. 2015 Nov 18;10(11):e0143354. doi: 10.1371/journal.pone.0143354

Table 1. Summary of biophysical properties of D1-D18 duplexes at various buffers pH values. ^a .

Sequences of duplexes and control oligonucleotides	Name of duplexes and control probes	Thermodynamic stabilities			Fluorescence measurements ^b						Analysis of CD spectra
		pH 5	pH 7		pH 5			pH 7			pH 5	pH 7
		-ΔG°₃₇ (kcal/mol)	-ΔG°₃₇ (kcal/mol)	ΔΔG°₃₇ (pH 5)–ΔΔG°₃₇ (pH 7)	Lifetime τ _DA (ns)	FRET efficiency E (%)	Distance R (Å)	Lifetime τ _DA (ns)	FRET efficiency E (%)	Distance R (Å)	h_1/2	h_1/2
`AGAAAGAGAAGA`	S1^*	-	-	-	2.5 ^τD	0	R ₀	3.8	0	R ₀	-	-
`AGAAAGAGAAGA/TCTTTCTCTTCT`	D1	6.25	4.67	-1.58	2.4	2	104	3.4	10	78	-0.50	3.25
`AGAAAGAGAAGA/TC^LTTTC^LTCTTC^LT`	D2	8.07	4.11	-3.96	2.5	0	>108	3.2	16	70	1.05	1.55
`AGAAAGAGAAGA/UCUUUCUCUUCU`	D3	6.77	3.27	-3.50	2.5	0	>108	3.7	2	106	-0.40	2.00
`AGAAAGAGAAGA/UC^LUUUC^LUCUUC^LU`	D4	9.42	5.26	-4.16	2.5	0	>108	3.7	2	106	-0.95	0.40
`AGAAAGAGAAGA/U^MC^MU^MU^MU^MC^MU^MC^MU^MU^MC^MU^M`	D5	7.70	3.42	-4.28	2.4	2	103	3.8	0	>108	-0.50	1.10
`AGAAAGAGAAGA/U^MCLU^MU^MU^MC^LU^MC^MU^MU^MC^LU^M`	D6	10.35	5.81	-4.54	2.5	0	>108	3.8	0	>108	-3.30	0.00
`AGAAAGAGAAGA`	S2^*	-	-	-	2.4 ^τD	0	R ₀	3.7	0	R ₀	-	-
`AGAAAGAGAAGA/TCTTTCTCTTCT`	D7	6.44	7.12	0.68	1.8	26	64	1.7	55	52	-1.50	0.90
`AGAAAGAGAAGA/TC^LTTTC^LTCTTC^LT`	D8	9.18	9.94	0.76	1.4	57	57	1.2	68	47	-1.25	0.45
`AGAAAGAGAAGA/UCUUUCUCUUCU`	D9	7.58	7.99	0.41	1.6	66	48	0.4	89	38	-2.05	-0.15
`AGAAAGAGAAGA/UC^LUUUC^LUCUUC^LU`	D10	9.64	10.51	0.87	1.2	50	54	0.1	96	32	-2.00	-0.75
`AGAAAGAGAAGA/U^MC^MU^MU^MU^MC^MU^MC^MU^MU^MC^MU^M`	D11	8.33	8.86	0.53	0.7	71	46	1.2	68	47	-1.45	-0.70
`AGAAAGAGAAGA/U^MC^LU^MU^MU^MC^LU^MC^MU^MU^MC^LU^M`	D12	11.46	11.70	0.24	0.6	77	44	0.4	89	38	-0.95	1.40
`A^MG^MA^MA^MA^MG^MA^MG^MA^MA^MG^MA^M`	S3^*	-	-	-	2.3^τD	0	R ₀	3.6	0	R ₀	-	-
`A^MG^MA^MA^MA^MG^MA^MG^MA^MA^MG^MA^M/TCTTTCTCTTCT`	D13	6.50	6.81	0.31	1.3	43	56	1.4	62	50	-0.30	0.60
`A^MG^MA^MA^MA^MG^MA^MG^MA^MA^MG^MA^M/TC^LTTTC^LTCTTC^LT`	D14	9.92	9.52	-0.40	1.0	54	52	0.9	74	45	-0.75	-0.40
`A^MG^MA^MA^MA^MG^MA^MG^MA^MA^MG^MA^M/UCUUUCUCUUCU`	D15	7.60	7.91	0.31	0.9	58	51	0.7	81	42	-1.65	-0.75
`A^MG^MA^MA^MA^MG^MA^MG^MA^MA^MG^MA^M/UC^LUUUC^LUCUUC^LU`	D16	10.06	10.82	0.76	0.5	76	46	0.6	83	42	-0.80	0.65
`A^MG^MA^MA^MA^MG^MA^MG^MA^MA^MG^MA^M/U^MC^MU^MU^MU^MC^MU^MC^MU^MU^MC^MU^M`	D17	7.24	9.15	1.91	0.6	75	45	0.3	92	36	-0.30	0.00
`A^MG^MA^MA^MA^MG^MA^MG^MA^MA^MG^MA^M/U^MC^LU^MU^MU^MC^LU^MC^MU^MU^MC^LU^M`	D18	11.11	12.54	1.43	0.6	75	45	0.1	96	32	-0.45	1.25

^a—solution: 40 mM boric acid, 40 mM phosphoric acid, 40 mM acetic acid, and 100 mM sodium chloride, pH 5.0 and pH 7.0;

^b—the value of χ²≤ 1.2;

τ_DA—fluorescence lifetimes of donor with acceptor; τ_D—fluorescence lifetime of donor (references values); R₀—Förster distance; R—distance between donor and acceptor fluorophores; h_1/2—value of half high maximum peak at 220 nm and minimum peak at 210 nm;

*—S1, S2, S3 control probes for D1-D6, D7-D12 and D13-D18 duplexes, respectively. Meaning of used fonts: italic—RNA, A^M, G^M, U^M and C^M—2’-O-Me RNA, C^L—LNA cytidine.

Table 1. Summary of biophysical properties of D1-D18 duplexes at various buffers pH values. a .

Table 1. Summary of biophysical properties of D1-D18 duplexes at various buffers pH values. ^a .