. Author manuscript; available in PMC: 2011 Feb 1.

Published in final edited form as: Biochemistry. 2009 May 26;48(20):4377–4387. doi: 10.1021/bi9002056

Table 1.

Thermodynamic parameters of helix formation with RNA and 2'-O-Me oligoribonucleotides. The effect of LNA 3'- and 5'-dangling ends^a.

LNA-2′OMe RNA/RNA duplexes		T_M⁻¹ vs log C_T plots					LNA-2′OMe RNA / RNA duplexes		T_M⁻¹ vs log C_T plots

LNA-2′OMe RNA (5′-3′)	RNA (3′-5′)	−ΔH° (kcal/mol)	−ΔS° (eu)	−ΔG°₃₇ (kcal/mol)	T_M^b (°C)	ΔΔG°₃₇ (kcal/ mol)	LNA-2′OMe RNA (5′-3′)	RNA (3′-5′)	−ΔH° (kcal/mol)	−ΔS° (eu)	−ΔG°₃₇ (kcal/mol)	T_M^b (°C)	ΔΔG°₃₇ (kcal/ mol)
A. Thermodynamic parameters of helix formation with various 3′-dangling ends at 2′-OMeRNA/RNA and 2′-OMeRNA/2′-OMeRNA helical cores.
C^MC^MG^MU^MC^MG^M	GGCAGC	51.6±1.7	138.9±5.4	8.49±0.05	49.2	0	C^MC^MG^MU^MC^MC^M	GGCAGG	57.9±3.3	157.0±9.9	9.21±0.15	52.1	0
C^MC^MG^MU^MC^MG^MD^M	GGCAGC	60.8±1.9	165.1±6.1	9.64±0.08	53.7	−1.15	C^MC^MG^MU^MC^MC^MD^M	GGCAGG	61.4±3.3	163.5±10.0	10.70±0.19	59.5	−1.49
C^MC^MG^MU^MC^MG^MD^M	GGCAGC	65.5±1.9	176.1±5.9	10.88±0.11	59.1	−2.39	C^MC^MG^MU^MC^MC^MD^L	GGCAGG	62.7±0.9	165.4±2.8	11.39±0.06	63.1	−2.18
C^MC^MG^MU^MC^MG^MA^M	GGCAGC	55.9±1.4	149.6±4.2	9.54±0.05	54.6	−0.96	C^MC^MG^MU^MC^MC^MA^M	GGCAGG	63.3±2.9	169.3±9.0	10.76±0.17	59.2	−1.55
C^MC^MG^MU^MC^MG^MA^L	GGCAGC	60.4±2.4	161.2±7.4	10.43±0.12	58.4	−1.94	C^MC^MG^MU^MC^MC^MA^L	GGCAGG	66.2±1.8	175.8±5.4	11.69±0.12	63.2	−2.48
C^MC^MG^MU^MC^MG^MG^M	GGCAGC	55.8±2.0	149.8±6.1	9.32±0.07	53.3	−0.83	C^MC^MG^MU^MC^MC^MG^M	GGCAGG	62.4±1.7	167.1±5.1	10.60±0.09	58.6	−1.39
C^MC^MG^MU^MC^MG^MG^L	GGCAGC	60.7±1.2	161.9±3.5	10.49±0.05	59.1	−2.00	C^MC^MG^MU^MC^MC^MG^L	GGCAGG	70.6±1.3	188.1±3.8	12.24±0.10	64.3	−3.03
C^MC^MG^MU^MC^MG^MU^M	GGCAGC	54.7±1.8	146.7±5.5	9.15±0.07	52.6	−0.66	C^MC^MG^MU^MC^MC^MU^M	GGCAGG	60.9±2.1	163.1±6.4	10.35±0.11	57.7	−1.14
C^MC^MG^MU^MC^MG^MU^L	GGCAGC	57.7±0.7	155.4±2.1	9.49±0.03	53.8	−1.00	C^MC^MG^MU^MC^MC^MU^L	GGCAGG	59.8±1.5	158.3±4.7	10.64±0.09	59.9	−1.43
C^MC^MG^MU^MC^MG^MC^M	GGCAGC	54.2±4.1	145.7±12.8	9.01±0.15	51.9	−0.52	C^MC^MG^MU^MC^MC^MC^M	GGCAGG	60.2±3.7	162.5±11.6	9.78±0.15	54.7	−0.57
C^MC^MG^MU^MC^MG^MC^L	GGCAGC	60.7±4.3	165.2±13.4	9.41±0.17	52.5	−0.92	C^MC^MG^MU^MC^MC^MC^L	GGCAGG	61.0±1.6	162.9±4.9	10.45±0.09	58.3	−1.24

C^MC^MG^MU^MC^MG^M	G^MG^MC^MA^MG^MC^M	47.6±1.2	125.9±3.9	8.57±0.04	50.9	0	C^MC^MG^MU^MC^MC^M	G^MG^MC^MA^MG^MG^M	54.6±1.0	145.8±3.0	9.40±0.05	54.2	0
C^MC^MG^MU^MC^MG^MG^M	G^MG^MC^MA^MG^MC^M	53.3±2.4	141.6±7.3	9.34±0.11	54.3	−0.77	C^MC^MG^MU^MC^MC^MG^M	G^MG^MC^MA^MG^MG^M	60.4±1.0	160.0±3.1	10.78±0.06	60.5	−1.38
C^MC^MG^MU^MC^MG^MG^L	G^MG^MC^MA^MC^M	55.6±1.6	145.5±4.7	10.46±0.09	60.6	−1.89	C^MC^MG^MU^MC^MC^MG^L	G^MG^MC^MA^MG^MG^M	66.5±1.1	174.8±+3.3	12.32±0.09	66.6	−2.92

C^MC^MG^MU^MC^MU^M	GGCAGA	43.2±1.2	114.7±3.9	7.63±0.02	45.1	0	C^MC^MG^MU^MC^MA^M	GGCAGU	47.5±1.6	127.8±5.1	7.83±0.04	45.7	0
C^MC^MG^MU^MC^MU^MD^M	GGCAGA	54.9±2.1	148.8±6.5	8.72±0.06	49.9	−1.09	C^MC^MG^MU^MC^MA^MD^M	GGCAGU	51.1±0.6	137.9±1.8	8.34±0.01	48.4	−0.61
C^MC^MC^MU^MC^MU^MD^L	GGCAGA	62.5±1.8	169.0±5.7	10.09±0.09	55.7	−2.46	C^MC^MG^MU^MC^MA^MD^L	GGCAGU	58.1±1.2	157.7±+3.8	9.24±0.04	52.2	−1.41
C^MC^MG^MU^MC^MU^MA^M	GGCAGA	56.5±1.2	154.3±3.8	8.67±0.03	49.2	−1.04	C^MC^MG^MU^MC^MA^MA^M	GGCAGU	51.8±0.8	140.2±2.4	8.35±0.02	48.3	−0.52
C^MC^MG^MU^MC^MU^MA^L	GGCAGA	62.5±1.3	169.7±3.9	9.87±0.05	54.5	−2.24	C^MC^MG^MU^MC^MA^MA^L	GGCAGU	54.5±1.2	146.9±3.7	8.95±0.05	51.4	−1.12
C^MC^MG^MU^MC^MU^MG^M	GGCAGA	52.4±0.9	141.6±2.8	8.48±0.02	49.0	−0.85	C^MC^MG^MU^MC^MA^MG^M	GGCAGU	51.3±3.1	138.1±9.8	8.50±0.09	49.4	−0.67
C^MC^MG^MU^MC^MU^MG^L	GGCAGA	58.3±1.0	157.6±3.2	9.44±0.04	53.3	−1.81	C^MC^MG^MU^MC^MA^MG^L	GGCAGU	56.1±1.1	151.7±3.5	9.00±0.04	51.3	−1.17
C^MC^MG^MU^MC^MU^MU^M	GGCAGA	62.3±5.7	172.6±5.7	8.81±0.10	48.8	−1.18	C^MC^MG^MU^MC^MA^MU^M	GGCAGU	47.2±1.2	125.3±3.9	8.31±0.03	49.2	−0.48
C^MC^MG^MU^MC^MU^MU^L	GGCAGA	54.0±2.2	146.6±6.9	8.53±0.07	48.9	−0.90	C^MC^MG^MU^MC^MA^MU^L	GGCAGU	50.5±1.9	135.4±6.0	8.50±0.08	49.6	−0.67
C^MC^MG^MU^MC^MU^MC^M	GGCAGA	50.5±2.7	136.4±8.4	8.17±0.05	47.4	−0.54	C^MC^MG^MU^MC^MA^MC^M	GGCAGU	49.8±1.0	133.5±3.3	8.44±0.03	49.4	−0.61
C^MC^MG^MU^MC^MU^MC^L	GGCAGA	51.5±1.8	138.2±5.6	8.64±0.06	50.3	−1.01	C^MC^MG^MU^MC^MA^MC^L	GGCAGU	50.4±2.1	135.1±6.6	8.54±0.05	49.9	−0.71

C^MC^MG^MU^MC^MU^M	C^MG^MC^MA^MG^MA^M	48.0±1.7	129.3±5.5	7.94±0.03	46.4	0	C^MC^MG^MU^MC^MA^M	G^MG^MC^MA^MG^MU^M	45.1±1.0	119.9±3.1	7.94±0.02	47.0	0
C^MC^MG^MU^MC^MU^MG^M	G^MG^MC^MA^MG^MA^M	51.8±0.8	139.5±2.7	8.55±0.02	49.6	−0.61	C^MC^MG^MU^MC^MA^MG^M	G^MG^MC^MA^MG^MU^M	51.1±0.5	137.3±1.6	8.51±0.01	49.5	−0.57
C^MC^MG^MU^MC^MU^MG^L	G^MG^MC^MA^MG^MA^M	57.6±0.9	154.5±2.7	9.72±0.04	55.2	−1.78	C^MC^MG^MU^MC^MA^MG^L	G^MG^MC^MA^MG^MU^M	57.2±1.5	154.1±4.5	9.42±0.06	53.5	−1.48

B. Thermodynamic parameters of helix formation with various 5’-dangling ends at 2’-OMeRNA/RNA and 2’-OMeRNA/2’-OMeRNA helical cores.							C. Thermodynamic parameters of helix formation with G^L 3’-dangling ends at RNA/RNA helical core.

C^MC^MG^MU^MC^MG^M	GGCAGC	51.6±1.7	138.9±5.4	8.49±0.05	49.2	0	CCGUCA	GGCAGU	51.2±2.5	142.3±8.1	7.09±0.05	40.4	0
G^MC^MC^MG^MU^MC^MG^M	GGCAGC	51.1±1.3	137.1±4.0	8.57±0.04	49.9	−0.08	CCGUCAG^L	GGCAGU	58.7±1.1	163.0±3.6	8.17±0.02	45.9	−1.08
G^LC^MC^MG^MU^MC^MG^M	GGCAGC	50.0±1.3	133.4±3.9	8.61±0.04	50.4	−0.12	CCGUCU	GGCAGA	46.0±1.0	126.3±3.3	6.88±0.01	39.4	0
C^MC^MG^MU^MC^MG^M	G^MG^MC^MA^MG^MC^M	47.6±1.2	125.9±3.9	8.57±0.04	50.9	0	CCGUCUG^L	GGCAGA	61.8±0.8	172.2±2.6	8.39±0.02	46.6	−1.51
G^MC^MC^MG^MU^MC^MG^M	G^MG^MC^MA^MG^MC^M	49.0±0.8	130.1±2.4	8.69±0.03	51.3	−0.12
G^LC^MC^MG^MU^MC^MG^M	G^MG^MC^MA^MG^MC^M	47.3±1.8	124.6±5.6	8.67±0.06	51.7	−0.10

– solutions are 100 mM NaCl, 20 mM sodium cacodylate and 0.5 mM Na₂EDTA, pH 7. Listed errors are standard deviations from reported measurements assuming no correlation of errors in slope and intercept and are therefore underestimates. Estimated errors from all sources are ±10%, ±10%, ±2%, and 1 °C for ΔH°, ΔS°, ΔG°, and T_m, respectively, b – calculated for 10⁻⁴M oligomer concentration.