Optimization of quantitative polymerase chain reactions for detection and quantification of eight periodontal bacterial pathogens

Decat, Ellen; Cosyn, Jan; De Bruyn, Hugo; Miremadi, Reza; Saerens, Bart; Van Mechelen, Els; Vermeulen, Stefan; Vaneechoutte, Mario; Deschaght, Pieter

doi:10.1186/1756-0500-5-664

Table 2 Primer sequences evaluated for specificity (BLAST) and primer annealing onto secondary structures (mFOLD) by in silico analysis for the eight different species

From: Optimization of quantitative polymerase chain reactions for detection and quantification of eight periodontal bacterial pathogens

Species	Primers	Target gene	Reference
Aggregatibacter actinomycetemcomitans ^a	F: GCGAACGTTACGCGTTTTAC	waaA	Hyvarinen et al. [33]
Aggregatibacter actinomycetemcomitans ^a	R: GGCAAATAAACGTGGGTGAC	waaA	Hyvarinen et al. [33]
Aggregatibacter actinomycetemcomitans	F: CTTACCTACTCTTGACATCCGAA	16S rRNA	Maeda et al. [35]
Aggregatibacter actinomycetemcomitans	RV: ATGCAGCACCTGTCTCAAAGC	16S rRNA	Maeda et al. [35]
Aggregatibacter actinomycetemcomitans ^b	F: CAGCATCTGCGATCCCTGTA	iktA	Yoshida et al. [36]
Aggregatibacter actinomycetemcomitans ^b	R: TCAGCCCTTTGTCTTTCCTAGGT	iktA	Yoshida et al. [36]
Fusobacterium spp.	F: AAGCGCGTCTAGGTGGTTATGT	16S rRNA	Martin et al. [37]
Fusobacterium spp.	R: TGTAGTTCCGCTTACCTCTCCAG	16S rRNA	Martin et al. [37]
Fusobacterium spp.^b	F: CGCAGAAGGTGAAAGTCCTGTAT	16S rRNA	Suzuki et al. [38]
Fusobacterium spp.^b	R: TGGTCCTCACTGATTCACACAGA	16S rRNA	Suzuki et al. [38]
Parvimonas micros	F: AAACGACGATTAATACCACATGAGAC	16S rRNA	Bartz et al. [39]
Parvimonas micros	R: ACTGCTGCCTCCCGTAGGA	16S rRNA	Bartz et al. [39]
Parvimonas micros ^b	F: AGTGGGATAGCCGTTGGAAA	16S rRNA	Martin et al. [37]
Parvimonas micros ^b	R: GACGCGAGCCCTTCTTACAC	16S rRNA	Martin et al. [37]
Porphyromonas gingivalis	F: TGGTTTCATGCAGCTTCTTT	waaA	Hyvarinen et al. [33]
Porphyromonas gingivalis	R: TCGGCACCTTCGTAATTCTT	waaA	Hyvarinen et al. [33]
Prevotella intermedia ^b	F: GACCCGAACGCAAAATACAT	waaA	Hyvarinen et al. [33]
Prevotella intermedia ^b	R: AGGGCGAAAAGAACGTTAGG	waaA	Hyvarinen et al. [33]
Prevotella intermedia	F: TCCACCGATGAATCTTTGGTC	16S rRNA	Maeda et al. [35]
Prevotella intermedia	R: ATCCAACCTTCCCTCCACTC	16S rRNA	Maeda et al. [35]
Tannerella forsythia ^a	F: CTCGCTCGGTGAGTTTGAA	waaA	Hyvarinen et al. [33]
Tannerella forsythia ^a	R: ATGGCGAAAAGAACGTCAAC	waaA	Hyvarinen et al. [33]
Tannerella forsythia	F: GGGTGAGTAACGCGTATGTAACCT	16S rRNA	Shelburne et al. [40]
Tannerella forsythia	R: ACCCATCCGCAACCAATAAA	16S rRNA	Shelburne et al. [40]
Tannerella forsythia ^b	F: TCCCAAAGACGCGGATATCA	bspA antigen	Morillo et al. [41]
Tannerella forsythia ^b	R: ACGGTCGCGATGTCATTGT	bspA antigen	Morillo et al. [41]
Tannerella forsythia ^a	F: AGCGATGGTAGCAATACCTGTC	16S rRNA	Kuboniwa et al. [42]
Tannerella forsythia ^a	R: TTCGCCGGGTTATCCCTC	16S rRNA	Kuboniwa et al. [42]
Tannerella forsythia ^a	F: ATCCTGGCTCAGGATGAACG	16S rRNA	Suzuki et al. [38]
Tannerella forsythia ^a	R: TACGCATACCCATCCGCAA	16S rRNA	Suzuki et al. [38]
Treponema denticola	F: CCTTGAACAAAAACCGGAAA	waaG	Hyvarinen et al. [33]
Treponema denticola	R: GGGAAAAGCAGGAAGCATAA	waaG	Hyvarinen et al. [33]
Streptococcus mutans ^b	F: AGCCATGCGCAATCAACAGGTT	gftB	Yano et al. [43]
Streptococcus mutans ^b	R: CGCAACGCGAACATCTTGATCAG	gftB	Yano et al. [43]
Streptococcus mutans	F: GCCTACAGCTCAGAGATGCTATTCT	gftB	Yoshida et al. [36]
Streptococcus mutans	R: GCCATACACCACTCATGAATTGA	gftB	Yoshida et al. [36]

Legend
^a: Primer pairs excluded for further in vitro testing on the basis of in silico analysis.
^b: Primer pairs excluded for further specificity testing on the basis of amplification efficiency.

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ISSN: 1756-0500

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