Cleavage Close to the End of DNA Fragments

Annealed 5´ FAM labeled oligos were incubated with the indicated enzyme (10 units/ 1pmol oligo) for 60 minutes at the recommended incubation temperature and NEBuffer. The digest was run on a TBE acrylamide gel and analyzed by fluorescent imaging. The double stranded oligos were designed to have the indicated number of base pairs from the end followed by the recognition sequence and an additional 12 bases. In some cases asymmetric cleavage was observed and interpreted as a negative result. Asymmetric cleavage decreased with increasing base pairs from the end.
Note: As a general rule and for enzymes not listed below, 6 base pairs should be added on on either side of the recognition site to cleave efficiently. The extra bases should be chosen so that palindromes and primer dimers are not formed. In most cases there is no requirement for specific bases.

Note: You may download the previous tables, which use a different methodology here:
Cleavage Close to the End of DNA Fragments (oligonucleotides) and
Cleavage Close to the End of DNA Fragments (linearized vector)

Chart Legend
 
0% + 0-20%
++ 20-50% +++ 50-100%
nt not tested  

* RE-Mix® master mix format available 

EnzymeBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
AccI-----
AciI-+++++++
AgeI+++++++++++++++
AgeI-HF®++++++++++++++
AluI-++++++++++++
ApaI+++++++++++++++
AscI+++++++++++++++
AvrII+++++++++++++
EnzymeBack to topBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
BamHI++++++++++++
BamHI-HF®+++++++++++
BbsI-HF®+++++++++++++++
BglII++++++++++++++
BmtI+++++++++++++++
BmtI-HF®+++++++++++++++
BsaI+++++++++++++++
BsaI-HF®+++++++++++++++
BsiWI++++++++++++++
BsiWI-HF®+++++++++++++++
BsmBI+++++++++++++++
BsrGI+++++++++++++++
EnzymeBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
BssHII+++++++++++++
BstZ17I-HF®+++++++++++++
EnzymeBack to topBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
ClaI--+++++++
EnzymeBack to topBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
DdeI+++++++++++++++
DpnI-++++ntnt
DraIII+++++++++++++++
DraIII-HF®+++++++++++++++
EnzymeBack to topBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
EagI++++++++++++++
EagI-HF®+++++++++++++
EcoRI+++++++++
EcoRI-HF®++++++++++
EcoRV+++++++++++
EcoRV-HF®++++++++++
EnzymeBack to topBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
FseI++++++++++++
EnzymeBack to topBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
HindIII-++++++++++
HindIII-HF®-++++++++++
HpaI+++++++++++++++
EnzymeBack to topBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
KpnI+++++++++++++
KpnI-HF®+++++++++++++
EnzymeBack to topBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
MfeI++++++++++++
EnzymeBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
MfeI-HF®++++++++++++
MluI++++++++++++
MseI+++++++++++++++
EnzymeBack to topBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
NcoI-+++++++++++
NcoI-HF®++++++++++++
NdeI+++++++++++
NheI++++++++++++
NheI-HF®+++++++++++++
NlaIII++++++++++++++
NotI++++++++++
NotI-HF®++++++++++
NsiI+++++++++++
NspI--+++++
EnzymeBack to topBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
PacI+++++++++++++++
PciI+++++++++++++++
PmeI+++++++++++++++
PstI+++++++++++++
PstI-HF®++++++++++++++
PvuI+++++++++++++++
PvuI-HF®+++++++++++++++
EnzymeBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
PvuII++++++++++++
PvuII-HF®-++++++++++
EnzymeBack to topBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
RsaI+++++++++++++
EnzymeBack to topBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
SacI-+++++++++++
SacI-HF®-++++++++++
SacII+++++++++++++++
SalI-+++++++++++
SalI-HF®-+++++++++++
SapI+++++++++++++++
Sau3AI+++++++++++++++
SbfI++++++++++++++
SbfI-HF®++++++++++++++
ScaI+++++++++++++++
ScaI-HF®+++++++++++++
SfiI+++++++++++++++
SmaI+++++++++++++++
SpeI+++++++++
SpeI-HF®+++++++++
SphI+++++++++++++++
SphI-HF®+++++++++++++
EnzymeBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
SspI+++++++++++++
SspI-HF®+++++++++++++
StuI+++++++++++++++
StyI++++++++++++
StyI-HF®+++++++++++++
EnzymeBack to topBase Pairs from end
1 bp2 bp3 bp4 bp5 bp
XbaI++++++++++
XhoI++++++++++++
XmaI+++++++++++++++
HF® is a registered trademark of New England Biolabs, Inc.
* AccI requires at least 13 base pairs beyond the end of its recognition sequence to cleave efficiently.