Use of aminoglycoside 3′ adenyltransferase as a selection marker for Chlamydia trachomatis intron-mutagenesis and in vivo intron stability

Table 1 PCR reactions used to map intron insertions in DFCT3, DFCT9, DFCT13, and DFCT16

Reaction	Primers	Target	Notes
1	V1F–V1R	rsbV1	Confirms intron insertion (primers flank insertion site)
2	incAF–incAR	incA	Confirms intron insertion (primers flank insertion site)
3	hyp08F–hyp08R	cryptic plasmid	Confirms that transformation has not resulted in loss of the native, cryptic plasmid
4	incAF–GIIR	Connects the 5′ region of incA to the intron	Confirms intron insertion and orientation
5	incAR–GIIF	Connects the 3′ region of incA to the intron	Confirms intron insertion and orientation
6	GIIF–GIIR	Intron	Confirms intron presence
7	incAF–aadAR	Connects incA to the aadA marker	Confirms marker type
8	catF–catR	Intron donor plasmid	Confirms loss of intron donor plasmid
9	V1F–GIIF	Connects the 5′ region of rsbV1 to the intron	Confirms intron insertion and orientation
10	V1R2–GIIR	Connects the 3′ region of rsbV1 to the intron	Confirms intron insertion and orientation
11	blaR2–VIR	Connects rsbV1 to the bla marker	Confirms marker type
12	blaF1–blaR1	Marker	Confirms presence of bla marker
13	aadAF–aadAR	Marker	Confirms presence of aadA marker