Synthesis and Biophysical Characterization of RNAs Containing 2′-Fluorinated Northern Methanocarbacyclic Nucleotides

Abstract

2′-Fluorinated Northern methanocarbacyclic (2′-F-NMC) nucleosides and phosphoramidites, based on a bicyclo[3.1.0]hexane scaffold bearing all four natural nucleobases (U, C, A, and G), were synthesized to enable exploration of this novel nucleotide modification related to the clinically validated 2′-deoxy-2′-fluororibonucleotides (2′-F-RNA). Biophysical properties of the 2′-F-NMC-containing oligonucleotides were evaluated. A duplex of 2′-F-NMC-modified oligonucleotide with RNA exhibited thermal stability similar to that of the parent RNA duplex, 2′-F-NMC-modified oligonucleotides had higher stability against 5′-and 3′-exonucleolytic degradation than the corresponding oligonucleotides modified with 2′-F-RNA, and 2′-F-NMC-modified oligonucleotides exhibited higher lipophilicity than the corresponding RNA oligonucleotides as well as those modified with 2′-F-RNA.

Difluorophosphonylated Allylic Ether Moiety as a 2′-Modification of RNA-Type Molecules: Synthesis, Thermal, and Metabolic Studies

“…Fluorinated ON 10 , having a much higher retention time compared to the unmodified ON 7 and its nonfluorinated analogue 13 , exhibited an increased lipophilic character. That could facilitate cellular uptake of such ONs as already mentioned in the literature …”

“…That could facilitate cellular uptake of such ONs as already mentioned in the literature. 21 The melting temperature study of each ON was next realized. After hybridization to their complementary unmodified RNA strands (rA 12 ), thermal stability of the formed duplex was measured by UV-melting experiments and compared to the unmodified duplex (Table 1 and Figures S20 and S21).…”

RNAs Containing Carbocyclic Ribonucleotides

“…Our laboratory has been interested in studying noncanonical nucleic acid modifications, and we recently reported the synthesis of small interfering RNAs (siRNAs) containing 2′-fluorinated northern -methanocarbacyclic (2′-F-NMC) nucleotides (Figure A). , The 2′-F-NMC scaffold preorganizes the carbocyclic sugar into a pseudo-boat C2′- exo (north) conformation . 2′-F-NMC was generally well tolerated in both the guide and passenger strands of siRNAs with some exceptions, such as positions 1 and 2 on the guide strand. , This prompted us to evaluate the carbocyclic nucleotides, the parent compounds of the NMC scaffold.…”

Synthesis and Evaluation of Artificial Nucleic Acid Bearing an Oxanorbornane Scaffold

“…The reduction of the azide group, using ammonium formate with Pd/C, underwent the removal of the TES group. A uracil ring was successively formed by a reaction with 3-methoxyacryloyl isocyanate, following the reported procedure [21][22][23]. The direct incorporation of the uracil nucleobase to the triflated compound of 6 was unsuccessful.…”