Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA

Abstract

The recent discovery of the RNA interference mechanism emphasizes the biological importance of short, isolated, double-stranded (ds) RNA helices and calls for a complete understanding of the biophysical properties of dsRNA. However, most previous studies of the electrostatics of nucleic acid duplexes have focused on DNA. Here, we present a comparative investigation of electrostatic effects in RNA and DNA. Using resonant (anomalous) and non-resonant small-angle X-ray scattering, we characterized the charge screening efficiency and counterion distribution around short (25 bp) dsDNA and RNA molecules of comparable sequence. Consistent with theoretical predictions, we find counterion mediated screening to be more efficient for dsRNA than dsDNA. Furthermore, the topology of the RNA A-form helix alters the spatial distribution of counterions relative to B-form DNA. The experimental results reported here agree well with ion-size-corrected non-linear Poisson–Boltzmann calculations. We propose that differences in electrostatic properties aid in selective recognition of different types of short nucleic acid helices by target binding partners.

Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids

“…The single strands were annealed using standard procedures used in previous studies 43 and were dialyzed extensively using spin dialysis 10 kDa cutoff columns (Amicon Ultra-0.5 mL, Millipore, Billerica, MA) in buffered salt solutions of either 100 mM NaCl, 100 mM RbCl, or 10 mM SrCl 2 with 1 mM Na-MOPS pH 7.0. All reagents were purchased from Sigma-Aldrich (St. Louis, MO).…”

Anomalous small-angle X-ray scattering from charged soft matter

“…As noted before, the cross-term only reveals the mean correlation between counterions and the macroion [5]. In a subsequent related work, the charge screening efficiency and counterion distribution around short double stranded DNA and RNA molecules of comparable sequence was characterized [29]. The counterion mediated screening was found to be more efficient for RNA than DNA which has been attributed to the ability of RNA helix to draw monovalent and divalent ions closer.…”

“…For the same potential surface close to the nucleic acids, they found more 'bound' ions close to RNA than DNA. This distinction is relevant in understanding selective recognition of different types of short nucleic acid helices by target binding partners [29]. More recent work also reported a quantitative estimate of the number of counterions around DNA [30].…”

3 Importance of Diffuse Metal Ion Binding to RNA

“…The first key issue in the ion electrostatics is how diffuse ions are distributed around the RNA molecule [9][10][11][12][13][14][15][16][17][18][19]. There have been several useful experimental methods developed for the quantification of the ion atmosphere around nucleic acids.…”

“…There have been several useful experimental methods developed for the quantification of the ion atmosphere around nucleic acids. The methods include small angle X-ray scattering (SAXS) [9][10][11][12], the ion-counting method [13], and the thermodynamic method [14][15][16][17][18][19]. These methods have been successfully used to quantify the ion distribution, the competition between the different species of the ions, and the folding thermodynamics [16,17]; see Table 1.…”