Formation of G-Wires: The Role of G:C-Base Pairing and G-Quartet Stacking

Abstract

G-wireslong, continuous G-quadruplexesare a promising element for use in nanotechnology, particularly in molecular electronics. The pairing of G-quadruplex structures through complementary GC-termini was tested. We designed four analogous G-quadruplexforming oligonucleotides with the same core sequence d(GGTG 4 TGG) and with different number and position of GC-ends. We used circular dichroism to determine the topology and relative orientation of G-quadruplexes, 1 H NMR to identify Watson−Crick base pairing, and dynamic light scattering to examine the size of the G-quadruplex assemblies. The quadruplexes associated through GC-base pairs forming (G:C:G:C)-quartets and by stacking of unhindered terminal (G:G:G:G)-quartets. These two modes of association had different specificities: stacking occurred at both the 5′-and 3′-faces of the quadruplex, whereas GC-base pairing occurred only at the 5′-face of the quadruplex. These insights may be employed to design Gquadruplex-based nanowires or more complex architectures.

Structure Validation of G‐Rich RNAs in Noncoding Regions of the Human Genome

“…The strong positive signal at 262 nm is also in agreement with the formation of G‐wires, as observed by Protozanova and Macgregor . For larger aggregates of those G‐wires, the detection of a broad signal in 1D 1 H NMR spectra is expected . In native PAGE experiments the bands of TGFB1 and MAPKAPK2 are strongly broadened, thus supporting the proposed folding scheme of highly polymorphic structures (Figure S2).…”

Self‐Assembly of G‐Rich Oligonucleotides Incorporating a 3′–3′ Inversion of Polarity Site: A New Route Towards G‐Wire DNA Nanostructures

“…Depending on the topological arrangement of the G‐rich strands participating in their formation, G‐wires can be classified into two categories: i) interlocked G‐wires , characterized by the cooperative assembly of interlocked slipped strands (Figure B) and ii) stacked G‐wires , characterized by the multimerization of G‐quadruplex building blocks held together by end‐to‐end π–π stacking (Figure C). Besides the well‐known interlocked G‐wires and G‐wires containing both topological motifs, only a few examples of exclusively stacked G‐wires have been reported so far …”

“…Depending on the topological arrangement of the G-rich strandsp articipating in their formation, G-wires can be classified into two categories:i )interlocked G-wires,c haracterizedb yt he cooperative assembly of interlocked slipped strands( Figure 1B)a nd ii) stacked G-wires,c haracterized by the multimerization of Gquadruplexb uilding blocks held together by end-to-end p-p stacking ( Figure 1C). Besides the well-known interlocked Gwires [29][30][31][32][33][34][35] and G-wires containing both topological motifs, [36][37][38] only af ew examples of exclusively stacked G-wires have been reported so far. [39][40][41] In ap revious study,w er eported that in the presenceo fK + cations the 7-mer d(CGGTGGT)c an assemble into the octameric higher-ordered G-quadruplex complex d(CGGTGGT) 8 (Figure S1 in the Supporting Information) through p-p stacking of two unusualG (:C):G(:C):G(:C):G(:C) planar octadsb elonging to two identicalt etramolecularp arallel G-quadruplexes.…”

Evaluation of the effect of polymorphism on G-quadruplex-ligand interaction by means of spectroscopic and chromatographic techniques

“…By contrast, the assignation of bands at 7.8 and 11.3 minutes was not straightforward. The band at 7.8 minutes corresponded to a tetramer or to another structure formed by a greater number of individual strands, such as the Gwire [36,37]. Finally, the band at 11.3 minutes, which corresponds to a structure with a smaller hydrodynamic volume than the unfolded strand, was assigned to a highly compact monomeric structure.…”