Abstract
G-quadruplexes (G4s) are unusual secondary structures of DNA occurring in guanosine-rich oligodeoxynucleotide (ODN) strands that are extensively studied for their relevance to the biological processes in which they are involved. In this study, we report the synthesis of a new kind of G4-forming molecule named double-ended-linker ODN (DEL-ODN), in which two TG4T strands are attached to the two ends of symmetric, non-nucleotide linkers. Four DEL-ODNs differing for the incorporation of either a short or long linker and the directionality of the TG4T strands were synthesized, and their ability to form G4 structures and/or multimeric species was investigated by PAGE, HPLC–size-exclusion chromatography (HPLC–SEC), circular dichroism (CD), and NMR studies in comparison with the previously reported monomeric tetra-ended-linker (TEL) analogues and with the corresponding tetramolecular species (TG4T)4. The structural characterization of DEL-ODNs confirmed the formation of stable, bimolecular DEL-G4s for all DEL-ODNs, as well as of additional DEL-G4 multimers with higher molecular weights, thus suggesting a way towards the obtainment of thermally stable DNA nanostructures based on reticulated DEL-G4s.
Highlights
Among the noncanonical secondary structures adopted by nucleic acids, the G-quadruplexes (G4s) are one of the most extensively studied
Molecules 2019, 24, 654 studies have demonstrated that guanosine-rich oligonucleotides (GRO) can form highly polymorphic G4 scaffolds that can differ by the number of the strands and by their mutual orientation, which lead to parallel, antiparallel, or mixed assemblies [4,5]
We reported the synthesis and the structural characterization of a new kind of G4 forming G-rich oligonucleotides, named double-ended-linker ODN (DEL-ODN), in which two TG4 T strands are attached either by their 50 or 30 end to the two ends of a bifunctional linker
Summary
Among the noncanonical secondary structures adopted by nucleic acids, the G-quadruplexes (G4s) are one of the most extensively studied. Molecules 2019, 24, 654 studies have demonstrated that GROs can form highly polymorphic G4 scaffolds that can differ by the number of the strands (one, two, or four) and by their mutual orientation, which lead to parallel, antiparallel, or mixed assemblies [4,5]. The wide polymorphism of G4s arises from the length and the base composition of GROs, from the glycoside conformation of the guanosines involved in each tetrad, and from the cation species used to stabilize the complex [6,7,8]. It is well documented that the duplex DNA motif can be used to build supramolecular structures of various shapes and sizes by a bottom-up process named DNA origami, which is controlled by the sequence and length of the DNA strands [31,32,33]. Supramolecular structures based on G4 building blocks are essentially confined to G4 hybrid structures, such as duplex–quadruplex repetitions and the so-called G-wires
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