Oligonucleotide Analogues with Integrated Bases and Backbones. Part 25

The ability of A*[s ]U dinucleosides to gel organic solvents and water is modulated by changing the nature of the substituents at O C(2′) and O C(3′), as evidenced by comparing the gelation of the dinucleosides 7 – 9 and the properties of the gels. A mere extension of the hydrophobic moiety, by replacing the isopropylidene groups of 2 by cyclohexylidene groups, as in 7 , has a small effect, while changing the conformation of the ribose ring and reducing the size of the hydrophobic moiety, as in 8 , has a strong effect on the scope of gelation, the minimum gelation concentration, as low as 0.07% for pentanol and decanol, and the properties of the gel. The fully deprotected dinucleoside 9 gels water at a minimal gelation concentration of 0.6%. A TEM of the corresponding xerogel shows the formation of fibers with a diameter of ca. 30 to 90 nm.     

Oligonucleotide Analogues with Integrated Bases and Backbones. Part 23

The sulfone 2 , and the sulfoxides (S)‐ 3 and (R)‐ 3 were obtained by oxidation of the thiomethylene‐linked A*[s ]U dinucleoside 1 . Conformational analysis and association studies of 2 , (S)‐ 3 , and (R)‐ 3 reveal a strong influence of the configuration on the conformation of the linking unit and on the self‐association of the dinucleosides.     

Oligonucleotide Analogues with Integrated Bases and Backbones. Part 26

The self‐complementary aminomethylene‐linked A*[n] U* dinucleosides 23 – 26 were prepared by reductive coupling of aldehyde 10 and azide 8 . The U*[n] A* sequence isomers 19 – 21 were similarly prepared from aldehyde 14 and azide 3 . The substituents at C(6/I) of 23 – 26 and at C(8/I) of 19 – 21 strongly favour the syn‐conformation. The A*[n] U* dinucleoside 23 associates more strongly than the sequence‐isomeric U*[n] A* dinucleoside 19 . The A*[n] U* dinucleosides 23 and 24 associate more strongly than the analogues devoid of the substituent at C(6/I), while the U*[n] A* dinucleoside 19 associates less strongly than the analogue devoid of the substituent at C(8/I). While 23 and 24 form cyclic duplexes mostly by Watson–Crick‐type base pairing, 25 only forms linear associates. The U*[n] A* dinucleoside 19 forms mostly linear duplexes and higher associates, and 21 forms cyclic duplexes showing both Watson–Crick‐ and Hoogsteen‐type base pairing. The cyclic duplexes of the aminomethylene‐linked dinucleosides show both the gg‐ and gt‐orientation of the linker, with the gg‐orientation being preferred.