Oligonucleotide Analogues with Integrated Bases and Backbone. Part 15

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AbstractThe self‐complementary (Z)‐configured U*[ce]A(*) dinucleotide analogues 6, 8, 10, 12, 14, and 16, and the A*[ce]U(*) dimers 19, 21, 23, 25, 27, and 29 were prepared by partial hydrogenation of the corresponding ethynylene linked dimers. Photolysis of 14 led to the (E)‐alkene 17. These dinucleotide analogues associate in CDCl3 solution, as evidenced by NMR and CD spectroscopy. The thermodynamic parameters of the duplexation were determined by van't Hoff analysis. The (Z)‐configured U*[ce]A(*) dimers 14 and 16 form cyclic duplexes connected by Watson–Crick H‐bonds, the (E)‐configured U*[ce]A dimer 17 forms linear duplexes, and the U*[ce]A(*) allyl alcohols 6, 8, 10, and 12 form mixtures of linear and cyclic duplexes. The C(6/I)‐unsubstituted A*[ce]U allyl alcohols 19 and 23 form linear duplexes, whereas the C(6/I)‐substituted A*[ce]U* allyl alcohols 21 and 25, and the C(5′/I)‐deoxy A*[ce]U(*) dimers 27 and 29 also form minor amounts of cyclic duplexes. The influence of intra‐ and intermolecular H‐bonding of the allyl alcohols and the influence of the base sequence upon the formation of cyclic duplexes are discussed.