User:Jessica Karen Wong/Primers
Scarring Primers
These will be used to PCR out T9002 in order to scar out the BB sites from a backbone plasmid.
- T9002_F -- CTTAGTAG CAATTG TCCCTATCAGTGATAGAGATTGACATC
- T9002_R -- TCAGCCAT ATGCAT TATAAACGCAGAAAGGCCCAC
Bold is the tail, italics is the restriction site.
- New T9002 Reverse that matches only GFP TCAGCCAT ATGCAT TTATTATTTGTATAGTTCATCCATGCC
- Melting Temp 55.0
- Original T9002_F CTTAGTAG CAATTG TCCCTATCAGTGATAGAGATTGACATC has melting temp 53.9
Bold is the tail, italics is the restriction site.
- New Longer I2055
- Fwd- CTTAGTAG CAATTG TCCCTATCAGTGATAGAGATTGACATCCCTATC melting temp 62
- Rev- TCAGCGAT ATGCAT TATAAACGCAGAAAGGCCCACCCG melting temp 63.6
- New Shorter I2055
- Fwd- CTTAGTAG CAATTG TCCCTATCAGTGATAGAGATTG melt 45.4
- Rev- TCAGCGAT ATGCAT TATAAACGCAGAAAGGCC melt 45.5
Keep same tails?
- Original I2055
- Fwd- CTTAGTAG CAATTG tccctatcagtgatagagattgacatc melt 53.9
- Rev- TCAGCGAT ATGCAT TATAAACGCAGAAAGGCCCAC melt 53.6 (is actually same primer as E0240R)
- I2056:
- F: Same as I2055
- R: same as I2055
- I2057:
- F: CTTAGTAG CAATTG TCACACAGGAAAGTACTAGATGGC (52.1)
- R: same as I2055
- I2057:
Also designed primers to PCR R0040 in if none of the colonies were successfully ligated
* Only ordered a forward primer with Tail including Mfe1 and R0040 * format: 8-mer.MfeI.promoter+mix.part of gfp (Tm) * CTTAGTAG.CAATTG.tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcactactag.ATGCGTAAAGGAGAAGAACTTTTC (52.4)
Ordered new I2056 primers to PCR in Promoter
- I2056_R0040_F 8mer.Mfe1.promoter+mix.part of RFP
- CTTAGTAG CAATTG tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcactactag ATGGCTTCCTCCGAAGACG (54.0)
BioBrick Primers
* E0240: o F (incl E0240, PstI): CTTAGTAG.ACTAGT.TCACACAGGAAAGTACTAGATGCG (53.1) o R (incl 3K3/1AK3, EcoRI): TCAGCGAT.GAATTC.CAGAAATCATCCTTAGCGAAAGC (54.2)
* I2057: o F (incl I2057, PstI): CTTAGTAG.ACTAGT.TCACACAGGAAAGTACTAGATGGC (52.1) o R: same as E0240
* I2055: o F (incl GFP, SpeI): CTTAGTAG.ACTAGT.ATGCGTAAAGGAGAAGAACTTTTC (52.4) o R (incl R0040, EcoRI): TCAGCGAT.GAATTC.GTGCTCAGTATCTCTATCACTGATAGG (52.0)
* I2056: o F (incl RFP, SpeI): CTTAGTAG.ACTAGT.ATGGCTTCCTCCGAAGACG (54.0) o R: Same as I2055
* For T9002: o F (incl RBS, GFP,EcoRI): TCAGCGAT.CTGCAG.TCACACAGGAAAGTACTAGATGCG (53.1) o R (incl lux pR, PstI) : CTTAGTAG.GAATTC.TTTATTCGACTATAACAAACCATTTTC (51.9)
Format: 8-mer.restriction site.primer
New Primers
T9002 pieces
- F2620-F 8mer mfe1 TCCCTATCAGTGATAGAGATTGACATC 53.9
- CTTAGTAG CAATTG TCCCTATCAGTGATAGAGATTGACATC
- F2620-R 8mer xba1 not1 eco1 TTTATTCGACTATAACAAACCATTTTC 51.9
- TCAGCGAT CTCTAGAAGCGGCCGCGAATTC TTTATTCGACTATAACAAACCATTTTC
- E0240-F 8mer spe1 NOT1 pst1 TCACACAGGAAAGTACTAGATGCG 53.1
- CTTAGTAG tactagtagcggccgctgcag TCACACAGGAAAGTACTAGATGCG
- E0240-R 8mer nsi1 GTGGGCCTTTCTGCGTTTATA 53.6
- TCAGCGAT ATGCAT GTGGGCCTTTCTGCGTTTATA
I2055/I2056 to account for RBS spacing
- I2055-F 8mer Xba1 ATGCGTAAAGGAGAAGAACTTTTC 52.4
- CTTAGTAG TCTAGA TGCGTAAAGGAGAAGAACTTTTC
- I2055-R 8mer xba1 NOT1 ecor1 GTGCTCAGTATCTCTATCACTGATAGG 52.0
- TCAGCGAT CTCTAGAAGCGGCCGCGAATTC GTGCTCAGTATCTCTATCACTGATAGG
- I2056-F 8mer Xba1 ATGGCTTCCTCCGAAGACG 54.0
- CTTAGTAG TCTAGA TGGCTTCCTCCGAAGACG
- I2056-R same as I2055-R
Nishant's Primers
1) TCAGCGAT GCGGCCGC GAATTC CAGAAATCATCCTTAGCGAAAGC, BB_P_Rev_Eco
2) CTTAGTAG GCGGCCGC ACTAGT TCACACAGGAAAGTACTAGATGCG, BB_E0240_Fwd_Spe
3) CTTAGTAG GCGGCCGC TCTAGA TCACACAGGAAAGTACTAGATGCG, BB_E0240_Fwd_Xba
4) TCAGCGAT GCGGCCGC ACTAGT GTGCTCAGTATCTCTATCACTGATAGG, BB_R_Rev_Spe
5) TCAGCGAT GCGGCCGC GAATTC GTGCTCAGTATCTCTATCACTGATAGG, BB_R_Rev_Eco
6) CTTAGTAG GCGGCCGC TCTAGA ATGCGTAAAGGAGAAGAACTTTTC, BB_I2055_Fwd_Xba
7) TCAGCGAT GCGGCCGC GAATTC TTTATTCGACTATAACAAACCATTTTC, BB_T9002_Rev_Eco
8) CTTAGTAG GCGGCCGC GAATTC TCACACAGGAAAGTACTAGATGCG, BB_T9002_Fwd_Pst
9) CTTAGTAG GCGGCCGC TCTAGA ATGGCTTCCTCCGAAGACG, BB_I2056_Fwd_Xba
10) CTTAGTAG GCGGCCGC ACTAGT TCACACAGGAAAGTACTAGATGGC, BB_I2057_Fwd_Spe
11) CTTAGTAG GCGGCCGC TCTAGA TCACACAGGAAAGTACTAGATGGC, BB_I2057_Fwd_Xba
REVISION 7-23
- CTTAGTAG GCGGCCGC ACTAGT G TCACACAGGAAAGTACTAGATGCG, BBbp_E0240_Fwd_Spe
- CTTAGTAG GCGGCCGC TCTAGA G TCACACAGGAAAGTACTAGATGCG, BBbp_E0240_Fwd_Xba
- CTTAGTAG GCGGCCGC ACTAGT G TCACACAGGAAAGTACTAGATGGC, BBbp_I2057_Fwd_Spe
- CTTAGTAG GCGGCCGC TCTAGA G TCACACAGGAAAGTACTAGATGGC, BBbp_I2057_Fwd_Xba
- TCAGCGAT GCGGCCGC ACTAGT A GTGCTCAGTATCTCTATCACTGATAGG, BBbp_R_Rev_Spe
- CTTAGTAG GCGGCCGC TCTAG ATGCGTAAAGGAGAAGAACTTTTC, BBbp_I2055_Fwd_Xba
- CTTAGTAG GCGGCCGC TCTAG ATGGCTTCCTCCGAAGACG, BBbp_I2056_Fwd_Xba