Altered PCA3 and TMPRSS2-ERG expression in histologically benign regions of cancerous prostates: a systematic, quantitative mRNA analysis in five prostates

Table 1 Sequences of the primers and probes used in this study

Oligonucleotide	Sequence (5’- > 3’)	GenBank database sequence number	Position in sequence
KLK3
5’ primer	TGA ACC AGA GGA GTT CTT GAC	X05332	523–543
3’ primer	CCC AGA ATC ACC CGA GCA G	X05332	667–685
reporter probe	CCT TCT GAG GGT GAA CTT GCG C	X05332	596–617
quencher probe	AAT CAC CCT CAG AAG G	X05332	600–601, 604–617
mmPSA
5’ primer	TGA ACC AGA GGA GTT CTT GCA	X05332	523–543
3’ primer	CCC AGA ATC ACC CGA GCG A	X05332	667–685
reporter probe	CCT TCT GAG GGT GAT TGC GCA C	X05332	594–601, 604–617
quencher probe	AAT CAC CCT CAG AAG G	X05332	600–601, 604–617
PCA3
5’ primer	GGT GGG AAG GAC CTG ATG ATA C	AF103907	95–116
3’ primer	GGG CGA GGC TCA TCG AT	AF103907	505–521
reporter probe	AGA AAT GCC CGG CCG CCA TC	AF103907	478–497
quencher probe	CCG GGC ATT TCT	AF103907	478–489
TMPRSS2-ERG III
5’ primer	TAG GCG CGA GCT AAG CAG GAG	NM_005656.3	4–24
3’ primer	GTA GGC ACA CTC AAA CAA CGA CTG G	NM_004449.4	338–362
reporter probe	AGC GCG GCA GGA AGC CTT ATC AGT T	NM_005656.3 and NM_004449.4	57–64 and 310–326
quencher probe	TTC CTG CCG CGC T	NM_005656.3 and NM_004449.4	57–64 and 310–314
TMPRSS2-ERG VI
5’ primer	CGG CAG GTC ATA TTG AAC ATT CC	NM_005656.3	73–95
3’ primer	GCA CAC TCA AAC AAC GAC TGG	NM_004449.4	338–358
reporter probe	CTT TGA ACT CAG AAG CCT TAT CAG TTG TGA	NM_005656.3 and NM_004449.4	139–149 and 312–330
quencher probe	GGC TTC TGA GTT CAA AG	NM_005656.3 and NM_004449.4	139–149 and 312–317

Lanthanide chelates were attached to the 5’ ends of the reporter probes via an amino group to enable signal measurement with time-resolved fluorescence and phosphate groups to the 3’ ends to prevent them from functioning as starting points for DNA synthesis. Quencher molecules were attached to the 3’ ends of the quencher probes. The oligonucleotide sequences have been previously published for KLK3 [12, 13], mmPSA [11–13], PCA3 [10, 20], TMPRSS2-ERG III [9, 21, 22], and TMPRSS2-ERG VI [9] assays

ISSN: 1471-2490