Table 1 Primer sequences

lam-up-f

loop 9 up

5'TGTACAAGTGGACGCCAATC 3'

lam-up-r

5'GTTATCGCCGTCTTTGATATAGCC 3'

lam-dn-f

loop 9 dn

5'ATTTCCCGTTATGCCGCAGC 3'

lam-dn-r

5'GTTAAACAGAGGGCGACGAG 3'

Km-f

I-SceI/Km^r gene

5'GCTATATCAAAGACGGCGATAAC TAACTATAACGGTCCTAAGGTAGCGAATTTCCGGGGATCCGTCGA 3'

Km-r

5'GCTGCGGCATAACGGGAAAT TGTAGGCTGGAGCTGCTTCG 3'

Kan4f

inside Km^r gene: sequencing

5'CAAAAGCGCTCTGAAGTTCC 3'

Kan4r

5'GCGTGAGGGGATCTTGAAGT 3'

lam-i1

M2e/loop 9 dn

5'GCTATATCAAAGACGGCGATAAC GAAGTTGAAACCCCGATTCGTAAC ATTTCC CGTTATGCCGCAGCG 3'

lam-i2

CD154s/loop 9 dn

5'GCTATATCAAAGACGGCGATAAC TGGGCAGAAAAAGGTTATTATACCATGTCT ATTTCCCGTTATGCCGCAGC 3'

i2-i1h-f

CD154s-(Gly)₃-LM2-(Gly)₃-loop 9 dn

5'TGGGCAGAAAAAGGTTATTATACCATGTCTGGTGGTGGTGAAGTTGAAACCCCGATTCGTAACGGTGGTGGT ATTTCCCGTTATGCCGCAGC 3'

i2-i1-r

CD154s-(Gly)₃-loop 9 Up

5'AGACATGGTATAATAACCTTTTTCTGCCCAACCACCACC GTTATCGCCGTCTT TGATATAGCC 3'

TJ1-f

CD154-(Ser)₄-LM2-(Ser)₄-LM2-(Ser)₄-loop 9 dn

5'TGGGCAGAAAAAGGTTATTATACCATGTCTTCCTCCTCCTCCGAAGTTGAAACCCCGATTCGTAACTCCTCCTCCTCCGAAGTTGAAACCCCGATTCGTAACTCCTCCTCCTCC ATTTCCCGTTATGCCGCAGC 3'

TJ1-r

CD154-(Ser)₄-M2eA-(Ser)₄-M2eA-(Ser)₄-loop 9 up

5'AGACATGGTATAATAACCTTTTTCTGCCCAGGAGGAGGAGGAGTTACGGGTCGGGGTTTCAACTTCGGAGGAGGAGGAGTTACGGGTCGGGGTTTCAACTTCGGAGGAGGAGGA GTTATCGCCGTCTTTGATATAGCC 3'

lam 3f

outer regions of loop 9: sequencing

5'GCCATCTCGCTTGGTGATAA 3'

lam 3r

5'CGCTGGTATTTTGCGGTACA 3'

aroA-1F

aroA up

5'CTGGACGTCTCTCGCTATGG 3'

aroA-1R

5'TAGGAACTTCGAAGCAGCTCCAGCCTACACATAAAAACC CCACAGACTGG 3'

aroA-2F

aroA dn

5'GGAATAGGAACTAAGGAGGATATTCATATGGTCTTCTGTTGCGCCAGT 3'

aroA-2R

5'CTTGCGAGAGTGCCCTAAAG 3'

htrA-1F

htrA up

5'GGTTTTAGCCGCCTGCTT 3'

htrA-1R

5'TAGGAACTTCGAAGCAGCTCCAGCCTACACTTGCTGTGTACGTCAGATTCA 3'

htrA-2F

htrA dn

5'GGAATAGGAACTAAGGAGGATATTCATATGTCACCTTTGTCCCCCTTC 3'

htrA-2R

5'GCATCATTTCGGCAGTCATA 3'

Kan 3F

Km^r gene

5'GTGTAGGCTGGAGCTGCTTC 3'

Kan 3R

5'CATATGAATATCCTCCTTAG 3'