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REBASE
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.

Cleavage Substrate:
LITMUS
Cleavage Substrate:
pBR322
Cleavage Substrate:
pUC19
Enzyme Units
to
Cleave
Reference
Substrate
AatII3λ DNA
Acc65I1λ DNA
AflII2λ DNA
AflIII1λ DNA
AgeI1λ DNA
AhdI1λ DNA
ApaI1λ DNA
AvrII1λ DNA
BaeI3λ DNA
BamHI5λ DNA
BglII8λ DNA
BsaXI2λ DNA
BsiWI3λ DNA
BspEI1λ DNA
BsrGI1λ DNA
BtgI5λ DNA
EagI10λ DNA
EcoRI4λ DNA
EcoRV1λ DNA
HindIII4λ DNA
KasI4λ DNA
KpnI2λ DNA
MluI2λ DNA
NcoI1λ DNA
NgoMIV2λ DNA
NheI1λ DNA
NheI-HF5λ DNA
NmeAIII***λ DNA
NsiI1λ DNA
PciI3λ DNA
PstI1λ DNA
SacI5λ DNA
SalI10λ DNA
SnaBI1λ DNA
SpeI1λ DNA
SphI4λ DNA
StuI3λ DNA
TliI2λ DNA
XhoI10λ DNA
*** NmeAIII cleaves single site substrates poorly. Even with 20 units/µg of LITMUS, less than 10% cleavage is possible.
Enzyme Units
to
Cleave
Reference
Substrate
AatII3λ DNA
AflIII1λ DNA
AhdI1λ DNA
AlwNI1λ DNA
AseI0.3λ DNA
AvaI10λ DNA
BamHI3λ DNA
BsaAI20λ DNA
BsaI2λ DNA
BsaXI2λ DNA
BsgI1λ DNA
BsmI1λ DNA
BspDI1λ DNA
BspMI**λ DNA
BspQI3λ DNA
ClaI5λ DNA
EagI10λ DNA
EcoNI3λ DNA
EcoRI2.5λ DNA
EcoRV1λ DNA
HindIII5λ DNA
NdeI3λ DNA
NheI10λ DNA
NheI-HF10λ DNA
NruI1λ DNA
PciI3λ DNA
PstI1λ DNA
PvuI2λ DNA
PvuII2λ DNA
PvuII-HF4λ DNA
SalI10λ DNA
SalI-HF2.5λ DNA
SapI1λ DNA
ScaI20λ DNA
ScaI-HF4λ DNA
SphI2λ DNA
SphI-HF3λ DNA
SspI2λ DNA
StyI4λ DNA
Tth111I10λ DNA
** BspMI cleaves pBR322 poorly.  Even with 100 units/µg of pBR322, less than 50% cleavage is possible.
Enzyme Units
to
Cleave
Reference
Substrate
AatII3λ DNA
AccI5λ DNA
AflIII1λ DNA
AhdI1λ DNA
AlwNI2λ DNA
ApoI1λ DNA
AvaI10λ DNA
BamHI1λ DNA
BanII1λ DNA
BpmI1λ DNA
BsaI1λ DNA
BspMI**λ DNA
BsrFI2λ DNA
EcoO109I8λ DNA
EcoRI2.5λ DNA
HincII4λ DNA
HindIII5λ DNA
KpnI2λ DNA
NarI20λ DNA
NdeI2λ DNA
NmeAIII***λ DNA
PciI3λ DNA
PstI1λ DNA
PvuII-HF2λ DNA
SacI5λ DNA
SalI10λ DNA
SalI-HF5λ DNA
SapI1λ DNA
ScaI15λ DNA
ScaI-HF4λ DNA
SmaI1λ DNA
SphI3λ DNA
SphI-HF3λ DNA
SspI5λ DNA
TspMI1λ DNA
XbaI2λ DNA
XmnI5λ DNA
** BspMI cleaves pUC19 poorly.  Even with 100 units/µg of pUC19, less than 50% cleavage is possible.
*** NmeAIII cleaves single site substrates poorly. Even with 20 units/µg of pUC19, less than 10% cleavage is possible.