. Author manuscript; available in PMC: 2010 Nov 24.

Published in final edited form as: Biochemistry. 2009 Nov 24;48(46):10882–10893. doi: 10.1021/bi901506f

Table 1.

Thermodynamic parameters of helix formation with RNA and 2'-O-Me oligoribonucleotides. The effect of 2'-O-methyl-2-thiouridine and LNA-2-thiouridine.^a

		Average of curve fits				T_M⁻¹ vs log C_T plots
RNA duplexes
(5'-3')	(3'-5')	−ΔH⁰ (kcal/mol)	−ΔS⁰ (eu)	−ΔG⁰₃₇ (kcal/mol)	T_M^b (⁰C)	−ΔH⁰ (kcal/mol)	−ΔS⁰ (eu)	−ΔG⁰₃₇ (kcal/mol)	T_M^b (⁰C)	ΔΔG⁰₃₇ (kcal/ mol)	ΔT_M^b (⁰C)	ΔΔG^0,₃₇^c (kcal/ mol)	ΔΔG⁰₃₇^c (kcal/ mol)
U^MC^MU^MA^MC^MC^MA^M, ^d	AGAUGGU^d	50.7±5.9	140.0±18.4	7.25±0.19	41.5	45.2±1.6	122.5±5.3	7.18±0.03	41.5	0	0	0	0
s²U^MC^MU^MA^MC^MC^MA^M	AGAUGGU	53.3±3.5	146.8±11.1	7.74±0.09	44.2	51.2±1.4	140.5±4.4	7.67±0.02	44.1	−0.49	2.6	−0.49	0
U^MC^MU^MA^MC^MC^MA^M	GGAUGGU	47.2±5.1	130.4±16.6	6.74±0.14	38.4	42.0±0.8	113.6±2.5	6.79±0.01	39.0	0.39	−2.5	0	0.39
s²U^MC^MU^MA^MC^MC^MA^M	GGAUGGU	(48.7 ±6.7)	(134.2±21.2)	(7.08±0.17)	(40.5)	(40.8±1.7)	(109.1±5.4)	(7.03±0.03)	(40.9)	(−0.24)	(−0.6)	(−0.24)	(0.64)

U^LC^MU^MA^MC^MC^MA^M, ^d	AGAUGGU^d	55.7±3.3	154.4±10.0	7.84±0.19	44.4	47.2±3.0	127.5±9.6	7.64±0.08	44.5	0	0	0	0
s²U^LC^MU^MA^MC^MC^MA^M	AGAUGGU	58.8±3.2	161.7±9.9	8.65±0.13	48.6	53.9±1.7	146.6±5.2	8.51±0.05	48.8	−0.87	4.3	−0.87	0
U^LC^MU^MA^MC^MC^MA^M	GGAUGGU	48.1±4.7	132.5±15.0	7.03±0.10	40.3	43.3±1.4	117.1±4.7	7.01±0.02	40.5	0.63	−4.0	0	0.63
s²U^LC^MU^MA^MC^MC^MA^M	GGAUGGU	47.9±8.7	130.2±27.6	7.55±0.16	43.7	44.2±4.4	118.6±14.2	7.45±0.18	43.6	−0.44	−0.9	−0.44	1.06

A^MC^MU^MA^MC^MC^MU^M, ^d	UGAUGGA^d	59.6±5.7	168.4±18.9	7.41±0.28	41.2	62.2±7.3	176.8±23.6	7.37±0.26	41.2	0	0	0	0
A^MC^MU^MA^MC^MC^Ms²U^M	UGAUGGA	49.9±5.9	137.7±18.5	7.28±0.19	41.7	44.1±0.8	119.1±2.7	7.20±0.01	41.8	0.17	0.6	0.17	0
A^MC^MU^MA^MC^MC^MU^M	UGAUGGG	48.6±4.0	134.2±12.5	6.96±0.11	39.8	44.4±1.5	121.0±5.0	6.93±0.03	39.8	0.44	−1.4	0	0.44
A^MC^MU^MA^MC^MC^Ms²U^M	UGAUGGG	45.2±7.4	123.6±23.3	6.84±0.15	39.1	41.7±0.8	112.5±2.5	6.78±0.01	38.9	0.59	−2.3	0.15	0.42

A^MC^MU^MA^MC^MC^MU^L, ^d	UGAUGGA^d	59.2±5.2	167.7±17.2	7.19±0.17	40.5	55.6±2.6	155.8±8.5	7.24±0.04	41.0	0	0	0	0
A^MC^MU^MA^MC^MC^Ms²U^L	UGAUGGA	54.5±3.3	150.3±10.3	7.92±0.15	45.1	48.4±1.2	130.9±3.9	7.84±0.02	45.6	−0.60	4.6	−0.60	0
A^MC^MU^MA^MC^MC^MU^L, ^d	UGAUGGG^d	57.6±11.2	161.3±35.9	7.52±0.29	42.4	58.4±9.0	164.6±29.0	7.38±0.38	41.6	−0.14	0.6	0	−0.14
A^MC^MU^MA^MC^MC^Ms²U^L	UGAUGGG	50.6±3.1	139.3±9.5	7.44±0.16	42.7	44.7±1.9	120.4±6.2	7.40±0.33	43.1	−0.02	2.1	−0.02	0.44

A^MC^MU^MU^MG^MC^MA^M	UGAACGU	61.2±3.3	172.4±10.0	7.71±0.15	43.1	52.7±0.7	145.3±2.3	7.59±0.01	43.4	0	0	0	0
A^MC^MU^Ms²U^MG^MC^MA^M	UGAACGU	60.9±5.3	167.4±16.3	8.97±0.22	50.0	62.4±5.2	172.4±16.3	9.00±0.17	49.8	−1.41	6.4	−1.41	0
A^MC^MU^MU^MG^MC^MA^M, ^d	UGAGCGU^d	62.5±4.1	186.3±13.5	4.76±0.17	28.4	66.4±11.1	199.2±37.2	4.60±0.58	28.2	2.99	−15.2	0	2.99
A^MC^MU^Ms²U^MG^MC^MA^M	UGAGCGU	46.2±2.8	132.2±9.4	5.16±0.16	28.1	46.6±1.8	133.7±6.1	5.17±0.09	28.2	2.42	−15.2	−0.57	3.83

A^MC^MU^MU^LG^MC^MA^M, ^d	UGAACGU^d	61.0±2.3	167.7±7.4	9.00±0.12	50.1	59.5±1.6	163.1±5.0	8.96±0.05	50.2	0	0	0	0
A^MC^MU^Ms²U^LG^MC^MA^M	UGAACGU	59.6±7.0	158.3±21.1	10.48±0.43	59.0	59.1±1.4	157.0±4.2	10.40±0.07	58.7	−1.44	8.5	−1.44	0
A^MC^MU^MU^LG^MC^MA^M, ^d	UGAGCGU^d	60.8±11.0	174.2±35.5	6.78±0.19	38.3	55.9±4.7	158.3±15.5	6.76±0.13	38.3	2.20	−11.9	0	2.20
A^MC^MU^Ms²U^LG^MC^MA^M	UGAGCGU	35.2±3.6	91.9±11.3	6.71±0.18	38.6	38.7±5.8	103.3±18.8	6.64±0.31	37.9	2.32	−12.3	0.12	3.76

G^MU^MU^MA^MC^MC^MA^M	CAAUGGU	55.3±3.5	156.0±11.1	6.88±0.10	39.0	49.9±1.2	138.6±3.9	6.85±0.01	39.0	0	0	0	0
G^Ms²U^MU^MA^MC^MC^MA^M	CAAUGGU	54.2±3.8	150.4±11.8	7.60±0.13	43.2	48.8±0.7	133.1±2.3	7.51±0.01	43.4	−0.66	4.4	−0.66	0
G^MU^MU^MA^MC^MC^MA^M	CGAUGGU	47.4±4.4	136.8±14.4	4.97±0.17	27.1	45.8±4.8	131.5±16.3	5.06±0.27	27.3	1.79	−11.7	0	1.79
G^Ms²U^MU^MA^MC^MC^MA^M	CGAUGGU	41.8±5.2	119.6±17.3	4.71±0.34	24.1	41.5±5.3	118.3±17.9	4.76±0.39	24.3	2.09	−14.7	0.30	2.75

G^MU^LU^MA^MC^MC^MA^M	CAAUGGU	58.4±3.1	161.6±9.4	8.27±0.16	46.5	53.7±2.0	146.7±6.4	8.15±0.05	46.7	0	0	0	0
G^Ms²U^LU^MA^MC^MC^MA^M	CAAUGGU	55.2±3.7	149.6±11.3	8.82±0.22	50.4	50.9±1.1	136.3±3.6	8.67±0.03	50.6	−0.52	3.9	−0.52	0
G^MU^LU^MA^MC^MC^MA^M	CGAUGGU	51.7±3.1	146.4±9.8	6.29±0.16	35.5	47.0±2.4	131.1±8.0	6.35±0.06	35.8	1.80	−10.9	0	1.80
G^Ms²U^LU^MA^MC^MC^MA^M	CGAUGGU	41.7±2.9	115.1±9.2	5.98±0.08	33.0	40.1±1.4	109.9±4.6	6.01±0.05	33.0	2.14	−13.7	0.34	2.66

solutions are 1 M NaCl, 20 mmol sodium cacodylate and 0.5 mmol Na₂EDTA, pH 7,

calculated for 10⁻⁴ M total strand concentration,

data with the same character of fonts belong to the same set,

data from ref. 16. The data in parenthesis indicate non–two state melting.