Orienting Tetramolecular G‐Quadruplex Formation: The Quest for the Elusive RNA Antiparallel Quadruplex

Abstract

DNA and RNA G-quadruplexes (G4) are unusual nucleic acid structures involved in a number of key biological processes. RNA G-quadruplexes are less studied although recent evidence demonstrates that they are biologically relevant. Compared to DNA quadruplexes, RNA G4 are generally more stable and less polymorphic. Duplexes and quadruplexes may be combined to obtain pure tetrameric species. Here, we investigated whether classical antiparallel duplexes can drive the formation of antiparallel tetramolecular quadruplexes. This concept was first successfully applied to DNA G4. In contrast, RNA G4 were found to be much more unwilling to adopt the forced antiparallel orientation, highlighting that the reason RNA adopts a different structure must not be sought in the loops but in the G-stem structure itself. RNA antiparallel G4 formation is likely to be restricted to a very small set of peculiar sequences, in which other structural features overcome the formidable intrinsic barrier preventing its formation.

Templated Formation of Discrete RNA and DNA:RNA Hybrid G‐Quadruplexes and Their Interactions with Targeting Ligands

“…A possible interpretation would be that the flexibility required to reorient the strand polarities might come at the cost of one G‐tetrad as some guanines might be involved in the formation of hairpin‐like structures. Regardless of the exact structure, and in line with previous unsuccessful attempts to govern the formation of antiparallel RNA G4, this unexpected major structural reorganization in the context of constrained template‐assembled nucleic acids further emphasizes that the formation of antiparallel RNA G4 is strongly disfavored.…”

“…As expected, both conjugates 1 and 2 were able to fold into highly stable parallel G4 topologies as validated by UV thermal difference spectra (TDS), circular dichroism (CD), and NMR spectroscopy, thereby expanding our collection of telomeric G4 mimics to RNA‐based structures. Strikingly, but in coherence with previous reports, the G‐rich RNA strands within conjugate 3 refused to adopt the forced antiparallel orientation as our experimental data instead support the formation of a peculiar mixture of parallel G4 architectures. The ability of four ligands, representative of well‐known classes of G4 binders, to associate with RNA and DNA:RNA G4 1 and 2 was assessed using surface plasmon resonance (SPR).…”

DNA–RNA Hybrid Quadruplexes Reveal Interactions that Favor RNA Parallel Topologies

“…In striking contrast, RNA quadruplexes have been found to almost exclusively form parallel structures and only few exceptions have been reported to date . Even attempts to enforce an RNA non‐parallel topology by template‐based approaches failed . The pronounced preference for parallel RNA structures with their all‐ anti G residues has been attributed to a ribose C3′‐ endo or north (N) sugar conformation found to be strongly correlated with an anti glycosidic torsion angle .…”

“…[5][6][7] Even attempts to enforce an RNA non-parallel top-ology by template-based approaches failed. [8,9] The pronounced preference for parallel RNA structures with their allanti Gr esidues has been attributed to ar ibose C3'-endo or north (N) sugar conformation found to be strongly correlated with an anti glycosidic torsion angle. [10] However,asurvey of availableh igh-resolution RNA G4 structures has revealed as ignificant population of riboguanosines (rG)i naC2'-endo or south (S) conformationt hat should allow for ah igher glycosidic conformational flexibility.…”

Antiparallel RNA G-quadruplex Formed by Human Telomere RNA Containing 8-Bromoguanosine

“…According to the crystallographic analysis, the unprecedented complex loops, and not the G-stem itself, were described as “non-parallel”. A recent study tried to govern the formation of a forced RNA antiparallel orientation in G-stem, suggesting that the RNA G-quadruplex was difficult to control in an antiparallel orientation in G-stem than the DNA G-quadruplex 22 . Until now, the studies on RNA G-quadruplexes showed that the RNA sequences can only adopt parallel G-quadruplex.…”