IGEM:IMPERIAL/2009/Primers

Primers to be used for PCR

Considerations for primer design http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html

Use this website to calculate temperatures and modify primers.

using oligonucleotides property calculator
http://www.basic.northwestern.edu/biotools/oligocalc.html

RcsB Sequence:

     ATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTG
     AGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGACTCTACAGCACTGATCAACAACCTGCCGAA
     ACTGGATGCGCATGTGTTGATTACCGATCTCTCCATGCCTGGCGATAAGTACGGCGATGGCATTACCTTA
     ATCAAGTACATCAAGCGCCATTTCCCAAGCCTGTCGATCATTGTTCTGACTATGAACAACAACCCGGCGA
     TTCTTAGTGCGGTATTGGATCTGGATATCGAAGGGATCGTGCTGAAACAAGGTGCACCGACCGATCTGCC
     GAAAGCTCTCGCCGCGCTGCAGAAAGGGAAGAAATTTACCCCGGAAAGCGTTTCTCGCCTGTTGGAAAAA
     ATCAGTGCTGGTGGTTACGGTGACAAGCGTCTCTCGCCAAAAGAGAGTGAAGTTCTGCGCCTGTTTGCGG
     AAGGCTTCCTGGTGACCGAGATCGCTAAAAAGCTGAACCGCAGTATTAAAACCATCAGTAGCCAGAAGAA
     ATCTGCGATGATGAAGCTGGGTGTCGAGAACGATATCGCCCTGCTGAATTATCTCTCTTCAGTGACCTTA
     AGTCCGGCAGATAAAGACTAA

Spec fwd: GCTCTAGATGAACAATATGAACGTAATTATTG 53.1C and 61.8

Spec rev: GGACTAGTATTA GTC TTT ATC TGC CGG 51.4C and 63.4

OtsB Sequence:

     ATGGTGGAGCTTGACGCACTGGCAAAACCTTATCGCTTCCCGTTAGCGGGCGTGCATGGGGC
     GGAGCGCCGTGACATCAATGGTAAAACACATATCGTTCATCTGCCGGATGCGATTGCGCGTGAT
     ATTAGCGTGCAACTGCATACAGTCATCGCTCAGTATCCCGGCGCGGAGCTGGAGGCGAAAGGGA
     TGGCTTTTGCGCTGCATTATCGTCAGGCTCCGCAGCATGAAGACGCATTAATGACATTAGCGCA
     ACGTATTACTCAGATCTGGCCACAAATGGCGTTACAGCAGGGAAAGTGTGTTGTCGAGATCAAA
     CCGAGAGGTACCAGTAAAGGTGAGGCAATTGCAGCTTTTATGCAGGAAGCTCCCTTTATCGGGC
     GAACGCCCGTATTTCTGGGCGATGATTTAACCGATGAATCTGGCTTCGCAGTCGTTAACCGACT
     GGGCGGAATGTCAGTAAAAATTGGCACAGGTGCAACTCAGGCATCATGGCGACTGGCGGGTGTG
     CCGGATGTCTGGAGCTGGCTTGAAATGATAACCACCGCATTACAACAAAAAAGAGAAAATAACA
     GGAGTGATGACTATGAGTCGTTTAGTCGTAGTATCTAA

Forward: GCTCTAGATGGTGGAGCTTGACG      51.7C (without) & 64.2C (with)
Backward: GGACTAGTAGCTCTAGATGGTGGAG      51.7C (without) & 64.6C (with)

B3023 Sequence:

     ATGACAAACCTGACACTGGATGTAAACATTATCGATTTCCCATCAATACCTGTGGCGATGTTGCCG
     CACCGCTGTAGCCCTGAATTGCTCAACTACAGCGTGGCGAAATTTATCATGTGGCGTAAAGAGACG
     GGGCTTTCTCCTGTTAACCAAAGCCAGACTTTTGGCGTCGCCTGGGACGACCCTGCCACCACCGCA
     CCGGAAGCGTTTCGCTTTGATATCTGCGGCAGCGTTAGCGAACCGATTCCCGATAATCGTTATGGT
     GTGAGCAATGGTGAACTTACCGGTGGACGTTATGCCGTGGCCCGCCACGTTGGCGAGCTGGACGAT
     ATTTCACACACGGTATGGGGCATCATTCGCCACTGGCTGCCTGCAAGCGGCGAGAAAATGCGTAAA
     GCACCGATTCTGTTTCACTACACCAATCTTGCCGAAGGGGTGACAGAGCAGCGACTGGAAACGGAT
     GTTTATGTGCCGTTGGCGTGA

Spec fwd: GCTCTAGATGACAAACCTGACACTGGATG 53C

Spec rev: GGACTAGTATCACGCCAACGGCACATAAAC 54C

WaaL Sequence:

      ATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAG
      ATAATAACTTATATATTATGTTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATA
      AAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGACAAGAAAATT
      ATAATATAAAAAACCTTATTCTTCCCCTTTCTATATTTTTAATAGGCTTGCTTGATTTAATTTGGTA
      TTCTGCGTTTAAAGTAGATAATTCGCCATTTCGTGCTACTTACCATAGTTATTTAAATACTGCCAAA
      ATATTTATATTTGGTTCTTTTATTGTTTTCTTGACACTAACTAGCCAGCTAAAATCAAAAAAAGAGA
      GTGTATTATACACTTTGTATTCTCTGTCATTTCTAATTGCTGGATATGCAATGTATATTAATAGCAT
      TCATGAAAATGACCGCATTTCTTTTGGTGTAGGAACGGCAACAGGAGCAGCATATTCAACAATGCTA
      ATAGGGATAGTTAGTGGCGTTGCGATTCTTTATACTAAGAAAAATCATCCTTTTTTATTTTTATTAA
      ATAGTTGCGCGGTACTTTATGTTCTGGCGCTAACACAAACCAGAGCAACCCTACTCCTGTTCCCTAT
      AATTTGTGTTGCTGCATTAATAGCTTATTATAATAAATCACCCAAGAAATTCACTTCCTCTATTGTT
      CTACTAATTGCTATATTAGCTAGCATTGTTATTATATTTAATAAACCAATACAGAATCGCTATAATG
      AAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGC
      AATGTACGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGC
      GCTGAAAGTATGAATTTGTTAGTTGCAGAACACAATAGGCTAAGAGGGGCATTGGAGTTTTCTAACG
      TACATCTACATAATGAGATAATTGAAGCAGGGTCACTGAAAGGTCTGATGGGAATTTTTTCCACACT
      TTTCCTCTATTTTTCACTATTTTATATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACG
      CTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTA
      TATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAA

Spec fwd: GCTCTAGATGCTAACATCCTTTAAACTTCATTC 52C

Spec rev: GGACTAGTATTAATTAATTGTATTGTTACGATTATTAATG 50C

OtsA Sequence:

      ATGAGTCGTTTAGTCGTAGTATCTAACCGGATTGCACCACCAGACGAGCACGCCGCCAGTGCCGGTGGCCTTGC
      CGTTGGCATACTGGGGGCACTGAAAGCCGCAGGCGGACTGTGGTTTGGCTGGAGTGGTGAAACAGGGAATGAGG
      ATCAGCCGCTAAAAAAGGTGAAAAAAGGTAACATTACGTGGGCCTCTTTTAACCTCAGCGAACAGGACCTTGAC
      GAATACTACAACCAATTCTCCAATGCCGTTCTCTGGCCCGCTTTTCATTATCGGCTCGATCTGGTGCAATTTCA
      GCGTCCTGCCTGGGACGGCTATCTACGCGTAAATGCGTTGCTGGCAGATAAATTACTGCCGCTGTTGCAAGACG
      ATGACATTATCTGGATCCACGATTATCACCTGTTGCCATTTGCGCATGAATTACGCAAACGGGGAGTGAATAAT
      CGCATTGGTTTCTTTCTGCATATTCCTTTCCCGACACCGGAAATCTTCAACGCGCTGCCGACATATGACACCTT
      GCTTGAACAGCTTTGTGATTATGATTTGCTGGGTTTCCAGACAGAAAACGATCGTCTGGCGTTCCTGGATTGTC
      TTTCTAACCTGACCCGCGTCACGACACGTAGCGCAAAAAGCCATACAGCCTGGGGCAAAGCATTTCGAACAGAA
      GTCTACCCGATCGGCATTGAACCGAAAGAAATAGCCAAACAGGCTGCCGGGCCACTGCCGCCAAAACTGGCGCA
      ACTTAAAGCGGAACTGAAAAACGTACAAAATATCTTTTCTGTCGAACGGCTGGATTATTCCAAAGGTTTGCCAG
      AGCGTTTTCTCGCCTATGAAGCGTTGCTGGAAAAATATCCGCAGCATCATGGTAAAATTCGTTATACCCAGATT
      GCACCAACGTCGCGTGGTGATGTGCAAGCCTATCAGGATATTCGTCATCAGCTCGAAAATGAAGCTGGACGAAT
      TAATGGTAAATACGGGCAATTAGGCTGGACGCCGCTTTATTATTTGAATCAGCATTTTGACCGTAAATTACTGA
      TGAAAATATTCCGCTACTCTGACGTGGGCTTAGTGACGCCACTGCGTGACGGGATGAACCTGGTAGCAAAAGAG
      TATGTTGCTGCTCAGGACCCAGCCAATCCGGGCGTTCTTGTTCTTTCGCAATTTGCGGGAGCGGCAAACGAGTT
      AACGTCGGCGTTAATTGTTAACCCCTACGATCGTGACGAAGTTGCAGCTGCGCTGGATCGTGCATTGACTATGT
      CGCTGGCGGAACGTATTTCCCGTCATGCAGAAATGCTGGACGTTATCGTGAAAAACGATATTAACCACTGGCAG
      GAGTGCTTCATTAGCGACCTAAAGCAGATAGTTCCGCGAAGCGCGGAAAGCCAGCAGCGCGATAAAGTTGCTAC
      CTTTCCAAAGCTTGCGTAG

Spec fwd: GCTCTAGATG AGT CGT TTA GTC GTA GTA TCT 52C

Spec rev: GGACTAGTACTA CGC AAG CTT TGG AAA GGT 52C

PAH Sequence:

      ATGTCCACTGCGGTCCTGGAAAACCCAGGCTTGGGCAGGAAACTCTCTGACTTTGGACAGGAAACAAGCTATAT
      TGAAGACAACTGCAATCAAAATGGTGCCATATCACTGATCTTCTCACTCAAAGAAGAAGTTGGTGCATTGGCCA
      AAGTATTGCGCTTATTTGAGGAGAATGATGTAAACCTGACCCACATTGAATCTAGACCTTCTCGTTTAAAGAAA
      GATGAGTATGAATTTTTCACCCATTTGGATAAACGTAGCCTGCCTGCTCTGACAAACATCATCAAGATCTTGAG
      GCATGACATTGGTGCCACTGTCCATGAGCTTTCACGAGATAAGAAGAAAGACACAGTGCCCTGGTTCCCAAGAA
      CCATTCAAGAGCTGGACAGATTTGCCAATCAGATTCTCAGCTATGGAGCGGAACTGGATGCTGACCACCCTGGT
      TTTAAAGATCCTGTGTACCGTGCAAGACGGAAGCAGTTTGCTGACATTGCCTACAACTACCGCCATGGGCAGCC
      CATCCCTCGAGTGGAATACATGGAGGAAGAAAAGAAAACATGGGGCACAGTGTTCAAGACTCTGAAGTCCTTGT
      ATAAAACCCATGCTTGCTATGAGTACAATCACATTTTTCCACTTCTTGAAAAGTACTGTGGCTTCCATGAAGAT
      AACATTCCCCAGCTGGAAGACGTTTCTCAATTCCTGCAGACTTGCACTGGTTTCCGCCTCCGACCTGTGGCTGG
      CCTGCTTTCCTCTCGGGATTTCTTGGGTGGCCTGGCCTTCCGAGTCTTCCACTGCACACAGTACATCAGACATG
      GATCCAAGCCCATGTATACCCCCGAACCTGACATCTGCCATGAGCTGTTGGGACATGTGCCCTTGTTTTCAGAT
      CGCAGCTTTGCCCAGTTTTCCCAGGAAATTGGCCTTGCCTCTCTGGGTGCACCTGATGAATACATTGAAAAGCT
      CGCCACAATTTACTGGTTTACTGTGGAGTTTGGGCTCTGCAAACAAGGAGACTCCATAAAGGCATATGGTGCTG
      GGCTCCTGTCATCCTTTGGTGAATTACAGTACTGCTTATCAGAGAAGCCAAAGCTTCTCCCCCTGGAGCTGGAG
      AAGACAGCCATCCAAAATTACACTGTCACGGAGTTCCAGCCCCTGTATTACGTGGCAGAGAGTTTTAATGATGC
      CAAGGAGAAAGTAAGGAACTTTGCTGCCACAATACCTCGGCCCTTCTCAGTTCGCTACGACCCATACACCCAAA
      GGATTGAGGTCTTGGACAATACCCAGCAGCTTAAGATTTTGGCTGATTCCATTAACAGTGAAATTGGAATCCTT
      TGCAGTGCCCTCCAGAAAATAAAGTAA

Spec fwd: GCTCTAGATG TCC ACT GCG GTC CTG 53C

Spec rev: GGACTAGTATTA CTT TAT TTT CTG GAG GGC ACT 52C