TABLE 1.

Oligonucleotide probes used to demonstrate the effect of probe elongation and moving the location of the fluorescein label

Probe namea	Sequence (5′-3′)d	Free energy change (kcal/mol)					Brightness (CBU)b		Quadrante
		ΔGo1	ΔGo2	ΔGo12	ΔGo3	ΔGooverall	3 hc	96 hc	Original	Elongated
E86-109	TCCGCCACTCGTCAGCAAAGAAGC	−27.1	0.2	−26.8	−13.0	−13.8	63 ± 1	70 ± 4	Q1	Q3
E251-271	GTGAGCCGTTACCCCACCTAC	−27.4	1.2	−27.3	−9.8	−17.5	NDf	24 ± 2	Q4	Q4
E312-332	CCGTGTCTCAGTTCCAGTGTG	−25.1	1.9	−25.1	−5.8	−19.3	87 ± 1	80 ± 6	Q4	Q3
E325-346	CGTAGGAGTCTGGACCGTGTCT	−25.7	0.4	−25.4	−11.5	−13.9	48 ± 2	63 ± 4	Q1	Q3
E483-506	CCGGTGCTTCTTCTGCGGGTAACG	−29.0	−0.2	−28.5	−8.5	−20.0	50 ± 1	81 ± 5	Q4	Q3
E595-618	GCCCGGGGATTTCACATCTGACTT	−28.4	0.5	−28.1	−16.1	−12.1	5 ± 4	63 ± 3	Q1	Q3
E615-634	GCAGTTCCCAGGTTGAGCCC	−27.6	0.2	−27.3	−12.4	−14.9	9 ± 3	67 ± 4	Q1	Q3
E631-655	TCAAGCTTGCCAGTATCAGATGCAG	−26.0	0.5	−25.8	−10.5	−15.3	8 ± 2	62 ± 3	Q1	Q3
E731-750	GTCTTCGTCCAGGGGGCCGC	−29.0	0.0	−28.6	−8.4	−20.1	ND	28 ± 2	Q4	Q4
E839-859	CCGGAAGCCACGCCTCAAGGG	−26.6	0.2	−26.3	−11.8	−14.5	6 ± 4	56 ± 3	Q1	Q3
E958-980	GGTTCTTCGCGTTGCATCGAATT	−24.3	0.0	−23.8	−6.2	−17.6	53 ± 1	56 ± 2	Q4	Q3
E1149-1172	GTTTATCACTGGCAGTCTCCTTTG	−25.9	0.5	−25.7	−8.7	−17.0	ND	28 ± 2	Q4	Q4
E1379-1400	GGTGTGTACAAGGCCCGGGAAC	−25.8	0.8	−25.6	−4.4	−21.2	59 ± 2	58 ± 2	Q4	Q3
E1425-1449	GGTTAAGCTACCTACTTCTTTTGCA	−26.9	0.2	−26.5	−9.6	−16.9	16 ± 2	52 ± 2	Q4	Q3
E1449-1469	GTGGTAAGCGCCCTCCCGAAG	−25.4	0.6	−25.2	−6.2	−18.9	16 ± 3	28 ± 2	Q4	Q3
E255-278	CGCCTAGGTGAGCCGTTACCCCAC	−32.9	0.4	−32.6	−12.4	−20.2	121 ± 4	97 ± 1	Q4	Q3
E734-755	CGTCAGTCTTCGTCCAGGGGGC	−29.1	0.4	−28.8	−7.7	−21.1	6 ± 6	63 ± 1	Q4	Q3
E1153-1178	CCTCCAGTTTATCACTGGCAGTCTCC	−32.0	−2.8	−29.3	−10.1	−19.2	8 ± 4	86 ± 1	Q4	Q3

^a“E” in the probe name indicates E. coli, and the numbers indicate the position of the target site on the 16S rRNA (5′ to 3′).

^bBrightness values were converted to the scale of Fuchs et al. (17). The values are means ± standard deviations of the means.

^cHybridization period.

^dUnderlining indicates bases added to elongate the original versions shown in Table S2 in the supplemental material.

^ePositions of the original and elongated probes according to Fig. 4.

^fND, not determined.