. 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 2.

Thermodynamic parameters of helix formation with RNA and 2'-O-Me oligoribonucleotides. The effect of LNA-2-thiouridine in the presence of 3'-pyrene^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)	ΔΔG⁰₃₇^c (kcal/mol)	ΔΔG⁰₃₇^c (kcal/mol)
U^LG^MU^MG^MU^M pyrene	GACACAG	48.6±3.1	133.0±9.9	7.37±0.10	42.4	43.9±1.6	117.8±5.2	7.35±0.02	42.9	0	0	0	0
s²U^LG^MU^MG^MU^Mpyrene	GACACAG	47.9±2.1	128.0±6.6	8.20±0.08	48.2	46.0±1.1	122.0±3.5	8.12±0.03	48.1	−0.77	5.2	−0.77	0
U^LG^MU^MG^MU^Mpyrene	GGCACAG	38.2±3.1	104.9±10.3	5.67±0.10	30.2	38.8±2.2	106.7±7.6	5.68±0.11	30.3	1.67	−12.6	0	1.67
s²U^LG^MU^MG^MU^Mpyrene	GGCACAG	35.7±8.9	94.9±30.3	6.28±0.61	34.8	36.9±4.2	99.3±13.8	6.12±0.24	33.6	1.23	−9.3	−0.44	2.00

U^MG^MU^MG^MU^Lpyrene	GACACAG	41.6±2.9	111.3±9.1	7.05±0.10	40.9	41.8±2.3	112.1±7.4	7.03±0.05	40.7	0	0	0	0
U^MG^MU^MG^Ms²U^Lpyrene	GACACAG	44.0±2.3	117.4±7.2	7.60±0.13	44.7	40.0±0.6	104.7±2.0	7.54±0.01	45.0	−0.51	4.3	−0.51	0
U^MG^MU^MG^MU^Lpyrene	GACACGG	44.3±2.2	122.4±7.1	6.33±0.09	35.6	40.3±1.5	109.3±5.1	6.42±0.05	36.1	0.61	−4.6	0	0.61
U^MG^MU^MG^Ms²U^Lpyrene	GACACGG	42.3±5.0	115.8±16.3	6.37±0.17	35.8	47.7±2.1	133.6±7.0	6.25±0.06	35.2	0.78	−5.5	0.17	1.29

C^MU^MU^LG^MC^Mpyrene	UGAACGU	54.8±5.9	145.4±17.9	9.71±0.32	56.1	51.1±1.2	134.2±3.7	9.52±0.06	56.3	0	0	0	0
C^MU^Ms²U^LG^MC^Mpyrene	UGAACGU	57.7±4.0	150.5±11.7	11.05±0.34	63.4	57.0±3.2	148.5±9.5	10.97±0.23	63.2	−1.45	6.9	−1.45	0
C^MU^MU^LG^MC^Mpyrene	UGAGCGU	48.9±2.6	134.4±8.3	7.20±0.10	41.3	45.6±1.1	124.1±3.4	7.18±0.01	41.5	2.34	−14.8	0	2.34
C^MU^Ms²U^LG^MC^Mpyrene	UGAGCGU	34.0±4.0	85.4±12.1	7.51±0.38	46.2	34.2±5.7	86.1±18.2	7.49±0.45	46.0	2.03	−10.3	−0.31	3.48

U^MG^MU^LG^MU^M pyrene	GACACAG	47.0±2.8	125.8±8.6	7.97±0.13	46.8	43.0±1.3	113.2±4.2	7.90±0.02	47.2	0	0	0	0
U^MG^Ms²U^LG^MU^Mpyrene	GACACAG	49.3±6.1	130.2±18.8	8.88±0.28	52.5	49.6±3.9	131.2±12.1	8.87±0.16	52.3	−0.97	5.1	−0.97	0
U^MG^MU^LG^MU^Mpyrene	GACGCAG	43.0±5.2	120.7±17.3	5.57±0.21	30.2	44.4±2.7	125.2±9.0	5.59±0.11	30.6	2.31	−16.6	0	2.31
U^MG^Ms²U^LG^MU^Mpyrene	GACGCAG	42.3±5.8	117.9±19.9	5.76±0.42	31.4	44.1±6.5	124.0±21.7	5.66±0.41	31.0	2.24	16.2	−0.07	3.21

U^MG^MU^LG^MU^Lpyrene	GACACAG	45.8±1.4	119.6±4.4	8.75±0.08	52.8	45.0±0.9	117.1±2.8	8.71±0.03	52.8	0	0	0	0
U^MG^Ms²U^LG^Ms²U^Lpyrene	GACACAG	49.3±4.0	126.3±12.1	10.10±0.29	61.2	50.1±2.2	128.8±6.7	10.12±0.13	60.9	−1.41	8.1	−1.41	0
U^MG^MU^LG^MU^Lpyrene	GACGCGG	53.4±4.8	152.4±15.9	6.14±0.17	34.7	50.8±2.9	144.0±9.4	6.21±0.07	35.0	2.50	−17.8	0	2.50
U^MG^Ms²U^LG^Ms²U^Lpyrene	GACGCGG	44.2±4.9	115.5±15.0	8.36±0.28	50.4	43.3±5.3	113.0±16.3	8.28±0.31	50.1	0.43	−2.7	−2.07	1.84

C^MU^LA^MU^LC^Mpyrene	UGAUAGU	54.9±2.5	148.6±7.6	8.83±0.14	50.6	55.8±2.8	151.5±8.8	8.85±0.10	50.5	0	0	0	0
C^Ms²U^LA^Ms²U^LC^Mpyrene	UGAUAGU	53.1±3.3	138.4±9.9	10.19±0.23	60.0	51.1±2.0	132.3±6.2	10.03±0.12	59.8	−1.18	9.3	−1.18	0
C^MU^LA^MU^LC^Mpyrene	UGGUGGU	48.5±6.3	142.3±21.2	4.37±0.27	23.8	44.6±5.3	129.2±18.1	4.57±0.36	24.0	4.28	−26.5	0	4.28
C^Ms²U^LA^Ms²U^LC^Mpyrene	UGGUGGU	25.4±5.1	61.0±17.1	6.51±0.69	36.7	28.4±11.6	70.6±37.2	6.55±1.76	37.2	2.30	−13.3	−1.98	3.48

C^MU^LA^MU^LC^Mpyrene	UGAUGGU	48.4±4.3	133.8±13.7	6.94±0.12	39.7	47.5±2.5	130.6±8.3	6.95±0.06	39.7	0	0	0	0
C^Ms²U^LA^Ms²U^LC^Mpyrene	UGAUGGU	40.7±2.5	109.5±8.1	6.74±0.10	38.6	41.3±1.6	111.6±5.2	6.70±0.04	38.3	0.25	−1.4	0.25	0
C^MU^LA^MU^LC^Mpyrene	UGGUAGU	47.0±4.6	132.1±15.2	6.02±0.19	33.6	45.5±3.4	127.1±11.2	6.08±0.13	34.0	0.87	−5.7	0	0.87
C^Ms²U^LA^Ms²U^LC^Mpyrene	UGGUAGU	38.7±4.8	105.3±15.5	6.06±0.15	33.3	41.2±5.7	113.3±18.6	6.03±0.29	33.3	0.92	−6.4	0.05	0.67

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

calculated for 10⁻⁴ M oligomer concentration,

the date with the same character of fonts belong to the same set.