Porphyrin Binding and Irradiation Promote G-Quadruplex DNA Dimeric Structure

Abstract

Nucleic acid sequences rich in guanines can organize into noncanonical DNA G-quadruplexes (G4s) of variable size. The design of small molecules stabilizing the structure of G4s is a rapidly growing area for the development of novel anticancer therapeutic strategies and bottom-up nanotechnologies. Among a multitude of binders, porphyrins are very attractive due to their light activation that can make them valuable conformational regulators of G4s. Here, a structure-based strategy, integrating complementary probes, is employed to study the interaction between TMPyP4 porphyrin and a 22-base human telomeric sequence (Tel22) before and after irradiation with blue light. Porphyrin binding is discovered to promote Tel22 dimerization, while light irradiation of the Tel22-TMPyP4 complex controls dimer fraction. Such a change in quaternary structure is found to be strictly correlated with modifications at the secondary structure level, thus providing an unprecedented link between the degree of dimerization and the underlying conformational changes in G4s.

Connecting Structure, Conformation and Energetics of Human Telomere G-quadruplex Multimers

“…On the other hand, in the intermediateand low-Q regions, the intensity I(Q) reflects the higher-order structure arising from the reversible multimerization process of G4 units. In particular, the contribution of Tel22 multimers is quite visible, as a clear deviation below Q < 1 nm −1 in Figure 1, where the scattering intensity of a solution of Tel22 monomers at DNA concentration C = 0.5 mM (data taken from Reference [28]) is compared with that of the present study. It is worth noting that the monomeric sample was prepared in such a way to rule out the presence of possible aggregates (see the Methods section).…”

“…Also in the high-Q region, where the SAXS signal is dominated by the form factor, the interpretation of the experimental data deserves great care. In a previous study [28], we found the form factor of Tel22 monomers in solution to be well described by that of a hard cylinder (HC). In this case the topology of Tel22 consists of a mixture of antiparallel and hybrid conformers, however, an increase of concentration above ≈ 1 mM drives a progressive shift toward the parallel (propeller) state, with concomitant decrease of the anti-parallel and hybrid forms [30,31,32,33].…”

“…In particular, to find the best agreement between simulations and ex-periments we explored the phase space corresponding to different G4 shapes and different strength of stacking interaction between units. As to the former, the starting point was a HC with a diameter of D 0 = 2.0 nm and a length of L 0 = 3.7 nm that best reproduces the monomeric form of Tel22 sequences [28]. To modulate the shape of the cylinder we introduced the parameter K, so that D = D 0 • K and L = L 0 /K (K ≥ 1).…”

“…Before measurements, samples where further annealed and left at room temperature overnight. It should be noted that the sample in monomeric state taken from Reference [28] was prepared starting from a stock solution with a lower concentration of C = 1 mM. Such a different procedure avoided the formation of aggregates.…”

Role of fast dynamics in the complexation of G-quadruplexes with small molecules

“…Within this context, a considerable body of research has been carried out to investigate the structural properties of different G4-forming DNA sequences [18][19][20][21] and how they are affected by small ligands. 1,[22][23][24][25] However, little is known about the dynamical features of G4s, an aspect that should play a relevant role given their transient nature. In the case of proteins and duplex DNA, the sub-nano-and nanosecond dynamics has been already linked to both structural and functional aspects.…”