Table 3.
Intra-basepair parameters for W-C basepairs
| Base Pair (n) | Buckle | Propeller-twist | Open | Shear | Stretch | Stagger | λ1 | λ2 | C1'-C1' | C6-C8 |
|---|---|---|---|---|---|---|---|---|---|---|
|
ModelRNA
| ||||||||||
| AU |
-1.5 |
-10.5 |
-0.2 |
0.0 |
2.9 |
-0.1 |
54.4 |
54.4 |
10.7 |
9.9 |
| GC |
-1.3 |
-10.5 |
-1.3 |
0.0 |
2.9 |
-0.1 |
54.4 |
54.4 |
10.7 |
9.9 |
|
free-RNA
| ||||||||||
| AU |
-1.5 |
-12.7 |
3.6 |
0.1 |
2.8 |
0.0 |
56.0 |
55.8 |
10.5 |
9.8 |
| (339) |
(5.6) |
(5.3) |
(3.9) |
(0.3) |
(0.1) |
(0.2) |
(2.6) |
(3.0) |
(0.2) |
(0.1) |
| GC |
-5.1 |
-10.9 |
0.9 |
-0.1 |
2.9 |
0.0 |
54.2 |
55.3 |
10.6 |
9.9 |
| (725) |
(6.5) |
(6.0) |
(3.3) |
(0.3) |
(0.1) |
(0.2) |
(2.4) |
(2.9) |
(0.2) |
(0.1) |
|
bound-RNA
| ||||||||||
| AU |
-2.8 |
-9.5 |
3.7 |
0.1 |
2.8 |
0.0 |
56.0 |
55.6 |
10.5 |
9.8 |
| (862) |
(8.8) |
(7.2) |
(4.8) |
(0.4) |
(0.2) |
(0.4) |
(3.3) |
(3.5) |
(0.3) |
(0.1) |
| GC |
-6.1 |
-8.9 |
0.9 |
-0.1 |
2.9 |
-0.1 |
54.3 |
55.1 |
10.6 |
9.9 |
| (2476) |
(8.8) |
(7.0) |
(3.9) |
(0.4) |
(0.1) |
(0.3) |
(3.1) |
(3.2) |
(0.2) |
(0.2) |
|
ADNA
| ||||||||||
| AT |
-0.3 |
-9.7 |
2.8 |
0.0 |
2.8 |
-0.1 |
55.1 |
56.5 |
10.4 |
9.8 |
| (43) |
(6.3) |
(5.6) |
(4.6) |
(0.2) |
(0.1) |
(0.2) |
(4.0) |
(3.3) |
(0.2) |
(0.1) |
| GC |
-6.6 |
-9.4 |
-0.2 |
-0.1 |
2.9 |
-0.1 |
55.2 |
55.1 |
10.6 |
9.8 |
| (273) |
(7.7) |
(6.5) |
(2.8) |
(0.2) |
(0.1) |
(0.3) |
(2.7) |
(2.7) |
(0.2) |
(0.1) |
|
BDNA
| ||||||||||
| AT |
-2.1 |
-13.7 |
4.2 |
0.1 |
2.8 |
-0.1 |
55.5 |
55.7 |
10.5 |
9.8 |
| (136) |
(7.8) |
(5.3) |
(4.1) |
(0.3) |
(0.1) |
(0.2) |
(3.2) |
(3.2) |
(0.2) |
(0.1) |
| GC |
0.1 |
-9.2 |
-0.7 |
-0.1 |
2.9 |
0.0 |
54.7 |
54.5 |
10.7 |
9.9 |
| (184) | (9.3) | (7.2) | (3.4) | (0.3) | (0.1) | (0.2) | (2.8) | (2.8) | (0.2) | (0.2) |
Mean and standard deviation (SD) values of intra-basepair parameters for all RNA and DNA datasets are tabulated. Frequency of occurrence of each base pair and SD of the parameters are given in parenthesis. Values for Buckle, Open, Propeller-twist, λ1 and λ2 are in degrees (°). Stagger, Shear, Stretch, C1′-C1′ and C6-C8 distances are in Angstroms (Å).