Seven-Membered Ring Nucleoside Analogues: Stereoselective Synthesis and Studies on Their Conformational Properties

Abstract

The synthesis of a novel series of seven-membered ring nucleoside analogues as candidates for biological screening and gene silencing applications is described. The key step in the synthetic approach is a stereoselective synthesis of an epoxide that is used as a common synthetic intermediate to prepare functionalized oxepane nucleoside derivatives. The conformational landscape and preferred ring-puckering of selected oxepane nucleosides was also studied by NMR, X-ray crystallography, and quantum mechanical calculations.

Gene editing with CRISPR-Cas12a guides possessing ribose-modified pseudoknot handles

“…To specifically investigate positions with predicted 2′-OH contacts, we synthesized crRNAs with RNA or 2′-F pseudoknots containing oxepane nucleic acid (OxN) and 2′-araOH in putative critical 2′-OH positions. OxN is a seven-membered ring structure that can be synthesized with multiple hydroxyl groups and a phosphodiester linkage at different ring positions 94 . We synthesized thymidine (OxT) nucleotide replacements with the phosphodiester linkage at three different positions, designated OxT-1, -2, and -3.…”

Recent progress in non-native nucleic acid modifications

“…These novel macrocyclizations open the door for new studies on even larger and more conformationally flexible rings in nucleic acids. Both 6-membered [47][48][49][50] and 7-membered [51][52][53] ring nucleic acids have been explored. Hexose nucleic acids (HNA) are among most notable.…”

Nucleoside Analogues with a Seven-Membered Sugar Ring: Synthesis and Structural Compatibility in DNA–RNA Hybrids

“…They find use as antiviral and anticancer agents, as structural probes for studying nucleic acid/protein interactions, and as precursors of therapeutic oligonucleotides (e.g., antisense, siRNA, crRNA, etc. ). − We previously reported on nucleosides containing a seven-membered sugar (oxepane) ring. , Elaboration to the phosphoramidite derivatives allowed for the solid-phase synthesis of oxepane nucleic acid (ONA) sequences connected via 5′-7′ linkages (OxT 0 , OxA 0 ; Scheme ).…”

“…Due to this limitation, we adopted two approaches to increase the thermal stability of ONA/RNA duplexes: (i) introduction of additional functional groups in the oxepane ring to steer the sugar conformation that may favor binding to RNA (e.g., OxT 1 ; Scheme ) and (ii) moving the location of phosphodiester backbone closer to the nucleobase to better mimic the native DNA or RNA backbone, e.g., 4′-7′ and 3′-7′ linked ONAs (OxT 2 and OxT 3 ; Scheme ). The choice of the nucleosides, alone or inside a duplex, is guided by classical molecular dynamics (MD) simulations and quantum mechanical calculations as reported recently by our groups. ,− Herein, we present the stereoselective functionalization of the unsaturated oxepine nucleosides, their elaboration into phosphoramidite derivatives by careful selection of orthogonal protecting groups, and microwave-assisted phosphitylation of their sterically hindered hydroxyl groups. We also describe the incorporation of oxepane nucleoside units into DNA and RNA strands via solid-phase synthesis and the impact of these modifications on the structure and thermal stability of dsRNA, dsDNA, and RNA–DNA hybrid duplexes.…”