Table 1.

Probe Sequences Used in This Work^a

name	sequence (5′-3′)b	predicted Tm (°C)c	predicted ΔGc(kcal/mol)	comments
HCV	thiol(CH2)6-GCG AGC ATA GTG GTC TGC GGA ACC GGT GAC TCG C-TAMRA	57.6	−6.26	probe specific for a 24-base region of HCV
SARS	thiol(CH2)6-GCG AGA GAT GCT GTG GGT ACT AAC CTA CCT CTC GC-TAMRA	65.1	−9.77	probe specific for a 25-base region of SARS, which extends the stem from 5 to 7 bases due to self-complementarity
HIV	thiol(CH2)6-GCG AGT GTT AAA AGA GAC CAT CAA TGA GCT CGC-TAMRA	57.1	−3.97	probe specific for a 23-base region of HIV
SBM	thiol(CH2)6-GCG AGA TAG TGG TCT GCG GAC TCG C-TAMRA	60.4	−4.50	probe used for mismatch assay; position of mismatch is bold
L14	thiol(CH2)6-GCG AGA TCA ATG AGG AAG CCT CGC-TAMRA	59.9	−4.24	probe with 14-base loop; specific for HIV
L24	thiol(CH2)6-GCG AGG AGA CCA TCA ATG AGG AAG CTG CACT CGC-TAMRA	53.8	−3.57	probe with 24-base loop; specific for HIV
L38	thiol(CH2)6-GCG AGA AAA GAG ACC ATC AAT GAG GAA GCT GCA GAA TGG GAT ACT CGC-TAMRA	46.8	−4.95	probe with 38-base loop; specific for HIV
DENV-2(4)	thiol(CH2)6-GCG AGT GTC TGT TAC CAA GGA TCT GTC GC-TAMRA	44.1	−1.80	probe with 4 base pair stem; for DENV-2
DENV-2(5)	thiol(CH2)6-GCG AGG TGT CTG TTA CCA AGG ATC TGC TCG C-TAMRA	56.6	−4.00	probe with 5 base pair stem; for DENV-2
DENV-2(6)	thiol(CH2)6-GCG AGC GTG TCT GTT ACC AAG GAT CTG GCT CGC-TAMRA	68.6	−6.27	probe with 6 base pair stem; for DENV-2
DENV-2(7)	thiol(CH2)6-GCG AGC GGT GTC TGT TAC CAA GGA TCT GCG CTC GC-TAMRA	74.7	−8.88	probe with 7 base pair stem; for DENV-2

^aTargets were synthetic oligonucleotides fully complementary to the loop region of each probe.

^bThe italic portions of the sequences indicate complementary stem regions.

^cGenerated by mfold for most stable secondary structure in 500 mM NaCl at 25 °C.