Small Angle X-ray Scattering Analysis of Deoxyguanosine 5′-Monophosphate Self-Assembing in Solution: Nucleation and Growth of G-Quadruplexes

Abstract

To solve details of the self-assembling process of guanosine in diluted aqueous solution and to derive a thermodynamical model for quadruplex formation, the structural behavior of deoxyguanosine 5'-monophosphate has been analyzed by in-solution small angle X-ray scattering. The experiments have been performed as a function of guanosine concentration and at fixed guanosine concentration but in the presence of varying amounts of KCl. As a result, the self-assembling process, in terms of both aggregate particle fractions and aggregate length, has been observed to be strongly dependent on composition and largely affected by excess potassium ions in the solution. In particular, the different aggregate forms have been resolved and their concentration derived as a function of sample composition. In accordance with a hierarchical aggregation process, a nucleation and elongation mechanism has been used to derive the thermodynamical parameters for self-assembling. The results show that the annealing and fragmentation steps play an important role in the aggregation process.

Guanosine Quadruplexes in Solution: A Small‐Angle X‐Ray Scattering Analysis of Temperature Effects on Self‐Assembling of Deoxyguanosine Monophosphate

“…In agreement with our previous results [24], solutions characterized by the lower number of particle components were preferred. As explained, above 26°C, we also included a nonzero structure factor.…”

“…Moreover, all the other common parameters are in very good agreement with previous reported structural data [17–19, 21, 24, 25, 27]. As expected, the main structural parameters of G-quadruplexes do not depend on the experimental conditions.…”

“…Samples were prepared in the absence of excess salt, at a concentration of 50.8 mg/mL, just above the critical concentration at which self-assembling occurs [24]. To derive composition and size distribution of the scattering particles, SAXS curves were analyzed by using a global fit approach [36].…”

“…The pathway that in dilute conditions governs the formation of d(pG) quadruplexes has been described as follows (see also Figure 1) [22, 24]:$\begin{array}{c}4\text{G}+\text{M}\rightleftharpoons {\text{G}}_4\text{M},\end{array}$$\begin{array}{c}2{\text{G}}_4\text{M}\rightleftharpoons {\text{G}}_8\text{M}+\text{M},\end{array}$$\begin{array}{c}{\text{G}}_8\text{M}+{\text{G}}_4\text{M}\rightleftharpoons {\text{G}}_{12}{\text{M}}_2,\end{array}$$\begin{array}{c}\cdots \\ {\text{G}}_{(n-1)4}{\text{M}}_{(n-2)}+{\text{G}}_4\text{M}\rightleftharpoons {\text{G}}_{4n}{\text{M}}_{(n-1)},\end{array}$where M indicates the monovalent counter-ion and the index on the G symbol represents the aggregation state of d(pG) molecules (G is for monomer, G 4 for G-quartet, G 8 for dimer of G-quartets, etc. ; note that in G 4 n , n corresponds to the number of stacked quartets).…”

Supramolecular Transcription of Guanosine Monophosphate into Mesostructured Silica

“…Previous measurements conducted in solution indicate that K + ions preferentially occupy the intertetramer sites, and thus increase the self-association constant significantly. [12][13][14] To confirm this in the present system, we varied the composition of the starting alkaline cation, which led to variations in the relative intensities and positions of the highangle diffraction peaks (see Figure S4 in the Supporting Information). When only Na + is used as the alkaline cation, the (002) peak is very broad and hardly detected.…”