3.7 Recognition Sites in Common DNA Substrates
Industry standards for enzyme unit definitions generally use DNA substrates other than
plasmid DNA. It is therefore necessary to determine how many units of enzyme will be
needed in cloning experiments involving plasmid vectors. Linear DNA such as lambda can be
cleaved more efficiently than closed circular plasmid DNA, and fewer units of enzyme per
microgram of DNA may be required for a complete digest. The number of sites per microgram
of DNA must also be considered. For example, 1µg of lambda contains 0.0317 picomoles of
DNA. For a 3,000bp plasmid there are 0.5pmol DNA in 1µg. Therefore, in 1µg of lambda DNA
there will be fewer cut sites to digest than in 1µg of plasmid DNA. Table 3.7 provides
information on the number of recognition sites for Promega's restriction enzymes in
various DNA substrates.
| Enzyme |
Recognition
Site |
Number of Sites in: |
lambda
|
Ad2
|
phiX174
|
pUC18
|
M13mp18
|
pBR322
|
| Aat II |
GACGT/C
|
10 |
3 |
1 |
1 |
0 |
1 |
| Acc I |
GT/MKAC
|
9 |
17 |
2 |
1 |
1 |
2 |
| Acc III |
T/CCGGA
|
24 |
8 |
0 |
0 |
0 |
1 |
| Acc65 I |
G/GTACC
|
2 |
8 |
0 |
1 |
1 |
0 |
| AccB7 I |
CCANNNN/NTGG
|
14 |
18 |
2 |
0 |
0 |
2 |
| Age I |
A/CCGGT
|
13 |
5 |
0 |
0 |
0 |
0 |
| Alu I |
AG/CT
|
143 |
158 |
24 |
16 |
27 |
17 |
| Alw26 I |
GTCTC(1/5)
|
37 |
60 |
4 |
4 |
5 |
3 |
| Alw44 I |
G/TGCAC
|
4 |
7 |
1 |
3 |
0 |
3 |
| Apa I |
GGGCC/C
|
1 |
12 |
0 |
0 |
0 |
0 |
| Ava I |
C/YCGRG
|
8 |
40 |
1 |
1 |
2 |
1 |
| Ava II |
G/GWCC
|
35 |
73 |
1 |
2 |
1 |
8 |
| Bal I |
TGG/CCA
|
18 |
17 |
0 |
0 |
1 |
1 |
| BamH I |
G/GATCC
|
5 |
3 |
0 |
1 |
1 |
1 |
| Ban I |
G/GYRCC
|
25 |
57 |
3 |
4 |
7 |
9 |
| Ban II |
GRGCY/C
|
7 |
57 |
0 |
1 |
2 |
2 |
| Bbu I |
GCATG/C
|
6 |
8 |
0 |
1 |
1 |
1 |
| Bcl I |
T/GATCA
|
8 |
5 |
0 |
0 |
0 |
0 |
| Bgl I |
GCCNNNN/NGGC
|
29 |
20 |
0 |
2 |
1 |
3 |
| Bgl II |
A/GATCT
|
6 |
11 |
0 |
0 |
1 |
0 |
| BsaM I |
GATTGCN/
|
46 |
10 |
4 |
0 |
1 |
1 |
| BsaO I |
CGRY/CG
|
22 |
50 |
1 |
5 |
4 |
7 |
| Bsp1286I |
GDGCH/C
|
38 |
105 |
3 |
10 |
5 |
10 |
| BsrBR I |
GATNN/NNATC
|
21 |
2 |
2 |
0 |
2 |
1 |
| BsrS I |
ACTGGN/
|
110 |
86 |
9 |
11 |
18 |
19 |
| BssH II |
G/CGCGC
|
6 |
52 |
1 |
0 |
0 |
0 |
| Bst71 I |
GCAGC(8/12)
|
199 |
179 |
14 |
12 |
10 |
21 |
| Bst98 I |
C/TTAAG
|
3 |
4 |
2 |
0 |
0 |
0 |
| BstE II |
G/GTNACC
|
13 |
10 |
0 |
0 |
0 |
0 |
| BstO I |
CC/WGG
|
71 |
136 |
2 |
5 |
7 |
6 |
| BstX I |
CCANNNNN/NTGG
|
13 |
10 |
3 |
0 |
0 |
0 |
| BstZ I |
C/GGCCG
|
2 |
19 |
0 |
0 |
0 |
1 |
| Bsu36 I |
CC/TNAGG
|
2 |
7 |
0 |
0 |
1 |
0 |
| Cfo I |
GCG/C
|
215 |
375 |
18 |
17 |
26 |
31 |
| Cla I |
AT/CGAT
|
15 |
2 |
0 |
0 |
2
|
1
|
| Csp I |
CG/GWCCG
|
5 |
2 |
0 |
0 |
0 |
0 |
| Csp45 I |
TT/CGAA
|
7 |
1 |
0 |
0 |
0 |
0 |
| Dde I |
C/TNAG
|
104 |
97 |
14 |
6 |
29 |
8 |
| Dpn I |
GmeA/TC
|
116 |
87 |
0 |
15 |
7 |
22 |
| Dra I |
TTT/AAA
|
13 |
12 |
2 |
3 |
5 |
3 |
| EclHK I |
GACNNN/NNGTC
|
9 |
9 |
1 |
1 |
0 |
1 |
| Eco47 III |
ACG/GCT
|
2 |
13 |
0 |
0 |
2 |
4 |
| Eco52 I |
C/GGCCG
|
2 |
19 |
0 |
0 |
0 |
1 |
| EcoICR I |
GAG/CTC
|
2 |
16 |
0 |
1 |
1 |
0 |
| EcoR I |
G/AATTC
|
5 |
5 |
0 |
1 |
1 |
1 |
| EcoR V |
GAT/ATC
|
21 |
9 |
0 |
0 |
0 |
1 |
| Fok I |
GGATG(9/13)
|
149 |
78 |
8 |
5 |
4 |
12 |
| Hae II |
RGCGC/Y
|
48 |
76 |
8 |
3 |
6 |
11 |
| Hae III |
GG/CC
|
149 |
216 |
11 |
11 |
15 |
22 |
| Hha I |
GCG/C
|
215 |
375 |
18 |
17 |
26 |
31 |
| Hinc II |
GTY/RAC
|
35 |
25 |
13 |
1 |
1 |
2 |
| Hind III |
A/AGCTT
|
7 |
12 |
0 |
1 |
1 |
1 |
| Hinf I |
G/ANTC
|
148 |
72 |
21 |
6 |
27 |
10 |
| Hpa I |
GTT/AAC
|
14 |
6 |
3 |
0 |
0 |
0 |
| Hpa II |
C/CGG
|
328 |
171 |
5 |
13 |
18 |
26 |
| Hsp92 I |
GR/YCGC
|
40 |
44 |
7 |
3 |
1 |
6 |
| Hsp92 II |
CATG/
|
181 |
183 |
22 |
11 |
16 |
26 |
| I-Ppo I |
CTCTCTTAA/GGTAGC
|
0 |
0 |
0 |
0 |
0 |
0 |
| Kpn I |
GGTAC/C
|
2 |
8 |
0 |
1 |
1 |
0 |
| Mbo I |
/GATC
|
116 |
87 |
0 |
15 |
7 |
22 |
| Mbo II |
GAAGA(8/7)
|
130 |
113 |
11 |
7 |
12 |
11 |
| Mlu I |
M/CGCGT
|
7 |
5 |
2 |
0 |
0 |
0 |
| Msp I |
C/CGG
|
328 |
171 |
5 |
13 |
18 |
26 |
| MspA I |
CMG/CKG
|
75 |
95 |
4 |
6 |
4 |
5 |
| Nae I |
GCC/GGC
|
1 |
13 |
0 |
0 |
1 |
4 |
| Nar I |
GG/CGCC
|
1 |
20 |
2 |
1 |
1 |
4 |
| Nci I |
CC/SGG
|
114 |
97 |
1 |
7 |
4 |
10 |
| Nco I |
C/CATGG
|
4 |
20 |
0 |
0 |
0 |
0 |
| Nde I |
CA/TATG
|
7 |
2 |
0 |
1 |
3 |
1 |
| Nde II |
/GATC
|
116 |
87 |
0 |
15 |
7 |
22 |
| NgoM IV |
G/CCGGC
|
1 |
13 |
0 |
0 |
1 |
4 |
| Nhe I |
G/CTAGC
|
1 |
4 |
0 |
0 |
0 |
1 |
| Not I |
GC/GGCCGC
|
0 |
7 |
0 |
0 |
0 |
0 |
| Nru I |
TCG/CGA
|
5 |
5 |
2 |
0 |
0 |
1 |
| Nsi I |
ATGCA/T
|
14 |
9 |
0 |
0 |
0 |
0 |
| Pst I |
CTGCA/G
|
28 |
30 |
1 |
1 |
1 |
1 |
| Pvu I |
CGAT/CG
|
3 |
7 |
0 |
2 |
1 |
1 |
| Pvu II |
CAG/CTG
|
15 |
24 |
0 |
2 |
3 |
1 |
| Rsa I |
GT/AC
|
113 |
83 |
11 |
3 |
19 |
3 |
| Sac I |
GAGCT/C
|
2 |
16 |
0 |
1 |
1 |
0 |
| Sac II |
CCGC/GG
|
4 |
33 |
1 |
0 |
0 |
0 |
| Sal I |
G/TCGAC
|
2 |
3 |
0 |
1 |
1 |
1 |
| Sau3A I |
G/ATC
|
116 |
87 |
0 |
15 |
7 |
22 |
| Sau96 I |
G/GNCC
|
74 |
164 |
2 |
6 |
4 |
15 |
| Sca I |
AGT/ACT
|
5 |
5 |
0 |
1 |
0 |
1 |
| Sfi I |
GGCCNNNN/NGGCC
|
0 |
3 |
0 |
0 |
0 |
0 |
| Sgf I(a) |
GCGAT/CGC
|
0 |
1 |
0 |
0 |
0 |
0 |
| Sin I |
G/GWCC
|
35 |
73 |
1 |
2 |
1 |
8 |
| Sma I |
CCC/GGG
|
3 |
12 |
0 |
1 |
1 |
0 |
| SnaB I |
TAC/GTA
|
1 |
0 |
0 |
0 |
1 |
0 |
| Spe I |
A/CTAGT
|
0 |
3 |
0 |
0 |
0 |
0 |
| Sph I |
GCATG/C
|
6 |
8 |
0 |
1 |
1 |
1 |
| Ssp I |
AAT/ATT
|
20 |
5 |
1 |
1 |
6 |
1 |
| Stu I |
AGG/CCT
|
6 |
11 |
1 |
0 |
0 |
0 |
| Sty I |
C/CWWGG
|
10 |
44 |
0 |
0 |
0 |
1 |
| Taq I |
T/CGA
|
121 |
50 |
10 |
4 |
13 |
7 |
| Tru9 I |
T/TAA
|
195 |
115 |
35 |
13 |
62 |
15 |
| Tth111 I |
GACN/NNGTC
|
2 |
12 |
0 |
0 |
0 |
1 |
| Vsp I |
AT/TAAT
|
17 |
3 |
2 |
3 |
6 |
1 |
| Xba I |
T/CTAGA
|
1 |
5 |
0 |
1 |
1 |
0 |
| Xho I |
C/TCGAG
|
1 |
6 |
1 |
0 |
0 |
0 |
| Xho II |
R/GATCY
|
21 |
22 |
0 |
7 |
3 |
8 |
| Xma I |
C/CCGGG
|
3 |
12 |
0 |
1 |
1 |
0 |
| Xmn I |
GAANN/NNTTC
|
24 |
5 |
3 |
1 |
2 |
2 |
|
