Comparison of different real-time PCR chemistries and their suitability for detection and quantification of genetically modified organisms

Table 1 Primers and probes for Q-PCR analyses

Detection method	Target	Amplicon (bp)	Primer/probe name	Oligo concentration (nM)	Sequence (5'-3')^a	Position^b	Reference
TaqMan^®	Ivr	79	Ivr_F	900	TGGCGGACGACGACTTGT	3376	[23]
			Ivr_R	900	AAAGTTTGGAGGCTGCCGT	3436	[23]
			Ivr_Taq_P	200	[FAM]-CGAGCAGACCGCCGTGTACTTCTACC-[TAMRA]	3395	[23]
	Mon	111	Mon_F	600	CCTTCATAACCTTCGCCCG	-87	[24]
			Mon_R	600	AATAAAGTGACAGATAGCTGGGCA	+5	[24]
			Mon_Taq_P	150	[FAM]-ACGAAGGACTCTAACGTTTAACATCCTTTGCCA-[TAMRA]	-30	[24]
LNA^®	Ivr	79	Ivr_F	900	TGGCGGACGACGACTTGT	3376	[23]
			Ivr_R	900	AAAGTTTGGAGGCTGCCGT	3436	[23]
			Ivr_LNA_P	200	[FAM]-CGAGC+AG+ACCGCCGTG-[BHQ1]	3395	this study
	Mon	111	Mon_F	600	CCTTCATAACCTTCGCCCG	-87	[24]
			Mon_R	600	AATAAAGTGACAGATAGCTGGGCA	+5	[24]
			Mon_LNA_P	150	[FAM]-TTT+AA+C+AT+C+CTTTG+C+CA-[BHQ1]	-14	this study
CPT	Ivr	79	Ivr_F	600	TGGCGGACGACGACTTGT	3376	[23]
			Ivr_R	600	AAAGTTTGGAGGCTGCCGT	3436	[23]
			Ivr_CP_P	200	[FAM]-CT(G)CTCAAGGG-[TAMRA]	3420	this study
	Mon	112	Mon_CP_F	600	GAAGGACGAAGGACTCTAAC	-35	this study
			Mon_CP_R	600	GCAATGATGGCATTTGTAG	+58	this study
			Mon_CP_P	200	[FAM]-AT(G)GCAAAGGAT-[TAMRA]	-8	this study
Lux™	Ivr	84	Ivr_Lux_F	300	CGTGAGAATTTCCGTCTACTCG	2312	this study
			Ivr_Lux_R	300	cacggAAAGTGTTGTGCTTGGACCGt-[FAM]-G	2369	this study
	Mon	65	Mon_Lux_F	300	cgttagGAAGGACGAAGGACTCTAAc-[FAM]-G	-35	this study
			Mon_R	200	AATAAAGTGACAGATAGCTGGGCA	+8	this study
Plexor™	Ivr	99	Ivr_Plex_F	100	GCCGTGTACTTCTACCTGCTCA	3405	this study
			Ivr_Plex_R	100	[FAM]-iso-dC-GCATGGTCATAAGTCATAACATACATACCT	3478	this study
	Mon	134	Mon_F	200	CCTTCATAACCTTCGCCCG	-87	[24]
			Mon_Plex_R	200	[FAM]-iso-dC-CCTTTTCCACTATCTTCACAATAAAGTGAC	18	this study

^a +N denotes the LNA^® base; (G) stands for RNA nucleotide; lowercase letters for Lux™ indicate the sequence required for the hairpin structure and iso-dC is synthetic base isocytosine. ^b A position in the invertase gene or a distance in nucleotides between the 5'-junction and the 5'-end of the primer/probe.

ISSN: 1472-6750