IGEM:MIT/2005/Sequences of primers specified
The melting temperatures were calculated mostly by the following site:Oligonucleotide Primer Check
Reverse Complement
Codon Table
Translation Tools
Check KO
- FecA/TetR
gacgttcccgctgaaaaata, FecAKO check left1
gcgactcctgcattaggaag, FecAKO check right1
gcttgcggtattcggaatcttg, FecAKO check left2
TGCGGGACTTAAGCAGCAGTAC, FecAKO check right2
Primers for Sequencing
- FecR'
VR1 5' attaccgcctttgagtgagc 3' T_m=68.2 VF2 5' tgccacctgacgtctaagaa 3' T_m=68.2 FecR'seq.fwd: 5' ctcactgctttagggacag 3' goes w/ VR1 T_m=67.6 FecR'seq.rev: 5' CTGGCCCTGACGGGTCAGG 3' goes w/ VF2 T_m=70.3
- FecA'
VR1 VF2 FecA'seq.fwd1: 5' cttacggtcagccgcagc 3' goes w/ FecA'seq.rev2 T_m=71.3 FecA'seq.rev1: 5' ACGGGGATGCCGTCCATC 3' goes w/ VF2 T_m=71.3 FecA'seq.fwd2: 5' cgagcctgggctaccag 3' goes w/ FecA'seq.rev3 T_m=70.7 FecA'seq.rev2: 5' CATACGGGCGGGTGGATTG 3' goes w/ FecA'seq.fwd1 T_m=71.9 FecA'seq.fwd3: 5' gtacagtacagccagattggc 3' goes w/ VR1 T_m=70.8 FecA'seq.rev3: 5' GAACGAGCCTTCAGTGTTTGC 3' goes w/ FecA'seq.fwd2 T_m=70.8
- PhoA
VR1 VF2 PhoAseq.fwd: 5' ggcaaccgctggtgaatggcag 3' goes w/ PhoAseq.rev2 T_m=76.9 PhoAseq.rev: 5' CAGCAAAGGTTTTTGCGCCGCCG 3' goes w/ VF2 T_m=77.1
- scFv-linker
scFv-L fwd: 5' gacgtcgttatgactcaaacaccac 3' T_m=74.2 scFv-L rev: 5' GCTGCCCGGCGCGCTGCT 3' T_m=78.2
Fur knockout with Chloramphenicol resistance marker
- NEW: 41bp homologus with Fur gene + 20-25bp primer to PCR Chloramphenicol gene
Cm fwd: 5' atgactgataacaataccgccctaaagaaagctggcctgaa ctggatctatcaacaggagtcc 3'T_m,i=71.3 T_m,f=89.7 Cm rev: 5' ttatttgccttcgtgcgcatgttcatcttcgcggcaatcgc GTTGATCGGGCACGTAAGAGGTT 3'T_m,i=73.6 T_m,f=92.1
- OLD:
Fwd: 5' atgactgataacaataccgccctaaagaaagctggcctgaa gctcgaggcttggattctcac 3' T_m,i=72.8 T_m,f= 90.5 Rev: 5' ttatttgccttcgtgcgcatgttcatcttcgcggcaatcgc ctcgagttgatcgggcacgta 3' t_m,i=72.8 T_m,f=92.4
FecA KO with Chloramphenicol resistance marker
- homologous to FecA gene + 20-25bp primer designed by Primer3
gtctctcgttttccgcttttgctgcacaggttaatatcgc ctggatctatcaacaggagtcc, FecA-Cm fwd
aggcatctatgcaggccagccgcgcacgctgtatatgcag GTTGATCGGGCACGTAAGAGGTT, FecA-Cm rev
ctggatctatcaacaggagtcc, Cm-left
GTTGATCGGGCACGTAAGAGGTT, Cm-right
FecA knockout with Tetracycline resistance marker
- homologous to FecA gene + 20-25bp primer designed by Primer3
gtctctcgttttccgcttttgctgcacaggttaatatcgc tgagtaaacttggtctgacagctc, TetR_fwd1
aggcatctatgcaggccagccgcgcacgctgtatatgcag cgctgagataggtgcctcac, TetR_rev1
gtctctcgttttccgcttttgctgcacaggttaatatcgc tgagtaaacttggtctgacagc , TetR_fwd2
aggcatctatgcaggccagccgcgcacgctgtatatgcag cgctgagataggtgcctcac , TetR_rev2
gtctctcgttttccgcttttgctgcacaggttaatatcgc tgagtaaacttggtctgacagc , TetR_fwd3
aggcatctatgcaggccagccgcgcacgctgtatatgcag gctgagataggtgcctcactg , TetR_rev3
gtctctcgttttccgcttttgctgcacaggttaatatcgc atgagtaaacttggtctgacagctc , TetR_fwd4
aggcatctatgcaggccagccgcgcacgctgtatatgcag cgctgagataggtgcctcac , TetR_rev4
- TetR primers designed by Primer3 (NO FecA homology)
left1 tgagtaaacttggtctgacagctc
right1 cgctgagataggtgcctcac
left2 tgagtaaacttggtctgacagc
right2 cgctgagataggtgcctcac
left3 tgagtaaacttggtctgacagc
right3 gctgagataggtgcctcactg
left4 atgagtaaacttggtctgacagctc
right4 cgctgagataggtgcctcac
- NEW 41bp homologous w/ FecA gene + 20-25bp primer to PCR Tetracycline resistance
Tet fwd: 5' gtctctcgttttccgcttttgctgcacaggttaatatcgc gagattctcatgtttgacagc 3' T_m,i=66.9 T_m,f=89.9 Tet rev: 5' aggcatctatgcaggccagccgcgcacgctgtatatgcag gcattggtaactcgagttagg 3' T_m,i=68.9 T_m,f=93.3
- OLD
Fwd: 5' atgacgccgttacgcgtttttcgtaaaacaacacctttggt gagattctcatgtttgacagc 3' T_m,i=66.9 T_m,f=88.5 Rev: 5' tcagaacttcaacgacccctgcatatacagcgtgcgcggct gcattggtaactcgagttagg 3' T_m,i=68.9 T_m,f=92.4
ToxR (ATCC)
Fwd: tctagatgttcggattaggacacaa
Rev: ctgcaggcggccgctactagtcgttaggggtttaaagctgga
scFv
- (pCT-4-4-20, pCT302 S101A, pCT-4M5.3 anti-fluorescein plasmids)
FWD: 5' CATCAT GAATTC GCGGCCGC T TCTAGA GACGTCGTTATGACTCAAACACC 3' T_m,i=71.8 T_m,f=88.5 rand EcoRI NotI XbaI Primer
REV: 5' GCTCAT ACTAGT TTATTA CTTATCATCATCATCCTTATAATC GGAGACGGTGACTGAGGTTCC 3' T_m,i=74.7 T_m,f=87.1 rand SpeI Stop FLAG Tag Primer
FWD-flag-test: CATCAT GAATTC GCGGCCGC T TCTAGA TG GACGTCGTTATGACTCAAACACC -rand- -EcoRI --NotI-- -XbaI[---] Primer start
FecA
fecA-Fwd 5’ CATCAT GAATTC GCGGCCGC TCTAGA TGACGCCGTTACGCGTTTTTCG 3’ T_m,i=73.2 T_m,f=89.6 rand EcoRI NotI XbaI primer fecA-Rev 5’ GCCATA ACTAGT TTATTA TCAGAACTTCAACGACCCCT 3’ T_m,i=68.2 T_m,f=79.9 rand SpeI stop primer
FecA'
Middle Fwd- 5'GGACGGCAGCGGACTGCAAGTAAAACCGCTGGGAAATAAC 3' T_m=84.7 Middle Rev- 5’GTTATTTCCCAGCGGTTTTACTTGCAGTCCGCTGCCGTCC 3' T_m=84.7
FecA Promoter
- registry specified 5'-3'
fecA Promoter Fwd- 5’CATCAT GAATTC GCGGCCGC T TCTAGA TGGATAAACATTTCACCACTG 3' T_m,i=65.0 T_m,f=86.2 rand EcoRI NotI XbaI primer fecA Promoter Rev- 5'GCCATA CTGCAG CGGCCGC T ACTAGT GTGTTCAGCTATGAGTCGAAC 3' T_m,i= 68.9 T_m,f=89.8 rand PstI NotI SpeI primer
- registry specified 3'-5'
fecA Promoter Fwd- 5’CATCAT GAATTC GCGGCCGC T TCTAGA CACAAGTCGATACTCAGCTTGCTC 3' T_m,i=73.9 T_m,f=87.9 rand EcoRI NotI XbaI primer fecA Promoter Rev- 5'GCCATA CTGCAG CGGCCGC T ACTAGT ACCTATTTGTAAAGTGGTGACATTCC 3' T_m,i=71.3 T_m,f=89 rand PstI NotI SpeI primer
FecR
fecR-Fwd 5' CATCAT GAATTC GCGGCCGC TCTAGA tgaatcctttgttaaccgattccc 3'T_m 66 rand EcoRI NotI XbaI primer fecR-Rev 5' GCCATA ACTAGT TTATTA ttacagtggtgaaatgtttatccag 3' T_m 68 rand SpeI stop primer
FecR'
Middle Fwd 5'gtgaaagcctacagttcagcgcctcag3' T_m 84 Middle Rev 5'ctgaggcgctgaactgtaggctttcac3' T_m 84
FecI
fecI-Fwd 5'CATCAT GAATTC GCGGCCGC T TCTAGA tgtctgaccgcgccactacc3' T_m 68 rand EcoRI NotI XbaI primer fecI-Rev 5'GCCATA CTGCAG CGGCCGC T ACTAGT A TTATTA tcataacccatactccagacggaa3' T_m 70 rand PstI NotI SpeI stop primer
==MalE== (updated/fixed)
fwd: 5' CCGTTA GAATTC GCGGCCGC T TCTAGA atgaaaataaaaacaggtgcacgc3' T_m,i=68.8 T_m,f=85.5 junk EcoRI NotI XbaI Primer rev: 5' ACTGAG CTGCAG GCGGCCGC T ACTAGT TTATTA TTACTTGGTGATACGAGTCTGC 3' T_m,i=69.5 T_m,f=89.4 junk PstI NotI SpeI Stop Primer
PhoA
- NEW:
fwd2: 5' CATGAG GAATTC GCGGCCGC T TCTAGA gtgaaacaaagcactattgcactggc 3' T_m,i=74.5 T_m,f=89.7 rev2: 5' AAGCTA CTGCAG GCGGCCGC T ACTAGT TTATTA TTATTTCAGCCCCAGAGCGGCTTTC 3' T_m,i=75.8 T_m,f=90.4 E1fwd: 5' cgatgctgcctcactgaactcggtgacggaagcgaatcag 3' T_m=88.2 E1rev: 5' CTGATTCGCTTCCGTCACCGAGTTCAGTGAGGCAGCATCG 3' T_m=88.2 E2fwd: 5' cgtacaacgggcgctggagttcgctaaaaaggagggtaac 3' T_m=87.2 E2rev: 5' GTTACCCTCCTTTTTAGCGAACTCCAGCGCCCGTTGTACG 3' T_m=87.2
- OLD:
fwd: 5' CATGAG GAATTC GCGGCCGC T TCTAGA ATGAAACAGAGCACCATTGCG 3' T_m,i=68.9 T_m,f=88.8 junk EcoRI NotI XbaI Primer rev: 5' AAGCTA CTGCAG GCGGCCGC T ACTAGT TTATTA TTATTTCAGGCCCAGCGCC 3' T_m,i=69.7 T_m,f=89.8 junk PstI NotI SpeI Stop Primer
Middle(1) fwd: 5' caccgcggaactgcaagatgcgaccccggcg 3' T_m=88.8 * rev: 5' CGCCGGGGTCGCATCTTGCAGTTCCGCGGTG 3' T_m=88.8 *
Middle(2) fwd: 5' aggcttttttctgcaagtggaaggcgcgagc 3' T_m=82.2 * rev: 5' GCTCGCGCCTTCCACTTGCAGAAAAAAGCCT 3' T_m=82.2 *
Adding Terminal Linker in scFv
linker fwd1: 5'GACGTCGTTATGACTCAAACACC 3' T_m,i= 71.8 primer linker rev1': 5' CGCGCTGCCGCTATGGCTCGCGCTGTTCGGGGAGACGGTGACTGAGGTTC 3' T_m,i=74.7 T_m,f=95.9 primer linker fwd2: 5' CATCAT GAATTC GCGGCCGC T TCTAGA GACGTCGTTATGACTCAAACACC 3' T_m,i=71.8 T_m,f=88.5 rand EcoRI NotI XbaI primer linker rev2': 5' GCTGCCCGGCGCGCTGCTGGTGTTCGGCGCGCTGCCGCTATGGCTCG 3' T_m,i=74.7 T_m,f=98.5 primer linker rev3: 5' GCTCAT ACTAGT CTTATCATCATCATCCTTATAATC TCCGGACCGTCGTCTAGTTCT 3' T_m,i=72.8 T_m,f=86.9 rand SpeI FLAG Tag Primer
- Verifying addition:
scFv-L fwd: 5' gacgtcgttatgactcaaacaccac 3' T_m=74.2 scFv-L rev1: 5' GCTGCCCGGCGCGCTGCT 3' T_m=78.2 scFv-L rev2: 5' CTATGGCTCGCGCTGTTCGG 3' T_m=74.7
FecA-scFv fusion
Note: scFv_rev_Tm=76.6 (44.8%); scFv_fwd_Tm=82.5 (81.0%)
Rev_primer=first_29_bp_of_scFv(reversecomplemented) + 21_bp_of_FecA(reversecomplemented)
Fwd_primer=last_21_bp_of_scFv + 21_bp_of_FecA
more documentation in http://web.mit.edu/ymk/Public/igem/feca_scfv_fusions2.txt
- Final: Type1s
Rev138: gatAGTGGTGTTTGAGTCATAACGACGTC GTCACGCGCGCCAGCATGTTC T_m=76.7 Fwd138: accagcagcgcgccgggcagc gtgatccgccgtgaggatttc T_m=72.8
Rev155: gatAGTGGTGTTTGAGTCATAACGACGTC ctcacgcatggtggttgcgcc T_m=76.7 Fwd155: accagcagcgcgccgggcagc gtacttaaccgcatccctggc T_m=72.8
Rev176: gatAGTGGTGTTTGAGTCATAACGACGTC caggtcgtggctgccggtgcc T_m,fec=80.6 Fwd176: accagcagcgcgccgggcagc gcgatgaactttggcatccggggc T_m,fec=79
Rev178: gatAGTGGTGTTTGAGTCATAACGACGTC catcgccaggtcgtggctgcc T_m=78.6 Fwd178: accagcagcgcgccgggcagc aactttggcatccggggcctg T_m=74.7
Rev180: gatAGTGGTGTTTGAGTCATAACGACGTC aaagttcatcgccaggtcgtggctg T_m,fec=77.5 Fwd180: accagcagcgcgccgggcagc ggcatccggggcctgaacccg T_m,fec=80.6
Rev527: gatAGTGGTGTTTGAGTCATAACGACGTC cgccggaagcggtgcgttata T_m=74.7 Fwd527: accagcagcgcgccgggcagc ttgaacgtgctctatcacctg T_m=68.9
Rev571: gatAGTGGTGTTTGAGTCATAACGACGTC tcgcgctttttccggttcaac T_m=70.8 Fwd571: accagcagcgcgccgggcagc acctgggaactcggtacccgc T_m=76.7
- Final: Type2s
Rev138-141: gatAGTGGTGTTTGAGTCATAACGACGTC acgcgcgccagcatgttcaaa T_m=72.8 Fwd138-141: accagcagcgcgccgggcagc cgtgaggatttcgccaaaacc T_m=70.8
Rev155-158: gatAGTGGTGTTTGAGTCATAACGACGTC acgcatggtggttgcgccggt T_m=76.7 Fwd155-158: accagcagcgcgccgggcagc cgcatccctggcgtcagcgcg T_m=80.6
Rev176-180: gatAGTGGTGTTTGAGTCATAACGACGTC gtcgtggctgccggtgccgtt T_m=78.6 Fwd176-180: accagcagcgcgccgggcagc ggcatccggggcctgaacccg T_m=80.6
Rev178-182: gatAGTGGTGTTTGAGTCATAACGACGTC cgccaggtcgtggctgccggt T_m=80.6 Fwd178-182: accagcagcgcgccgggcagc cggggcctgaacccgcgcctc T_m=82.5
Rev180-184: gatAGTGGTGTTTGAGTCATAACGACGTC gttcatcgccaggtcgtggct T_m=74.7 Fwd180-184: accagcagcgcgccgggcagc ctgaacccgcgcctcgccagc T_m=80.6
Rev521-529: gatAGTGGTGTTTGAGTCATAACGACGTC gctcacttcttcgtgcgtgcc T_m=74.7 Fwd521-529: accagcagcgcgccgggcagc gtgctctatcacctgactgac T_m=70.8
Rev523-531: gatAGTGGTGTTTGAGTCATAACGACGTC gttatagctcacttcttcgtg T_m=66.9 Fwd523-531: accagcagcgcgccgggcagc tatcacctgactgacagctgg T_m=70.8
Rev527-531: gatAGTGGTGTTTGAGTCATAACGACGTC cggaagcggtgcgttatagct T_m=72.8 Fwd527-531: accagcagcgcgccgggcagc tatcacctgactgacagctgg T_m=70.8
Rev567-576: gatAGTGGTGTTTGAGTCATAACGACGTC ttcaacattgccgctttgcacagc T_m,fec=73.9 Fwd567-576: accagcagcgcgccgggcagc acccgctacgacgacggcgcg T_m,fec=80.6
Rev571-574: gatAGTGGTGTTTGAGTCATAACGACGTC cgctttttccggttcaacattgccgc T_m,fec=77.6 Fwd571-574: accagcagcgcgccgggcagc ctcggtacccgctacgacgac T_m,fec=76.7