. 2014 Aug;196(16):2921–2933. doi: 10.1128/JB.01747-14

TABLE 1.

Oligonucleotides used in this study

Oligonucleotide	Sequence (5′–3′)^a (location)	Relevant property	Restriction site
22F	GCAATTGAGCAATACGAACA	Primer pair to amplify pXO1 region overlapping ORF 22
22R	AATTGTAGACATTGCGCGAC	Primer pair to amplify pXO1 region overlapping ORF 22
flpF	ACTGCATATGAGCCAGTTCGACATCCTGTGCAAGACC	Primer pair to amplify the flp gene	NdeI
flpR	ACTGCCCGGGAAAAGCTGGAGCTCGATATCTCATCAGATC	Primer pair to amplify the flp gene	XmaI
190F	ACTGACTAGTCAGCTTATGGTATAGCAACG	Primer pair to amplify left fragment of ORF 29–190 deletion	XhoI
191R	ACTGCTCGAGGTCTTGGATAACCACTATCATA	Primer pair to amplify left fragment of ORF 29–190 deletion	SpeI
26FS	ACTGACTAGTCATTTTAATTGTTCCAGGGG	Primer pair to amplify right fragment of ORF 29–190 deletion	SpeI
29RX	ACTGCTCGAGATTGCCCGTCACTCCTTTCT		XhoI
26seqF	TCCTCATCTATCTTTTTAATTGCAGCTTCG	Primer pair to verify ORF 29–190 deletion
190seqR	GCAGCTAACTTAGGGTCTTTCATTATTTGT	Primer pair to verify ORF 29–190 deletion
26FX	ACTGCTCGAGCATTTTAATTGTTCCAGGGG	Primer pair to amplify left fragment of ORF 29–133 deletion	XhoI
29RS	ACTGACTAGTATTGCCCGTCACTCCTTTCT	Primer pair to amplify left fragment of ORF 29–133 deletion	SpeI
133F	ACTGCTCGAGGGTGTTTTTCGTTTGAAGAC	Primer pair to amplify right fragment of ORF 29–133 deletion and left fragment of ORF 137–17 deletion	XhoI
137R	ACTGACTAGTTACTTTTCGGCCTCTTCCTG		SpeI
27seqF	CTATCTTTTTAATTGCAGCT	Primer pair to verify ORF 29–133 deletion
134seqR	ATTGTTTTCCTACAGTTTGT	Primer pair to verify ORF 29–133 deletion
17F	ACTGCTCGAGGGCTATTTACACCAGATAAG	Primer pair to amplify right fragments of ORF 137–17, 89–17, and 79–17 deletions	XhoI
18R	ACTGACTAGTATTCTTCACAGGCTGTAAAA		SpeI
222seqF	TATTAGAATTACCACGTTCC	Primer pair to verify ORF 137–17 deletion
18seqR1	AGATTCTTCAAAGCTATTCC	Primer pair to verify ORF 137–17 deletion
86F	ACTGCTCGAGGTATCTGACAGAAGAAAAGAAAGAG	Primer pair to amplify left fragment of ORF 89–17 deletion	XhoI
87R	ACTGACTAGTGGATACTAGCTTCTTATATACTTGC	Primer pair to amplify left fragment of ORF 89–17 deletion	SpeI
87seqF	TCGACCGTATGTATCTACAC	Primer pair to verify ORF 89–17 deletion
17seqR	CTTAATCCTTCGTTTTGTAG	Primer pair to verify ORF 89–17 deletion
79F	ACTGCTCGAGATTTGGAGGAACAAACAATGGCTAA	Primer pair to amplify left fragment of ORF 79–17 deletion	XhoI
79R	ACTGACTAGTAAAACGTCTGGCTTTGTTTCTGGCT	Primer pair to amplify left fragment of ORF 79–17 deletion	SpeI
79seqF	GGCAAGTGGCGCGTATGATT	Primer pair to verify ORF 79–17 deletion
18seqR2	GCTGAGTTGGGATGACGAAA	Primer pair to verify ORF 79–17 deletion
80F	ACTGCGATCGGGTTGGAAAGGAACATATTA	Primer pair to amplify ORF 81–86 fragment for cloning	PvuI
87R	ACTGCGATCGCAATAACCATTGGATACATC	Primer pair to amplify ORF 81–86 fragment for cloning
84F	ACTGCTCGAGGGCAGACCTTGTTGTTCATG	Primer pair to amplify left fragment of ORF 85–19 deletion	XhoI
85R	ACTGACTAGTACAGCTGCTCTCTTTTCTTT	Primer pair to amplify left fragment of ORF 85–19 deletion	SpeI
19F	ACTGCTCGAGCCTTACTTCAAAAGCTGTAT	Primer pair to amplify right fragment of ORF 85–19 deletion	XhoI
19R	ACTGACTAGTGTATTTCAATGTTGCTAGGA	Primer pair to amplify right fragment of ORF 85–19 deletion	SpeI
85seqF	AGGAAAAACAAATCGCCTTA	Primer pair to verify ORF 85–19 deletion
19seqR1	CCAGCCATACTATTTCACAT	Primer pair to verify ORF 85–19 deletion
25F	ACTGCTCGAGATGGTCGTACTTGAAAATAC	Primer pair to amplify left fragment of ORF 26–68 deletion	XhoI
26R	ACTGACTAGTGCTGTTGTGTATCTTCCATA	Primer pair to amplify left fragment of ORF 26–68 deletion	SpeI
68F	ACTGCTCGAGTGCTCCCTCAAGTCGTGCAGTCATA	Primer pair to amplify right fragment of ORF 26–68 deletion	XhoI
69R	ACTGACTAGTCCATCGCTTAACTGCTCATCAATCA	Primer pair to amplify right fragment of ORF 26–68 deletion	SpeI
26seqF1	CCTTAATTCCGGATCAATCA	Primer pair to verify ORF 26–68 deletion
68seqR	TGTACTATACGCTGAAGGTG	Primer pair to verify ORF 26–68 deletion
83F	ACTGCTCGAGGGCTACATAAGGAGGAATAC	Primer pair to amplify left fragment of ORF 84–19 deletion	XhoI
83R	ACTGACTAGTCGAATGCTTCTCTACATAGT	Primer pair to amplify left fragment of ORF 84–19 deletion	SpeI
83seqF	CATTCCCGTTACTCGTTGAT	Primer pair to verify ORF 84–19 deletion
19seqR2	CCAGCCATACTATTTCACAT	Primer pair to verify ORF 84–19 deletion
69F	ACTGCTCGAGCGGGAAAAAATAAAAGAGAC	Primer pair to amplify right fragment of ORF 26–69 deletion	XhoI
71R	ACTGACTAGTGCGAACTATACAGTTATAGTGA	Primer pair to amplify right fragment of ORF 26–69 deletion	SpeI
26seqF2	AGGTGATTATAATGAACGAG	Primer pair to verify ORF 26–69 deletion
70seqR	GTGTCCTAAGGATTTAGAAA	Primer pair to verify ORF 26–69 deletion
68F	ACTGCGATCGGAATATACTTCCGAAGTATCGTATGTATTA	Primer pair to amplify ORF 69 and 70 fragment for cloning	PvuI
70R	ACTGCGATCGATATGGATATAGAACTGCTAAACCAAAGTT	Primer pair to amplify ORF 69 and 70 fragment for cloning
23F	ACTGGATATCTTTAATCCTCCACTTGTTAA	Primer pair to amplify ORF 23 downstream area for cloning	EcoRV
24R	CACGCAATGGAAATAAAATA	Primer pair to amplify ORF 23 downstream area for cloning
81F	ATTGTAAAGATAGTTTTCGC	Primer pair to amplify fragment containing separated 67-bp stem-loop for cloning	SalI
82R	ACTGGTCGACTTTACCATTTCAAATCTCTG
82F	ACTGGCCGGCAGAAATGATTGACATGAAAC	Primer pair to amplify fragment containing separated 45-bp stem-loop for cloning	NaeI
83R	CTTTTACAACCTGTTTGAAA

Restriction enzyme recognition sites are underlined.