Table 3.

Al-Quds University 16S General PCR and Sequencing Primers (QUGP-16S; this study^a) based on 16S sequence of H. pylori gi|108562424:c1140006-1138506

Primer	PCR and sequencing primers	Oligomer: location	Tm (ºC)
QUGP-F1	5′-AGTTTGATCCTGGCTCAG-3′	18: 10–27a	53.7
QUGP-F1b	5′-AGTTTGATCATGGCTCAG-3′	18: 10–27	51.40
QUGP-F3	5′-GATACCCTGGTAGTCCA-3′	17: 753–769	52.80
QUGP-R3	5′-TGGACTACCAGGGTATC-3′	17: 769–752	52.80
QUGP-F4	5′-CCGCCTGGGGAGTACG-3′	16: 840–856	59.55
QUGP-R4	5′- CGTACTCCCCAGGCGG-3′	16: 856–840	59.55
QUGP-F5	5′-CCTACGGGAGGCAGCAG-3′	17: 326–343	54.54
QUGP-R5	5′-CTGCTGCCTCCCGTAGG-3′	17: 343–326	54.30
QUGP-F6	5′-GCAGCCGCGGTAATAC-3′	16: 481–497	54.51
QUGP-R6	5′-GTATTACCGCGGCTGC-3′	16: 497–481	54.30
QUGP-R7	5′-CGATTACTAGCGATTCC-3′	17:1319–1302	47.13
QUGP-R2	5′-GACGGGCGGTGTGTAC-3′	16: 1376–1392	54.85
QUGP-R1	5′-TACCTTGTTACGACTTCACCC-3′	17: 1468–1447	57.90
QUGP-R1b	5′-TACCTTGTTACGACTTC-3′	17: 1468–1451	47.90

Bold italicized sequences are homologous to Human GENE ID: 100008588 LOC100008588 | 18S ribosomal RNA. The potential products QUGP-Fn6. Rn2, 1096 bp and QUGP-Fn6.Rn1, 1226 bp are unlikely to form at 58°C due to 3′-mismatches to human 18S rDNA when clinical samples contain human DNA. This justifies switching from the short QUGP to the new longer sequences; while QUGP-R2 will match human DNA, QUGP-Rn2 presents a critical mismatch at its 3′-end

^aSome of the primers overlapped those used by others, see Table 1. Primer location differ slightly in different bacteria and may be absent from others (QUGP R2/Rn2 is absent from H. pylori, the shown location is for P. fluorescens, some bacteria will mismatch with 5′-end of primer(s)