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Molecules 2019, 24(3), 654; https://doi.org/10.3390/molecules24030654

New G-Quadruplex-Forming Oligodeoxynucleotides Incorporating a Bifunctional Double-Ended Linker (DEL): Effects of DEL Size and ODNs Orientation on the Topology, Stability, and Molecularity of DEL-G-Quadruplexes

1
Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy
2
Dipartimento di Chimica, Università degli Studi di Milano, via Camillo Golgi 19, 20133 Milano, Italy
3
Istituto di Biostrutture e Bioimmagini, CNR, Via Tommaso De Amicis 95, 80145 Napoli, Italy
4
Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, via Sergio Pansini 5, 80131 Napoli, Italy
*
Author to whom correspondence should be addressed.
Received: 23 January 2019 / Revised: 4 February 2019 / Accepted: 6 February 2019 / Published: 12 February 2019
(This article belongs to the Special Issue Molecules for Biotechnologies)
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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. View Full-Text
Keywords: G-quadruplexes; double-ended linkers; DEL-ODNs; TEL-ODNs; supramolecular G-quadruplexes; NMR; CD; size-exclusion chromatography G-quadruplexes; double-ended linkers; DEL-ODNs; TEL-ODNs; supramolecular G-quadruplexes; NMR; CD; size-exclusion chromatography
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Marzano, M.; Falanga, A.P.; D’Errico, S.; Pinto, B.; Roviello, G.N.; Piccialli, G.; Oliviero, G.; Borbone, N. New G-Quadruplex-Forming Oligodeoxynucleotides Incorporating a Bifunctional Double-Ended Linker (DEL): Effects of DEL Size and ODNs Orientation on the Topology, Stability, and Molecularity of DEL-G-Quadruplexes. Molecules 2019, 24, 654.

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