Table 3.

Oligonucleotide primers and molecular beacon probes used in this study^a

Primer/probeb	Sequence (5′ to 3′)c	Size (bp)	5′ fluorescent dye	3′ quencher
KPC-F107	TCGAACAGGACTTTGGCGGCT	260
KPC-R366	GGACAGCTCCGCCACCGTCATG
MB147G	gcgct CGATGGATACCGGCTCA agcgc		FAM	DABCYL
MB308C	cgcga CTGGTTCCGTGGTCAC tcgcg		HEX	DABCYL
MB308T	cgcga CTGGTTCTGTGGTC tcgcg		Quasar 670d	BHQ-2
KPC-F684	GGCAGTCGGAGACAAAACC	177
KPC-R860	CCCTCGAGCGCGAGTCTA
MB716T	cgcga AACCTGCGGAGTGTATGG tcgcg		Atto 425	DABCYL
MB716C	cgcga AACCTGCGGAGCGTATGG tcgcg		Quasar 670d	BHQ-2
MB814C	cgacg GACAAGCACAGCGAGG cgtcg		CAL Fluor Red 610	BHQ-2

^aFAM, fluorescein; HEX, hexachlorofluorescein; DABCYL, 4-(4′-dimethylaminophenylazo)benzoic acid; BHQ, black hole quencher.

^bOligonucleotide primer sets spanning nucleotide positions 107 to 366 and 684 to 860 were used to amplify two segments, each containing two molecular beacon target positions. Positions 308 and 716 are targeted by more than one molecular beacon probe.

^cMolecular beacon hairpin sequences are shown in lowercase letters. Single nucleotide polymorphism target positions are underlined, as in Table 2.

^dQuasar 670 dye is used for both MB308T and MB716C, as explained in Table 2.