A case of adaptation through a mutation in a tandem duplication during experimental evolution in Escherichia coli

Table 2 List of primers used in this study

Primer name	Direction	Genome position^a	Sequence (5'-3')^b	Used for
IS3F1	Forward	2,057,888	CGCTGTACCGACTCATAAGT	Detection of ogrK-yegSR deletion
IS3R1	Reverse	2,061,063	GATGCTGAACTCAGCCTGATG	Detection of ogrK-yegSR deletion
IS3R2	Reverse	2,059,299	CATTCCTTCCTCACGCAAC	Detection of ogrK-yegSR deletion
IS5F1	Forward	2,172,688	CACCATCAACTGTCTCACCA	Detection of duplication
IS5R1	Reverse	1,993,645	GACCCGCAGATGATGATTAC	Detection of duplication
DelF	Forward	2,057,748	CACCGTAACGCTGTTTTGACCG	Detection of ogrK-yegSR deletion
DelR	Reverse	2,062,009	GGATCTTGAGCTCAATTACGCGC	Detection of ogrK-yegSR deletion
IS3EF	Forward	NA^c	GCTGCTACGATAATGCCTGCG	Inverse PCR
IS3ER	Reverse	NA^c	GCGTTCAGCAAGCTTCAGGG	Inverse PCR
FrontR	Forward	1,993,555	GTACATTATGCCTGTTCCGAG	Detection of duplication
FrontF	Reverse	2,172,636	TCGTATTATTGGCGGTCCC	Detection of duplication
ogrKAmpF1	Forward	2,057,979	GGCTTGTACGCGCATGTGCGGCATGCTGGCATAAGAGTTGGTAGCTCTTGATC	Strain construction
yegSAmpF2	Forward	2,058,495	CTCACTCTCCACATTTGAATGTCAGACGAGCGACAGAGTTGGTAGCTCTTGATC	Strain construction
yegRAmpF3	Forward	2,059,218	CATGGCAGAATTTCCCGCCAGCTTACTGATTCTTAGAGTTGGTAGCTCTTGATC	Strain construction
ogrKAmpR1	Reverse	2,058,472	GGTAAGCGTCAAATATGCGCGTTCTGGCTGTGCCATTCAAATATGTATCCGCT	Strain construction
yegSAmpR2	Reverse	2,059,189	TGATTGGTCTGTAGATAGTGTAGAGCAGAAAACCATTCAAATATGTATCCGCT	Strain construction
yegRAmpR3	Reverse	2,060,666	GACCGTTATTCTCGACAGCGGAAGTACGACAATGCATTCAAATATGTATCCGCT	Strain construction

^aThe positions are given according to the genome sequence of the ancestor strain BW2952 [29]. ^bSequences in bold are homologous to the bla antibiotic resistance gene. ^cNot applicable; these primers are complementary to sequences inside the IS3 elements.

ISSN: 1471-2164