Oligonucleotide analogues with integrated bases and backbone. Part 16: Synthesis and association of ethylene-linked self-complementary dimers

Abstract

The self‐complementary, ethylene‐linked U*[ca]A(*) dinucleotide analogues 8, 10, 12, 14, 16, and 18, and the sequence‐isomeric A*[ca]U(*) analogues 20, 22, 24, 26, 28, and 30 were obtained by Pd/C‐catalyzed hydrogenation of the corresponding, known ethynylene‐linked dimers. The association of the ethylene‐linked dimers was investigated by NMR and CD spectroscopy. The U*[ca]A(*) dimers form linear duplexes and higher associates (K between 29 and 114M−1). The A*[ca]U(*) dimers, while associating more strongly (K between 88 and 345M−1), lead mostly to linear duplexes and higher associates; they form only minor amounts of cyclic duplexes. The enthalpy–entropy compensation characterizing the association of the U*[cx]A(*) and A*[cx]U(*) dimers (x=y, e, and a) is discussed.