Oligonucleotides Containing 9-(2-Deoxy-2-Fluoro-β-D-Arabinofuranosyl)-Adenine and -Guanine: Synthesis, Hybridization and Antisense Properties

• Published in: Nucleosides, nucleotides & nucleic acids nucleotides & nucleic acids, 2000-10, Vol.19 (10-12), p.1861-1884
• Main Authors: Tennilä, Tuula, Azhayeva, Elena, Vepsäläinen, Jouko, Laatikainen, Reino, Azhayev, Alex, Mikhailopulo, Igor A.
• Format: Article
• Language: English
• Subjects: Arabinonucleosides - chemistry; Base Sequence; Gene Expression Regulation, Enzymologic - drug effects; Luciferases - genetics; Magnetic Resonance Spectroscopy; Nucleic Acid Hybridization; Oligonucleotides - chemistry; Oligonucleotides, Antisense - chemical synthesis; Oligonucleotides, Antisense - chemistry; Oligonucleotides, Antisense - pharmacology; Thermodynamics
• ISSN: 1525-7770; 1532-2335
• DOI: 10.1080/15257770008045466

Synthesis of 9-(2-deoxy-2-fluoro-β-D-arabinofuranosyl)-adenine (7, ara-A 2′F ) and -guanine (12 ara-G 2′F ) was accomplished via the condensation of 2, 6-dichloropurine (1) with 2-deoxy-2-fluoro-1, 3, 5-tri-O-benzoyl-α-D-arabinofuranose (2) as a key chemical step. Condensation of silylated N 6 -benzoyladenine (6) with 2 gave, after deblocking and chromatographic separation, ara-A 2,F (7) (14%), it's α-anomer 8 (14%) and N 7 -α-isomer 9 (25%). The PSEUROT analysis of N 9 -β-D-arabinosides 7 and 12 manifested slight preference for the S rotamer (64%) for the former, and an equal population of the N and S rotamers for the latter. The arabinosides 7 and 12 were used for the preparation of the respective phosphoamidite building blocks 13 and 14 for automated oligonucleotide synthesis. Four 15-mer oligonucleotides (ONs) complementary to the initiation codon region of firefly luciferase mRNA were prepared: unmodified 2′-deoxy-ON (AS1) and containing (i) ara-A 2,F instead of the only A (AS2), (ii) ara-G 2,F vs. 3-G from the 5′-terminus (AS3), and (iii) both arabinosides at the same positions (AS4). All these ONs display practically the same (i) affinity to both complementary DNA and RNA, and (ii) ability to inhibit a luciferase gene expression in a cell-free transcription-translation system.