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Oligonucleotide Analogues with Integrated Bases and Backbone. Part 14
Authors:Xiaomin Zhang  Bruno Bernet  Andrea Vasella
Affiliation:Laboratorium für Organische Chemie, ETH Zürich, Wolfgang‐Pauli Strasse 10, CH‐8093 Zürich
Abstract:The self‐complementary tetrameric propargyl triols 8, 14, 18 , and 21 were synthesized to investigate the duplex formation of self‐complementary, ethynylene‐linked UUAA, AAUU, UAUA, and AUAU analogues with integrated bases and backbone (ONIBs). The linear synthesis is based on repetitive Sonogashira couplings and C‐desilylations (34–72% yield), starting from the monomeric propargyl alcohols 9 and 15 and the iodinated nucleosides 3, 7, 11 , and 13 . Strongly persistent intramolecular H‐bonds from the propargylic OH groups to N(3) of the adenosine units prevent the gg‐type orientation of the ethynyl groups at C(5′). As such, an orientation is required for the formation of cyclic duplexes, this H‐bond prevents the formation of duplexes connected by all four base pairs. However, the central units of the UAUA and AAUU analogues 18 and 14 associate in CDCl3/(D6)DMSO 10 : 1 to form a cyclic duplex characterized by reverse Hoogsteen base pairing. The UUAA tetramer 8 forms a cyclic UU homoduplex, while the AUAU tetramer 21 forms only linear associates. Duplex formation of the O‐silylated UUAA and AAUU tetramers is no longer prevented. The self‐complementary UUAA tetramer 22 forms Watson–Crick‐ and Hoogsteen‐type base‐paired cyclic duplexes more readily than the sequence‐isomeric AAUU tetramer 23 , further illustrating the sequence selectivity of duplex formation.
Keywords:Ribonucleotide analogues  Oligonucleotides  Conformational analysis  Hydrogen bonds  Dinucleotides  Sonogashira coupling  Base pairing  Watson–  Crick base pairing  Hoogsteen base pairing
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