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Table 1 List of primers used in this study

From: Characterization of the dsDNA prophage sequences in the genome of Neisseria gonorrhoeae and visualization of productive bacteriophage

Primer Sequence (5'-3') Description PCR conditions
F1TerD F AATCACCATGCGCCAATCT GCAACGCGCTCGA Amplifies the 5' end of NGO0495 (putative terminase) without any restriction sites 94°C, 5 min.; 2× (94°C, 48° 45 sec, 72°C 1 min); 30× (94°C, 45 sec.; 63°C,45 sec.; 72°C, 3 min.); 72°C, 10 min.
F1TerD R TCCGTGTCCCATGTGCCG TCATCCAACACCAT Amplifies the 3' end of NGO0495 (putative terminase) without any restriction sites  
F2Reg8L2 GCGAATTC GATGTCTGAA TTTAAAGACCGCCTGAAAG AG Amplifies the 5' end of NGO1116 (putative repressor cI) with EcoRI site 94°C, 5 min.; 2×(94°C, 30 sec.; 48°C, 45 sec.; 72°C, 2 min.); 28× (94°C, 15 sec.; 50°C, 45 sec.; 72°C, 2 min.); 72°C, 10 min.
F2Reg8Rt ATTCTGCAG TCACATCAAT CCAACACGCTCCACCAAA AG Amplifies the 3' end of NGO1116 (putative repressor cI) with PstI site  
F2TerD F AATATTCGTCGTGCAGCG GCCCCATTGCCACG Amplifies the 5' end of NGO1098 (putative terminase) without any restriction sites 94°C, 5 min; 30× (94°C, 45 sec.; 63°C, 45 sec.); 72°C, 3 min.; 72°C, 10 min.
F2TerD R CGGGCTGTTCAAGCCTTG CCGGTACAAGGTTA Amplifies the 3' end of NGO1098 (putative terminase) without any restriction sites  
F2antrep F GCCGGAATTC TCCAAGTT TTAAACTTTCAAC Amplifies the 5' end of NGO1085 (putative antirepressor) with EcoRI site 94°C, 5 min.; 3×(94°C, 1 min.; 44°C, 45 sec.; 72°C, 3 min.); 27× (94°C, 1 min.; 59°C, 45 sec.; 72°C,3 min.); 72°C, 10 min
F2antrep R TTATCTGCAG TTACCTTAC CGTAGCCTTGCC Amplifies the 3' end of NGO1085 (putative antirepressor) with PstI site  
F3dnaC F ACGCGCTGGAAAAACGCA TC Amplifies the 5' end of NGO1636 (putative replication protein DnaC) without any restriction sites 94°C, 2 min; 3× (94°C, 1 min.; 48°C, 45 sec.; 72°C, 3 min.28× (94°C, 45 sec.; 52°C, 45 sec.; 72°C, 2 min.); 72°C, 10 min.
F3dnaC R TCCCAGTCGAACGGAATC AG Amplifies the 3' end of NGO1636 (putative replication protein DnaC) without any restriction sites  
Fag4cI F TCACTTTACCAAGCGCAGT TT Amplifies the 5' end of NGO1013 (putative repressor cI) without any restriction sites 94°C, 2 min; 3× (94°C, 1 min.; 48°C, 45 sec.; 72°C, 3 min), 28×(94°C, 45 sec.; 50°C, 45 sec.; 72°C, 2 min.); 72°C, 10 min.
Fag4cI R AATTAGGCTTGAACCAAGC AG Amplifies the 3' end of NGO1013 (putative repressor cI) without any restriction sites  
Fag5cI F TCTATCCAATCGAGGAACT GCC Amplifies the 5' end of NGO0729 (putative repressor cI) without any restriction sites 94°C, 2 min; 28× (94°C, 45 sec.; 52°C, 45 sec.; 72°C, 2 min.); 72°C, 10 min.
Fag5cI R CTACACGCCTTACAACCTT TCG Amplifies the 3' end of NGO0729 (putative repressor cI) without any restriction sites  
RNFGF1c TATCTGCAGTCTAGAACTG GCTCAAACGCCAT Amplifies the 5' end of NGO0477 (putative repressor cI) 94°C, 2 min; 28× (94°C, 45 sec.; 52°C, 45 sec.; 72°C, 2 min.); 72°C, 10 min.
FNGF1C1 GCGAATTCGATGCCTTTTA TTATCGATTACCAATGC Amplifies the 3' end of NGO0477  
HPPRL_F CGCGGAATTCGACCCAGT CAAATATATTCC Amplifies the 5' region of PL promoter of phage HP1 94°C, 5 min; 27×(94°C, 45 sec.; 56°C, 45 sec.; 72°C, 1 min.); 72°C, 10 min.
HPPRL_R CGGGATCCTCGCAAAAAT CGCCGAAAG Amplifies the 3' region of PL promoter of phage HP1  
HPPR_F CGGGATCCCAGGTAACAC AGTGATATAAC Amplifies the 5' region of PR promoter of Φ HP1 94°C, 5 min; 27× (94°C, 45 sec.; 56°C, 45 sec.; 72°C, 1 min.); 72°C, 10 min.
HPPR_R CGCGGAATTCCCCGTATT GGTAAATAATGG Amplifies the 3' region of PR promoter of Φ HP1  
HO488T4 F GCGAATTCGATGGATACC CTGTTAAGCATCATCA Amplifies the 5' region of putative holin of NgoΦ1 94°C, 2 min; 2× (94°C, 48° 45 sek, 72°C 1 min); 28 × (94°C, 45 sec.; 56°C, 45 sec.; 72°C, 1 min.); 72°C, 10 min.
HO488T4 B ATTCTGCAGCTTAATATCC GAAGCCGTCGAAGT Amplifies the 3' region of putative holin of NgoΦ1