Table 4. Backbone and pseudorotation ring pucker parameters of calculated structure of nicked decamera.
| Glycosidic and backbone torsions (deg) | Ribose ring parameters | |||||||||
| C1′-N | P-O5′ | O5′-C5′ | C5′-C4′ | C4′-C3′ | C3′-O3′ | O3′-P | Phase | Amplitude | Pucker | |
| |
χ |
α |
β |
γ |
δ |
ɛ |
ζ |
P |
Φ |
|
| Scissile strand | |
|
||||||||
| G1-5′ | –113 ± 3 | –76 ± 11 | 174 ± 5 | 59 ± 5 | 141 ± 1 | –179 ± 2 | –93 ± 2 | 163 ± 2 | 38 ± 1 |
C2′-endo(S) |
| C2 | –116 ± 1 | –78 ± 1 | –175 ± 2 | 51 ± 1 | 132 ± 1 | –158 ± 3 | –157 ± 3 | 144 ± 1 | 42 ± 1 |
C1′-exo(S) |
| G3 | –114 ± 4 | –68 ± 1 | 150 ± 6 | 71 ± 3 | 142 ± 1 | –177 ± 1 | –87 ± 1 | 171 ± 1 | 37 ± 1 |
C2′-endo(S) |
| T4 | –131 ± 5 | –74 ± 2 | 170 ± 1 | 58 ± 1 | 116 ± 1 | 178 ± 2 | –98 ± 3 | 118 ± 2 | 33 ± 1 |
C1′-exo(S) |
| T5-3′ | –130 ± 3 | –61 ± 8 | 174 ± 9 | 75 ± 11 | 125 ± 2 | 168 ± 3 | 33 ± 1 |
C2′-endo(S) |
||
| G6-5′ | –157 ± 1 | 64 ± 2 | 86 ± 1 | –178 ± 1 | –72 ± 1 | 45 ± 2 | 35 ± 1 |
C4′-exo(N) |
||
| T7 | –134 ± 1 | –64 ± 1 | 179 ± 1 | 73 ± 1 | 128 ± 1 | 179 ± 1 | –83 ± 1 | 180 ± 1 | 38 ± 1 |
C3′-exo(S) |
| C8 | –129 ± 1 | –76 ± 1 | 178 ± 1 | 48 ± 1 | 120 ± 1 | 178 ± 1 | –91 ± 1 | 131 ± 1 | 33 ± 1 |
C1′-exo(S) |
| G9 | –125 ± 1 | –64 ± 1 | 179 ± 1 | 55 ± 1 | 132 ± 1 | –178 ± 1 | –100 ± 1 | 146 ± 1 | 36 ± 1 |
C2′-endo(S) |
| C10-3′ | –135 ± 2 | –69 ± 1 | –179 ± 3 | 59 ± 5 | 98 ± 2 | 179 ± 2 | –93 ± 2 | 82 ± 4 | 33 ± 1 |
O4′endo(S) |
| Non-scissile strand | |
|
||||||||
| C20-3′ | –119 ± 3 | –71 ± 1 | 165 ± 2 | 64 ± 3 | 94 ± 3 | –173 ± 18 | –93 ± 20 | 77 ± 4 | 33 ± 1 |
O4′-endo(S) |
| G19 | –85 ± 1 | –66 ± 1 | 178 ± 2 | 64 ± 1 | 133 ± 1 | –179 ± 2 | –109 ± 2 | 155 ± 1 | 30 ± 1 |
C2′-endo(S) |
| C18 | –136 ± 1 | –72 ± 2 | 177 ± 1 | 54 ± 2 | 113 ± 1 | –170 ± 1 | –90 ± 1 | 104 ± 1 | 33 ± 1 |
O4′-endo(S) |
| A17 | –124 ± 1 | –65 ± 1 | 179 ± 2 | 68 ± 2 | 121 ± 2 | –179 ± 1 | –102 ± 2 | 131 ± 2 | 39 ± 1 |
C1′-exo(S) |
| A16 | –105 ± 2 | –62 ± 1 | 167 ± 1 | 64 ± 2 | 139 ± 2 | 169 ± 1 | –94 ± 2 | 156 ± 2 | 39 ± 1 |
C2′-endo(S) |
| C15 | –118 ± 3 | –75 ± 5 | 171 ± 1 | 63 ± 2 | 120 ± 2 | –179 ± 1 | –91 ± 3 | 124 ± 2 | 32 ± 1 |
C1′-exo(S) |
| A14 | –112 ± 2 | –74 ± 5 | –174 ± 1 | 50 ± 1 | 132 ± 2 | –179 ± 2 | –101 ± 2 | 144 ± 2 | 34 ± 1 |
C1′-exo(S) |
| G13 | –131 ± 1 | –70 ± 1 | 174 ± 1 | 61 ± 1 | 118 ± 1 | 178 ± 2 | –99 ± 2 | 126 ± 1 | 40 ± 1 |
C1′-exo(S) |
| C12 | –132 ± 1 | –76 ± 1 | –180 ± 2 | 54 ± 1 | 120 ± 1 | –174 ± 2 | –93 ± 1 | 124 ± 1 | 36 ± 1 |
C1′-exo(S) |
| G11-5′ | –117 ± 3 | –159 ± 90 | –177 ± 11 | 119 ± 60 | 141 ± 3 | –179 ± 2 | –95 ± 1 | 163 ± 3 | 37 ± 1 | C2′-endo(S) |
aThe backbone torsion definition in agreement with IUPAC recommendation. Average parameters for the 30 lowest energy refined structures (± standard deviations).