TABLE 1.

Primers used in this studya

PrimerSequenceApplication
ccpa5′5′-GACAGGATCTGAAAGGACAGCAGC-3′ccpA amplification
ccpa3′5′-CTGGATTAGCTCATCAGTAAATG-3′ccpA amplification
fruA5′5′-GAGCATTAATGAACTATGTCATATTAAGG-3′PfruA amplification
fruA3′5′-TTTTCAAATTTATGAAACTGACAAACTC-3′PfruA amplification
cat3′5′-CGGAAATCGTCGTGGTATTCACTC-3′Fusion confirmation
mtA5′-CTGCTCGAAACTCTGCTATACCTC-3′Mutations of SL1
mtB5′-GAGGTATAGCAGAGTTTCGAGCAG-3′Mutations of SL1
cw15′-GGAAGATAGACGATACTTTGGTATACTGAGG-3′Mutations of CRE-W
cw25′-CCTCAGTATACCAAAGTATCGTCTATCTTCC-3′Mutations of CRE-W
dCS5′-CTATCTTATCCTCAGTATACCAAATC-3′Deletion of CRE-S
dT5′-CTATTTAGGTCGGTCAGTATTTAAC-3′Deletion of SL1 and SL2 and their 3′ sequences
mcA5′-AGATGGTACCTAAAACATTTTAAATAAATTTTTGAAAC-3′Mutations of CRE-S
mcB5′-TTTAGGTACCATCTTATCCTCAGTATACCAAATCGCTAT-3′Mutations of CRE-S
dtA5′-CTCTAATTAAATACCTCATTTCTTTCCTATTTAGGTC-3′Deletion of SL1 and SL2
dtB5′-GAAATGAGGTATTTAATTAGAGTTTGTCAGTTTC-3′Deletion of SL1 and SL2
up15′-AGGAAATGACAATTGCTAGATG-3′Deletion of DS
mDS5′-GAGCATTAATTCGTTCTGTCATATTAAGG-3′Mutations of DS
gtfC3′5′-AAAAATAGTTAGAGTTAGTG-3′Amplification of PgtfC
gtfC5′5′-GATGCTAACTCTGGAGAACG-3′Amplification of PgtfC
DSR5′5′-CTGACCGACCTAAATAGGAAAG-3′Amplification of 3′UTR
  • a See the text and Fig. 1 and 2 for more detail about the individual cis elements that were deleted and/or mutated by PCR or recombinant PCR with the primers list here.