pPrime (linearized)

Linearized vector with 3'-U overhangs for UA cloning of PCR products produced by non-proofreading DNA polymerases.

Sequence Author: 5 Prime

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BspQI - SapI (3527) PciI (3410) PspFI (3110) BseYI (3106) AlwNI (3001) PflMI (2560) Bpu10I (2314) BsmBI (2313) AsiSI (2297) EcoNI (2209) SmaI (2171) TspMI - XmaI (2169) BspDI - ClaI (1988) NruI (1954) AhdI (1647) BsaI (1581) lac operator Acc65I (3802) KpnI (3806) SphI (3814) PstI (3819) MluI (3821) SnaBI (3829) BamHI (3835) EcoRI (3842) End (3853) Start (1) EcoRI (6) SalI (12) AccI (13) HincII (14) HindIII (18) PaeR7I - XhoI (24) AvrII - StyI (30) NheI (35) BmtI (39) XbaI (41) AleI - PmlI (52) BstXI (54) EcoO109I - PspOMI (59) ApaI (63) Eco53kI (67) SacI (69) EagI - NotI (72) SP6 promoter AanI - PsiI (369) DraIII (497) BtgZI (498) NgoMIV (598) NaeI (600) BsaHI (1107) TatI (1164) ScaI (1166) NmeAIII (1500) BpmI (1578) pPrime 3852 bp
BspQI  (3527)
1 site
G C T C T T C N C G A G A A G N N N N

Sticky ends from different BspQI sites may not be compatible.
SapI  (3527)
1 site
G C T C T T C N C G A G A A G N N N N

Sticky ends from different SapI sites may not be compatible.
SapI gradually settles in solution, so a tube of SapI should be mixed before removing an aliquot.
PciI  (3410)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
PspFI  (3110)
1 site
C C C A G C G G G T C G
BseYI  (3106)
1 site
C C C A G C G G G T C G

After cleavage, BseYI can remain bound to DNA and alter its electrophoretic mobility.
AlwNI  (3001)
1 site
C A G N N N C T G G T C N N N G A C

Sticky ends from different AlwNI sites may not be compatible.
PflMI  (2560)
1 site
C C A N N N N N T G G G G T N N N N N A C C

Sticky ends from different PflMI sites may not be compatible.
Bpu10I  (2314)
1 site
C C T N A G C G G A N T C G

Cleavage may be enhanced when more than one copy of the Bpu10I recognition sequence is present.
This recognition sequence is asymmetric, so ligating sticky ends generated by Bpu10I will not always regenerate a Bpu10I site.
Sticky ends from different Bpu10I sites may not be compatible.
BsmBI  (2313)
1 site
C G T C T C N G C A G A G N ( N ) 4

Sticky ends from different BsmBI sites may not be compatible.
BsmBI-v2 is an improved version of BsmBI.
AsiSI  (2297)
1 site
G C G A T C G C C G C T A G C G
EcoNI  (2209)
1 site
C C T N N N N N A G G G G A N N N N N T C C

The 1-base overhangs produced by EcoNI may be hard to ligate.
Sticky ends from different EcoNI sites may not be compatible.
SmaI  (2171)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
TspMI  (2169)
1 site
C C C G G G G G G C C C
XmaI  (2169)
1 site
C C C G G G G G G C C C

Cleavage may be enhanced when more than one copy of the XmaI recognition sequence is present.
BspDI  (1988)
1 site
A T C G A T T A G C T A
ClaI  (1988)
1 site
A T C G A T T A G C T A
NruI  (1954)
1 site
T C G C G A A G C G C T
AhdI  (1647)
1 site
G A C N N N N N G T C C T G N N N N N C A G

The 1-base overhangs produced by AhdI may be hard to ligate.
Sticky ends from different AhdI sites may not be compatible.
BsaI  (1581)
1 site
G G T C T C N C C A G A G N ( N ) 4

Sticky ends from different BsaI sites may not be compatible.
BsaI can be used between 37°C and 50°C.
Acc65I  (3802)
1 site
G G T A C C C C A T G G
KpnI  (3806)
1 site
G G T A C C C C A T G G
SphI  (3814)
1 site
G C A T G C C G T A C G
PstI  (3819)
1 site
C T G C A G G A C G T C
MluI  (3821)
1 site
A C G C G T T G C G C A
SnaBI  (3829)
1 site
T A C G T A A T G C A T
BamHI  (3835)
1 site
G G A T C C C C T A G G

After cleavage, BamHI-HF® (but not the original BamHI) can remain bound to DNA and alter its electrophoretic mobility.
EcoRI  (3842)
2 sites
G A A T T C C T T A A G
End  (3853)
0 sites
Start  (1)
0 sites
EcoRI  (6)
2 sites
G A A T T C C T T A A G
SalI  (12)
1 site
G T C G A C C A G C T G
AccI  (13)
1 site
G T M K A C C A K M T G

Efficient cleavage with AccI requires ≥13 bp on each side of the recognition sequence.
Sticky ends from different AccI sites may not be compatible.
HincII  (14)
1 site
G T Y R A C C A R Y T G
HindIII  (18)
1 site
A A G C T T T T C G A A
PaeR7I  (24)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
XhoI  (24)
1 site
C T C G A G G A G C T C
AvrII  (30)
1 site
C C T A G G G G A T C C
StyI  (30)
1 site
C C W W G G G G W W C C

Sticky ends from different StyI sites may not be compatible.
NheI  (35)
1 site
G C T A G C C G A T C G
BmtI  (39)
1 site
G C T A G C C G A T C G
XbaI  (41)
1 site
T C T A G A A G A T C T
AleI  (52)
1 site
C A C N N N N G T G G T G N N N N C A C
PmlI  (52)
1 site
C A C G T G G T G C A C
BstXI  (54)
1 site
C C A N N N N N N T G G G G T N N N N N N A C C

Sticky ends from different BstXI sites may not be compatible.
EcoO109I  (59)
1 site
R G G N C C Y Y C C N G G R

Sticky ends from different EcoO109I sites may not be compatible.
PspOMI  (59)
1 site
G G G C C C C C C G G G
ApaI  (63)
1 site
G G G C C C C C C G G G

ApaI can be used between 25°C and 37°C.
Eco53kI  (67)
1 site
G A G C T C C T C G A G
SacI  (69)
1 site
G A G C T C C T C G A G
EagI  (72)
1 site