >Technical Resource  > Restriction Endonucleases Cleavage of Supercoiled DNA

Cleavage of Supercoiled DNA

Restriction endonucleases cleave different DNA substrates with varying efficiency. The supercoiled forms of pBR322, pUC19 and pLITMUS often require more units of enzyme for complete digestion than lambda DNA. Below is a table reporting the results of this comparison using standard reaction conditions. The enzymes listed are those which have single sites on pBR322, pUC19 or the appropriate LITMUS vector.

LITMUS pBR322 pUC19
Enzyme Units to Cleave
LITMUS Lambda
AatII 3 1
Acc65I 1 1
AflII 2 1
AflIII 1 1
AgeI 1 1
AhdI 1 1
ApaI 1 1
AvaII 1 1
BaeI 3 1
BamHI
5
1
BglII 8 1
BsaXI
2
1
BsiWI 3 1
Bsp120I 8 1
BspEI 1 1
BsrGI 1 1
BssHI 4 1
BtgI
5
1
EagI 10 1
EcoRI 4 1
EcoRV 1 1
HaeIII 4 1
KasI 4 1
KpnI 2 1
MluI 2 1
MunI 1 1
NcoI 1 1
NgoMIV 2 1
NheI 1 1
NsiI 1 1
PciI 3 1
PsiI
3
1
PstI
1
1
SacI 5 1
SalI 10 1
SnaBI 1 1
SpeI 1 1
SphI 4 1
StuI 3 1
TliI
2
1
XhoI 10 1
Enzyme Units to Cleave
pBR322 Lambda
AatII 3 1
AflIII 1 1
AhdI 1 1
AlwNI 1 1
AscI 0.3 1
AvaI 10 1
BamHI 3 1
BsaI 2 1
BsaAI 20 1
BsaXI
2
1
BsgI 1 1
BsmI 1 1
BspDI 1 1
BspMI ** 1
ClaI 5 1
EagI 10 1
EcoNI 3 1
EcoRI 2.5 1
EcoRV 1 1
HaeIII 5 1
NdeI 3 1
NheI 10 1
NruI 1 1
PciI 3 1
PstI
1
1
PvuI 2 1
PvuII 2 1
SalI 10 1
SapI 1 1
ScaI 20 1
SphI 2 1
SspI 2 1
StyI 4 1
Tth111I 10 1
** BspMI cleaves pBR322 poorly.  Even with 100 units/µg of pBR322, less than 50% cleavage is possible.
Enzyme Units to Cleave
pUC19 Lambda
AatII 3 1
AccI 5 1
AflIII 1 1
AhdI 1 1
AlwNI 2 1
ApoI 1 1
AvaI 10 1
BamHI 1 1
BanII 1 1
BpmI 1 1
BsaI 1 1
BspMI ** 1
BsrFI 2 1
EcoO109I 8 1
EcoRI 2.5 1
HaeII 4 1
HaeIII 5 1
KpnI 2 1
NarI 20 1
NdeI 2 1
PciI 3 1
PstI
1
1
SacI 5 1
SalI 10 1
SapI 1 1
ScaI 15 1
SmaI 1 1
SphI 3 1
SspI 5 1
XbaI 2 1
XmnI 5 1
** BspMI cleaves pUC19 poorly.  Even with 100 units/µg of pUC19, less than 50% cleavage is possible.