pPrime (linearized)

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

Sequence Author: 5 Prime

Try SnapGene for Free
|Download SnapGene Viewer
Explore Over 2.7k Plasmids: TA and GC Cloning Vectors | More Plasmid Sets
No matches
HomePlasmidsTA and GC Cloning VectorspPrime (linearized)
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		 C G G C C G G C C G G C
NotI  (72)
1 site		 G C G G C C G C C G C C G G C G
AanI  (369)
1 site		 T T A T A A A A T A T T
PsiI  (369)
1 site		 T T A T A A A A T A T T
DraIII  (497)
1 site		 C A C N N N G T G G T G N N N C A C
Sticky ends from different DraIII sites may not be compatible.
BtgZI  (498)
1 site		 G C G A T G ( N ) 10 C G C T A C ( N ) 10 ( N ) 4
Sticky ends from different BtgZI sites may not be compatible.
After cleavage, BtgZI can remain bound to DNA and alter its electrophoretic mobility.
BtgZI is typically used at 60°C, but is 75% active at 37°C.
NgoMIV  (598)
1 site		 G C C G G C C G G C C G
Efficient cleavage requires at least two copies of the NgoMIV recognition sequence.
NaeI  (600)
1 site		 G C C G G C C G G C C G
Efficient cleavage requires at least two copies of the NaeI recognition sequence.
BsaHI  (1107)
1 site		 G R C G Y C C Y G C R G
BsaHI is typically used at 37°C, but is even more active at 60°C.
TatI  (1164)
1 site		 W G T A C W W C A T G W
ScaI  (1166)
1 site		 A G T A C T T C A T G A
NmeAIII  (1500)
1 site		 G C C G A G ( N ) 18-19 N N C G G C T C ( N ) 18-19
Efficient cleavage requires at least two copies of the NmeAIII recognition sequence.
Sticky ends from different NmeAIII sites may not be compatible.
For full activity, add fresh S-adenosylmethionine (SAM).
BpmI  (1578)
1 site		 C T G G A G ( N ) 14 N N G A C C T C ( N ) 14
Efficient cleavage requires at least two copies of the BpmI recognition sequence.
Sticky ends from different BpmI sites may not be compatible.
After cleavage, BpmI can remain bound to DNA and alter its electrophoretic mobility.
BpmI quickly loses activity at 37°C.
AmpR
860 .. 1720  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
   Segment 1:  signal sequence  
   860 .. 928  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
860 .. 1720  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
   Segment 2:  
   929 .. 1720  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
860 .. 1720  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
KanR
1866 .. 2681  =  816 bp
271 amino acids  =  31.0 kDa
Product: aminoglycoside phosphotransferase
confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes
KanR
1866 .. 2681  =  816 bp
271 amino acids  =  31.0 kDa
Product: aminoglycoside phosphotransferase
confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes
ori
2766 .. 3354  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
2766 .. 3354  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
f1 ori
273 .. 728  =  456 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
f1 ori
273 .. 728  =  456 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
AmpR promoter
755 .. 859  =  105 bp
AmpR promoter
755 .. 859  =  105 bp
LacZα
3752 .. 3852  =  101 bp
33 amino acids  =  3.9 kDa
Product: LacZα fragment of β-galactosidase
LacZα
3752 .. 3852  =  101 bp
33 amino acids  =  3.9 kDa
Product: LacZα fragment of β-galactosidase
MCS
2 .. 78  =  77 bp
multiple cloning site
MCS
2 .. 78  =  77 bp
multiple cloning site
lac promoter
3678 .. 3708  =  31 bp
3 segments
   Segment 1:  -35  
   3678 .. 3683  =  6 bp
promoter for the E. coli lac operon
lac promoter
3678 .. 3708  =  31 bp
3 segments
   Segment 2:  
   3684 .. 3701  =  18 bp
promoter for the E. coli lac operon
lac promoter
3678 .. 3708  =  31 bp
3 segments
   Segment 3:  -10  
   3702 .. 3708  =  7 bp
promoter for the E. coli lac operon
lac promoter
3678 .. 3708  =  31 bp
3 segments
promoter for the E. coli lac operon
SP6 promoter
84 .. 102  =  19 bp
promoter for bacteriophage SP6 RNA polymerase
SP6 promoter
84 .. 102  =  19 bp
promoter for bacteriophage SP6 RNA polymerase
M13 fwd
116 .. 132  =  17 bp
common sequencing primer, one of multiple similar variants
M13 fwd
116 .. 132  =  17 bp
common sequencing primer, one of multiple similar variants
lac operator
3716 .. 3732  =  17 bp
The lac repressor binds to the lac operator to inhibit transcription in E. coli. This inhibition can be relieved by adding lactose or isopropyl-β-D-thiogalactopyranoside (IPTG).
lac operator
3716 .. 3732  =  17 bp
The lac repressor binds to the lac operator to inhibit transcription in E. coli. This inhibition can be relieved by adding lactose or isopropyl-β-D-thiogalactopyranoside (IPTG).
LacZα
2 .. 281  =  280 bp
92 amino acids  =  10.5 kDa
Product: LacZα fragment of β-galactosidase
LacZα
2 .. 281  =  280 bp
92 amino acids  =  10.5 kDa
Product: LacZα fragment of β-galactosidase
MCS
3802 .. 3852  =  51 bp
multiple cloning site
MCS
3802 .. 3852  =  51 bp
multiple cloning site
T7 promoter
3775 .. 3793  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
3775 .. 3793  =  19 bp
promoter for bacteriophage T7 RNA polymerase
M13 rev
3740 .. 3756  =  17 bp
common sequencing primer, one of multiple similar variants
M13 rev
3740 .. 3756  =  17 bp
common sequencing primer, one of multiple similar variants
ORF:  860 .. 1720  =  861 bp
ORF:  286 amino acids  =  31.6 kDa
ORF:  3 .. 281  =  279 bp
ORF:  92 amino acids  =  10.5 kDa  (no start codon)
ORF:  1866 .. 2681  =  816 bp
ORF:  271 amino acids  =  31.0 kDa
ORF:  1324 .. 1590  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
Click here to try SnapGene

Download pPrime (linearized).dna file

SnapGene

SnapGene is the easiest way to plan, visualize and document your everyday molecular biology procedures

  • Fast accurate construct design for all major molecular cloning techniques
  • Validate sequenced constructs using powerful alignment tools
  • Customize plasmid maps with flexible annotation and visualization controls
  • Automatically generate a rich graphical history of every edit and procedure
Download SnapGene

SnapGene Viewer

SnapGene Viewer is free software that allows molecular biologists to create, browse, and share richly annotated sequence files.

  • Gain unparalleled visibility of your plasmids, DNA and protein sequences
  • Annotate features on your plasmids using the curated feature database
  • Store, search, and share your sequences, files and maps
Download SnapGene Viewer

Individual Sequences & Maps

Allele TA Vector (linearized)
pCR2.1-TOPO (linearized)
pJAZZ-OK GC (left arm)
pSpark TA
pBAD-TOPO (linearized)
pCR4-TOPO (linearized)
pJAZZ-OK GC (right arm)
pSpark TA Done
pBAD Thio-TOPO (linearized)
pCR8 GW TOPO (linearized)
pLenti6.3 V5-TOPO (linearized)
pSTBlue-1 AccepTor
pBlue-TOPO (linearized)
pCRII-TOPO (linearized)
pLenti7.3 V5-TOPO (linearized)
pT7Blue T-Vector
pcDNA3.1 CT-GFP-TOPO (linearized)
pDrive (linearized)
pLPS-T (linearized)
pTA Plus (linearized)
pcDNA3.1 NT-GFP-TOPO (linearized)
pEF6 V5-His-TOPO (linearized)
pLUG (linearized)
pTargeT (linearized)
pcDNA3.1 V5-His-TOPO (linearized)
pENTR5'-TOPO (linearized)
pLUG-Multi (linearized)
pTOP TA V2 (linearized)
pcDNA3.3-TOPO (linearized)
pET SUMO (linearized)
pMT V5-His-TOPO (linearized)
pTrcHis-TOPO (linearized)
pcDNA3.4-TOPO (linearized)
pETBlue-1 AccepTor
pOptiVEC-TOPO (linearized)
pTrcHis2-TOPO (linearized)
pcDNA4 HisMax-TOPO (linearized)
pEXP5-CT TOPO (linearized)
pPrime (linearized)
pTZ57R_T
pcDNA5 FRT TO-TOPO (linearized)
pEXP5-NT TOPO (linearized)
pQE-30 UA (linearized)
pUC57-T
pcDNA5 FRT V5-His-TOPO (linearized)
pGC Blue (linearized)
pSC-A-amp kan (linearized)
pYES2.1 V5-His-TOPO (linearized)
pcDNA6.2 C-EmGFP-GW TOPO (linearized)
pGEM-T (linearized)
pSecTag FRT V5-His-TOPO (linearized)
RBC T&A Cloning Vector (linearized)
pcDNA6.2 C-YFP-GW TOPO (linearized)
pGEM-T Easy (linearized)
pSMART GC HK (linearized)
T-Vector pMD19 (Simple)
pcDNA6.2 N-EmGFP-GW TOPO (linearized)
pGlow-TOPO (linearized)
pSMART GC LK (linearized)
T-Vector pMD20
pCR-XL-TOPO (linearized)
pIB V5-His-TOPO (linearized)

Plasmid Sets

Basic Cloning Vectors
I.M.A.G.E. Consortium Plasmids
pET & Duet Vectors (Novagen)
TA and GC Cloning Vectors
Coronavirus Resources
Insect Cell Vectors
pGEX Vectors (GE Healthcare)
TOPO Cloning Vectors
CRISPR Plasmids
Luciferase Vectors
Plant Vectors
Viral Expression & Packaging Vectors
Fluorescent Protein Genes & Plasmids
Lucigen Vectors
Qiagen Vectors
Yeast Plasmids
Gateway® Cloning Vectors
Mammalian Expression Vectors
Structural Genomics Vectors

The maps, notes, and annotations in the zip file on this page are copyrighted material. This material may be used without restriction by academic, nonprofit, and governmental entities, except that the source must be cited as ’’www.snapgene.com/resources’’. Commercial entities must contact GSL Biotech LLC for permission and terms of use.

Discover the most user-friendly molecular biology experience.
Try for Free