Table 1.
LNA-2′OMe RNA/RNA duplexes | TM−1 vs log CT plots | LNA-2′OMe RNA / RNA duplexes | TM−1 vs log CT plots | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
LNA-2′OMe RNA (5′-3′) |
RNA (3′-5′) |
−ΔH° (kcal/mol) |
−ΔS° (eu) |
−ΔG°37 (kcal/mol) |
TMb (°C) |
ΔΔG°37 (kcal/ mol) |
LNA-2′OMe RNA (5′-3′) |
RNA (3′-5′) |
−ΔH° (kcal/mol) |
−ΔS° (eu) |
−ΔG°37 (kcal/mol) |
TMb (°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. | |||||||||||||
CMCMGMUMCMGM | GGCAGC | 51.6±1.7 | 138.9±5.4 | 8.49±0.05 | 49.2 | 0 | CMCMGMUMCMCM | GGCAGG | 57.9±3.3 | 157.0±9.9 | 9.21±0.15 | 52.1 | 0 |
CMCMGMUMCMGMDM | GGCAGC | 60.8±1.9 | 165.1±6.1 | 9.64±0.08 | 53.7 | −1.15 | CMCMGMUMCMCMDM | GGCAGG | 61.4±3.3 | 163.5±10.0 | 10.70±0.19 | 59.5 | −1.49 |
CMCMGMUMCMGMDM | GGCAGC | 65.5±1.9 | 176.1±5.9 | 10.88±0.11 | 59.1 | −2.39 | CMCMGMUMCMCMDL | GGCAGG | 62.7±0.9 | 165.4±2.8 | 11.39±0.06 | 63.1 | −2.18 |
CMCMGMUMCMGMAM | GGCAGC | 55.9±1.4 | 149.6±4.2 | 9.54±0.05 | 54.6 | −0.96 | CMCMGMUMCMCMAM | GGCAGG | 63.3±2.9 | 169.3±9.0 | 10.76±0.17 | 59.2 | −1.55 |
CMCMGMUMCMGMAL | GGCAGC | 60.4±2.4 | 161.2±7.4 | 10.43±0.12 | 58.4 | −1.94 | CMCMGMUMCMCMAL | GGCAGG | 66.2±1.8 | 175.8±5.4 | 11.69±0.12 | 63.2 | −2.48 |
CMCMGMUMCMGMGM | GGCAGC | 55.8±2.0 | 149.8±6.1 | 9.32±0.07 | 53.3 | −0.83 | CMCMGMUMCMCMGM | GGCAGG | 62.4±1.7 | 167.1±5.1 | 10.60±0.09 | 58.6 | −1.39 |
CMCMGMUMCMGMGL | GGCAGC | 60.7±1.2 | 161.9±3.5 | 10.49±0.05 | 59.1 | −2.00 | CMCMGMUMCMCMGL | GGCAGG | 70.6±1.3 | 188.1±3.8 | 12.24±0.10 | 64.3 | −3.03 |
CMCMGMUMCMGMUM | GGCAGC | 54.7±1.8 | 146.7±5.5 | 9.15±0.07 | 52.6 | −0.66 | CMCMGMUMCMCMUM | GGCAGG | 60.9±2.1 | 163.1±6.4 | 10.35±0.11 | 57.7 | −1.14 |
CMCMGMUMCMGMUL | GGCAGC | 57.7±0.7 | 155.4±2.1 | 9.49±0.03 | 53.8 | −1.00 | CMCMGMUMCMCMUL | GGCAGG | 59.8±1.5 | 158.3±4.7 | 10.64±0.09 | 59.9 | −1.43 |
CMCMGMUMCMGMCM | GGCAGC | 54.2±4.1 | 145.7±12.8 | 9.01±0.15 | 51.9 | −0.52 | CMCMGMUMCMCMCM | GGCAGG | 60.2±3.7 | 162.5±11.6 | 9.78±0.15 | 54.7 | −0.57 |
CMCMGMUMCMGMCL | GGCAGC | 60.7±4.3 | 165.2±13.4 | 9.41±0.17 | 52.5 | −0.92 | CMCMGMUMCMCMCL | GGCAGG | 61.0±1.6 | 162.9±4.9 | 10.45±0.09 | 58.3 | −1.24 |
CMCMGMUMCMGM | GMGMCMAMGMCM | 47.6±1.2 | 125.9±3.9 | 8.57±0.04 | 50.9 | 0 | CMCMGMUMCMCM | GMGMCMAMGMGM | 54.6±1.0 | 145.8±3.0 | 9.40±0.05 | 54.2 | 0 |
CMCMGMUMCMGMGM | GMGMCMAMGMCM | 53.3±2.4 | 141.6±7.3 | 9.34±0.11 | 54.3 | −0.77 | CMCMGMUMCMCMGM | GMGMCMAMGMGM | 60.4±1.0 | 160.0±3.1 | 10.78±0.06 | 60.5 | −1.38 |
CMCMGMUMCMGMGL | GMGMCMAMCM | 55.6±1.6 | 145.5±4.7 | 10.46±0.09 | 60.6 | −1.89 | CMCMGMUMCMCMGL | GMGMCMAMGMGM | 66.5±1.1 | 174.8±+3.3 | 12.32±0.09 | 66.6 | −2.92 |
CMCMGMUMCMUM | GGCAGA | 43.2±1.2 | 114.7±3.9 | 7.63±0.02 | 45.1 | 0 | CMCMGMUMCMAM | GGCAGU | 47.5±1.6 | 127.8±5.1 | 7.83±0.04 | 45.7 | 0 |
CMCMGMUMCMUMDM | GGCAGA | 54.9±2.1 | 148.8±6.5 | 8.72±0.06 | 49.9 | −1.09 | CMCMGMUMCMAMDM | GGCAGU | 51.1±0.6 | 137.9±1.8 | 8.34±0.01 | 48.4 | −0.61 |
CMCMCMUMCMUMDL | GGCAGA | 62.5±1.8 | 169.0±5.7 | 10.09±0.09 | 55.7 | −2.46 | CMCMGMUMCMAMDL | GGCAGU | 58.1±1.2 | 157.7±+3.8 | 9.24±0.04 | 52.2 | −1.41 |
CMCMGMUMCMUMAM | GGCAGA | 56.5±1.2 | 154.3±3.8 | 8.67±0.03 | 49.2 | −1.04 | CMCMGMUMCMAMAM | GGCAGU | 51.8±0.8 | 140.2±2.4 | 8.35±0.02 | 48.3 | −0.52 |
CMCMGMUMCMUMAL | GGCAGA | 62.5±1.3 | 169.7±3.9 | 9.87±0.05 | 54.5 | −2.24 | CMCMGMUMCMAMAL | GGCAGU | 54.5±1.2 | 146.9±3.7 | 8.95±0.05 | 51.4 | −1.12 |
CMCMGMUMCMUMGM | GGCAGA | 52.4±0.9 | 141.6±2.8 | 8.48±0.02 | 49.0 | −0.85 | CMCMGMUMCMAMGM | GGCAGU | 51.3±3.1 | 138.1±9.8 | 8.50±0.09 | 49.4 | −0.67 |
CMCMGMUMCMUMGL | GGCAGA | 58.3±1.0 | 157.6±3.2 | 9.44±0.04 | 53.3 | −1.81 | CMCMGMUMCMAMGL | GGCAGU | 56.1±1.1 | 151.7±3.5 | 9.00±0.04 | 51.3 | −1.17 |
CMCMGMUMCMUMUM | GGCAGA | 62.3±5.7 | 172.6±5.7 | 8.81±0.10 | 48.8 | −1.18 | CMCMGMUMCMAMUM | GGCAGU | 47.2±1.2 | 125.3±3.9 | 8.31±0.03 | 49.2 | −0.48 |
CMCMGMUMCMUMUL | GGCAGA | 54.0±2.2 | 146.6±6.9 | 8.53±0.07 | 48.9 | −0.90 | CMCMGMUMCMAMUL | GGCAGU | 50.5±1.9 | 135.4±6.0 | 8.50±0.08 | 49.6 | −0.67 |
CMCMGMUMCMUMCM | GGCAGA | 50.5±2.7 | 136.4±8.4 | 8.17±0.05 | 47.4 | −0.54 | CMCMGMUMCMAMCM | GGCAGU | 49.8±1.0 | 133.5±3.3 | 8.44±0.03 | 49.4 | −0.61 |
CMCMGMUMCMUMCL | GGCAGA | 51.5±1.8 | 138.2±5.6 | 8.64±0.06 | 50.3 | −1.01 | CMCMGMUMCMAMCL | GGCAGU | 50.4±2.1 | 135.1±6.6 | 8.54±0.05 | 49.9 | −0.71 |
CMCMGMUMCMUM | CMGMCMAMGMAM | 48.0±1.7 | 129.3±5.5 | 7.94±0.03 | 46.4 | 0 | CMCMGMUMCMAM | GMGMCMAMGMUM | 45.1±1.0 | 119.9±3.1 | 7.94±0.02 | 47.0 | 0 |
CMCMGMUMCMUMGM | GMGMCMAMGMAM | 51.8±0.8 | 139.5±2.7 | 8.55±0.02 | 49.6 | −0.61 | CMCMGMUMCMAMGM | GMGMCMAMGMUM | 51.1±0.5 | 137.3±1.6 | 8.51±0.01 | 49.5 | −0.57 |
CMCMGMUMCMUMGL | GMGMCMAMGMAM | 57.6±0.9 | 154.5±2.7 | 9.72±0.04 | 55.2 | −1.78 | CMCMGMUMCMAMGL | GMGMCMAMGMUM | 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 GL 3’-dangling ends at RNA/RNA helical core. | ||||||||||||
CMCMGMUMCMGM | 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 |
GMCMCMGMUMCMGM | GGCAGC | 51.1±1.3 | 137.1±4.0 | 8.57±0.04 | 49.9 | −0.08 | CCGUCAGL | GGCAGU | 58.7±1.1 | 163.0±3.6 | 8.17±0.02 | 45.9 | −1.08 |
GLCMCMGMUMCMGM | 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 |
CMCMGMUMCMGM | GMGMCMAMGMCM | 47.6±1.2 | 125.9±3.9 | 8.57±0.04 | 50.9 | 0 | CCGUCUGL | GGCAGA | 61.8±0.8 | 172.2±2.6 | 8.39±0.02 | 46.6 | −1.51 |
GMCMCMGMUMCMGM | GMGMCMAMGMCM | 49.0±0.8 | 130.1±2.4 | 8.69±0.03 | 51.3 | −0.12 | |||||||
GLCMCMGMUMCMGM | GMGMCMAMGMCM | 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 Tm, respectively, b – calculated for 10−4M oligomer concentration.