Table 1. Oligonucleotides used in C2CA.

	Sequence 5′-3′
Padlock probes
ppFD+	P-CCTCCCATCATATTAAAGGCTTTCTCTATGTTAAGTGACCTACGACCTCAATGCTGCTGCTGTACTACTCTTCCTAAGGCATTCTGCAAACAT
ppMT+	P-CTGCCATCTTAACAAACCCTCATGATTAGAGCGCATCTGCAATAGCTGCTGTACTACTCTCTTCTTCTATGCGATTACCGGGCC
ppREF+	P-CTGCCATCTTAACAAACCCTTACATCTCGGAATCATGCTGGCTGCTGTACTACTCTCTTCTTCTATGCGATTACCGGGCT
Targets
tFD-	GCCTTTAATATGATGGGAGGATGTTTGCAGAATGCCTTAG
tMT-	GTTTGTTAAGATGGCAGGGCCCGGTAATCG
tREF-	TTGTTAAGATGGCAGAGCCCGGTAATCGCA
Molecular beacons
mbFD+	HEX-ccucAAUGCUGCUGCUGUACUACgagg-DABCYL
mbFD-	HEX-ccucCGUAGUACAGCAGCAGCAUUgagg-DABCYL
mbREF+	HEX-cagctACATCTCGGAATCAagcug-DABCYL
mbMT+	FAM-gcagCATGATTAGAGCGCATcugc-DABCYL
Replication oligonucleotides
RSA-	GCTGCTGTACTACTCTCTT
RSA+	AAGAGAGTAGTACAGCAGC
FNU-	GACCGTTAGCAGCATGATTCCG
FNU+	GAATCATGCTGCTAACGGT
Sandwich primers
WDP-F+	FITC-CCGAGATGTACCGCTATCGT
WDP-T+	TAMRA-AGAGCGCATGAATCCGTAGT

P, 5′ phosphate; the stem parts of 2′-O-Me-RNA molecular beacons are shown in lowercase.