IGEM:IMPERIAL/2009/Primers

Primers to be used for PCR

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

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: GCTCTAGATGAACAATATGAACGTAATTATTGCC 52C

Spec rev: GGACTAGTATTA GTC TTT ATC TGC CGG ACT TAA GG 56C

OtsB Sequence:

     ATGGTGGAGCTTGACGCACTGGCAAAACCTTATCGCTTCCCGTTAGCGGGCGTGCATGGGGC
     GGAGCGCCGTGACATCAATGGTAAAACACATATCGTTCATCTGCCGGATGCGATTGCGCGTGAT
     ATTAGCGTGCAACTGCATACAGTCATCGCTCAGTATCCCGGCGCGGAGCTGGAGGCGAAAGGGA
     TGGCTTTTGCGCTGCATTATCGTCAGGCTCCGCAGCATGAAGACGCATTAATGACATTAGCGCA
     ACGTATTACTCAGATCTGGCCACAAATGGCGTTACAGCAGGGAAAGTGTGTTGTCGAGATCAAA
     CCGAGAGGTACCAGTAAAGGTGAGGCAATTGCAGCTTTTATGCAGGAAGCTCCCTTTATCGGGC
     GAACGCCCGTATTTCTGGGCGATGATTTAACCGATGAATCTGGCTTCGCAGTCGTTAACCGACT
     GGGCGGAATGTCAGTAAAAATTGGCACAGGTGCAACTCAGGCATCATGGCGACTGGCGGGTGTG
     CCGGATGTCTGGAGCTGGCTTGAAATGATAACCACCGCATTACAACAAAAAAGAGAAAATAACA
     GGAGTGATGACTATGAGTCGTTTAGTCGTAGTATCTAA

Forward: GCTCTAGATGGTGGAGCTTGACGCAC 53C
Backward: GGACTAGTATTAGATACTACGACTAAACGACTC 52C

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