Table 3.
Hydrodynamic Radii for Nucleic Acids and Complexes
| Molecule (PDB ID) | M (Da) | RT,expa (Å) | RT,calc (Å) | % Signed Error | RR,expa (Å) | RR,calc (Å) | a/bb | Reference(s) | |
|---|---|---|---|---|---|---|---|---|---|
| DNA duplex 8merc | 4850 | 14.1 | 13.8 | −1.9 | 14.5 | 14.8 | 1.13 | (33, 65) | |
| DNA duplex 12mer (5NT5) | 7331 | 16.6d | 16.4 | −1.2 | 18.3 | 18.0 | 1.61 | (33, 35, 36) | |
| DNA duplex 20mer (5F9I) | 12,288 | 19.7 | 20.5 | +4.1 | 25.0 | 24.7 | 2.62 | (33) | |
| DNA duplex 24mere | 14,758 | 22.5 | 22.6 | +0.4 | ND | ND | 2.92 | (34) | |
| tRNA-HisRS (4RDX) | 70,463 | 37.4 | 37.8 | +1.1 | ND | ND | 1.60 | (39) | |
| Bacteria ribosome 50S (5HKV) | 1,263,178f | 92.9 | 95.32 | +2.6 | ND | ND | 1.26 | (40) | |
| mean % signed error | +0.85 | ||||||||
ND, not determined.
a
Experimental hydrodynamic coefficients as reported in the references were converted to RT or RR for comparison.
b
Axial ratio of prolate ellipsoid with maximum dimension and volume equal to the respective convex hull.
c
The structure in PDB file 5NT5 was edited to be equivalent to an 8mer.
d
Average of values reported in cited references.
e
The structure in PDB file 5F9I was used to model a 24mer with the same pitch.
f
Molar mass of the structure in 5HKV. A reported actual molar mass of 1,364,954 g mol−1 (107) was used with a sedimentation coefficient of 50.0 and partial specific volume of 0.614 to calculate RT,exp.