2-Aminopyridine as a Nucleobase Substitute for Adenine in DNA-like Architectures: Synthesis of Alkynyl C-Nucleotides and Their Hybridization Characteristics

Halogenated 2-aminopyridine was attached to the acetylene terminal of ethynyl C-2-deoxy-β-d-ribofuranoside as a nucleobase substitute, and then, the C-nucleoside was incorporated into natural DNAs. The resulting chimeric DNA constructed double helical structures with the complementary chimeric DNA. In the duplex, 2-aminopyridine functioned as an adenine analogue that formed a base pair with a non-natural thymine isostere. Artificial homooligomers were also prepared only from the adenine-type C-nucleoside and proven to form completely artificial double helices with the corresponding artificial thymine-type homooligomers.

Synthesis of RNA Crosslinking Oligonucleotides Modified with 2-Amino-7-Deaza-7-Propynyl-6-Vinylpurine

This article describes procedures to synthesize 2'-OMe-RNA modified with cross-linkable 2-amino-7-deaza-7-propynyl-6-vinylpurine (ADpVP) and preparation of the RNA-crosslinking experiment in vitro. All synthesis steps yield the desired compound in moderate or high yield without expensive chemical reagents or specific devices. The crosslink-active form of modified RNA can also be purified by commonly used reversed-phase HPLC, can be stored at -80°C after lyophilization for a few days, and is ready to use for crosslinking experiments. This crosslink-active RNA can efficiently form covalent bonds with complementary RNA in a sequence-specific manner. © 2019 by John Wiley & Sons, Inc.

Synthesis of Nonnatural Oligonucleotides Made Exclusively of Alkynyl C-Nucleosides with Nonnatural Bases

This unit describes detailed procedures for the preparation of nonnatural C-nucleosides comprising seven types of nonnatural nucleobases attached to 1'-position of 2'-deoxyribose through an acetylene bond with the β-configuration. In addition, derivatization of these alkynyl C-nucleosides into the corresponding phosphoramidites and the subsequent oligonucleotide synthesis are also presented. The processes are depicted in three parts. The first basic protocol deals with the synthesis of a key intermediate, 5-O-DMTr-protected 1-ethynyl-2-deoxy-β-D-ribofuranoside. The second basic protocol mentions the procedures of the preparation of nonnatural C-nucleosides by a palladium-catalyzed coupling reaction of the ethynyl intermediate and halogen-attached nonnatural nucleobases. The synthetic procedures of the corresponding nonnatural phosporamidites are also described. The third basic protocol presents the solid-phase, automated synthesis of nonnatural oligonucleotides composed exclusively of the nonnatural C-nucleotides.