Stacking Interactions and Flexibility of Human Telomeric Multimers

G-quadruplexes (G4s)are helical four-stranded structuresformingfrom guanine-rich nucleic acid sequences, which are thought to playa role in cancer development and malignant transformation. Most currentstudies focus on G4 monomers, yet under suitable and biologicallyrelevant conditions, G4s undergo multimerization. Here, we investigatethe stacking interactions and structural features of telomeric G4multimers by means of a novel low-resolution structural approach thatcombines small-angle X-ray scattering (SAXS) with extremely coarse-grained(ECG) simulations. The degree of multimerization and the strengthof the stacking interaction are quantitatively determined in G4 self-assembledmultimers. We show that self-assembly induces a significant polydispersityof the G4 multimers with an exponential distribution of contour lengths,consistent with a step-growth polymerization. On increasing DNA concentration,the strength of the stacking interaction between G4 monomers increases,as well as the average number of units in the aggregates. We utilizedthe same approach to explore the conformational flexibility of a modelsingle-stranded long telomeric sequence. Our findings indicate thatits G4 units frequently adopt a beads-on-a-string configuration. Wealso observe that the interaction between G4 units can be significantlyaffected by complexation with benchmark ligands. The proposed methodology,which identifies the determinants that govern the formation and structuralflexibility of G4 multimers, may be an affordable tool aiding in theselection and design of drugs that target G4s under physiologicalconditions.