Nucleic acids can adopt diverse 3D structures, which enables them to perform various functions in cells. The 3D structure of completely modified 2'-F/2'-OMe 42-nt dimeric siRNA construct was determined. The siRNA construct adopts an antiparallel double helical structure with 19 Watson-Crick base pairs. The structure of the construct is not significantly altered by the 2'-F/2'-OMe modifications with respect to unmodified siRNA. The main consequence of the modifications is the preorganization of sugar moieties, which results in high stability and affinity of the construct towards target mRNA. NMR data suggests a difference in stabilities of both duplex ends, which determines the correct incorporation of the antisense strand into RISC. Nuclear magnetic resonance was used in order to demonstrate that the affinities of 15NH4+ ions towards binding sites of various G-quadruplex structures can differ by two orders of magnitude. The differences in affinities of 15NH4+ ions towards individual binding sites of a single G-quadruplex species indicate partial occupancy of binding sites and are a result of loop effects on the electrostatic properties of individual binding sites and relative positions of syn and anti guanine residues near the binding sites. Heteronuclear NMR experiments were used to quantify precisely the movement of 15NH4+ ions within uni- and bimolecular G-quadruplexes. Our data show that ion movement through the G-quadruplex in not unidirectional. Instead, cations randomly exchange between individual binding sites and the bulk solution. Our data show that the rate of cation exchange between binding sites within G-quadruplex structures is limited by the exchange of ions with the bulk solution, which ultimately depends on the structure of the loops.
D.09 Tutoring for postgraduate students
COBISS.SI-ID: 4724762In a lecture at the most important conference in the world focused on G-quadruplexes with exceptional international attendance, we presented our latest findings and results of interactions and the effects of inorganic salts on the structure and dynamic properties of G-quadruplexes.
B.04 Guest lecture
COBISS.SI-ID: 4882714We have presented our results on oligonucleotides that contain only a single run of guanines that are able to form G-quadruplex structures consisting of four strands. By the use of solution-state NMR spectroscopy we have deepened our understanding of the structural diversity of a simple oligonucleotide d(TG4T) as well as its uridine analogues. To date, a single form of d(TG4T)4 in solution has been described, whereas the current NMR study has demonstrated the coexistence of two forms, which are in slow exchange on the NMR time-scale. Substitution of U for T in the parent sequence provides further insights into dimerization and macromolecular association of G-quadruplex units. In addition, we have unequivocally proven that 15NH4+ ion movement inside the central ion cavities of tetramolecular G-quadruplexes is ca. 10 times faster than in bimolecular and monomolecular G-quadruplexes.
B.04 Guest lecture
COBISS.SI-ID: 4846874