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

Abstract

G-rich RNA and DNA oligonucleotides derived from the human telomeric sequence were assembled onto addressable cyclopeptide platforms through oxime ligations and copper-catalyzed azide-alkyne cycloaddition (CuAAc) reactions. The resulting conjugates were able to fold into highly stable RNA and DNA:RNA hybrid G-quadruplex (G4) architectures as demonstrated by UV, circular dichroism (CD), and NMR spectroscopic analysis. Whereas rationally designed parallel RNA and DNA:RNA hybrid G4 topologies could be obtained, we could not force the formation of an antiparallel RNA G4 structure, thus supporting the idea that this topology is strongly disfavored. The binding affinities of four representative G4 ligands toward the discrete RNA and DNA:RNA hybrid G4 topologies were compared to the one obtained with the corresponding DNA G4 structure. Surface plasmon resonance (SPR) binding analysis suggests that the accessibility to G4 recognition elements is different among the three structures and supports the idea that G4 ligands might be shaped to achieve structure selectivity in a biological context.

New Ruthenium‐Based Probes for Selective G‐Quadruplex Targeting

“…This technique is also relevant in the present case, as it does not rely on the luminescence of the complexes. We used a recently reported method based on a template‐assembled synthetic G‐quadruplex (TASQ) strategy that allows the formation of highly stable G‐quadruplex structures with precise control of G‐quadruplex topology through the assembly of constrained structures on a template (Figure ) . This method has been successfully used to probe the interaction modes of several G4‐binding ligands .…”

Template‐Mediated Stabilization of a DNA G‐Quadruplex formed in the HIV‐1 Promoter and Comparative Binding Studies

“…To explore the propensity of G4‐binding ligands to interact with the viral G4 structure formed by HIV‐PRO1 and to assess the selectivity of recognition, we collected six low molecular weight compounds, archetypes of important families of G4 ligands, and we studied, by SPR, their interactions with HIV conjugate 2 , telomeric conjugate 1 , and a control hairpin structure 9 (Supporting Information, Figure S42) (Table ). Template assembled DNA and RNA G4 model structures have been successfully exploited in the past, along with the hairpin structure 9 , to probe the interaction modes of several G4‐binding ligands –…”

“…template assembled synthetic G‐quadruplexes) . Those stable structural mimics have been extensively used to probe the binding mode of various families of G4 binding ligands . The scaffolds used to site‐specifically connect the DNA and RNA strands consist of cyclic decapeptides with two independent and addressable faces (as in Figure B) .…”

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 .…”