Double-Stranded RNA Resists Condensation

Much attention has been focused on DNA condensation because of its fundamental biological importance. The recent discovery of new roles for RNA duplexes demands efficient packaging of double-stranded RNA for therapeutics. Here we report measurements of short DNA and RNA duplexes in the presence of trivalent ions. Under conditions where UV spectroscopy indicates condensation of DNA duplexes into (insoluble) precipitates, RNA duplexes remain soluble. Small angle x-ray scattering results suggest that the differing surface topologies of RNA and DNA may be crucial in generating the attractive forces that result in precipitation.

Figure 1

The concentration of DNA and RNA molecules in the supernatant as a function of Co-hex is calculated from UV absorption. Short 16 and 25 bp DNA molecules are more easily condensed than 25 bp RNA. The 16 bp DNA, used as a control, indicates that the changing length of the double-stranded nucleic acid has a smaller effect in generating condensation than the type of nucleic acid used.

Figure 2

To assess interparticle interactions, solution SAXS profiles of (a) DNA and (b) RNA samples in Cobalt hexamine are compared with the form factor, the scattering from apparently noninteracting molecules (at infinite dilution). Only marginal repulsion between DNA molecules is measured when Co-hex $\sim 0.8\mathrm{mM}$. Comparatively, the sharp and smooth low $Q$ upturn in (b) can be interpreted as end-to-end stacking of RNA molecules when Co-hex is present at concentrations above 0.5 mM (see supplementary material, Ref. 7, for a detailed discussion of this effect). The calculated DNA and RNA form factors (shown) match the experimentally measured form factors [7].

Figure 3

Solution SAXS data of RNA samples in NaCl or Co-hex are displayed along with scattering profiles that simulate RNA duplex association in different modes. The purple and cyan curves represent the configurations of RNAs, stacked either end-to-end or placed side-by-side to mimic relative placement in hexagonal arrays, respectively. The end-to-end stacking model (supplementary material Ref. 7) is in better agreement with experimental SAXS profiles, though clearly not all duplexes participate in stacking interactions.