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The tritylated and silylated self-complementary A*[s]U*[s]A*[s]U* and U*[s]A*[s]U*[s]A* tetramers 18 and 24, linked by thiomethylene groups (abbreviated as [s]) between a nucleobase and C(5') of the neighbouring nucleoside unit were prepared by a linear synthesis based on S-alkylation of 5'-thionucleosides by 6-(chloromethyl)uridines, 7 or 10, or 8-(chloromethyl)adenosines, 12 or 15. The tetramers 18 and 24 were detritylated to the monoalcohols 19 and 25, and these were desilylated to the diols 20 and 26, respectively. The association of the tetramers 18-21 and 24-26 in CDCl3 or in CDCl3/(D-6)DMSO 95 :5 was investigated by the concentration dependence of the chemical shifts for H-N(3) or H2N-C(6). The formation of cyclic duplexes connected by four base pairs is favoured by the presence of one and especially of two OH groups. The diol 20 with the AUAU sequence prefers reverse-Hoogsteen, and diol 26 with the UAUA sequence Watson-Crick base pairing. The structure of the cyclic duplex of 26 in CDCl3 at 2 degrees was derived by a combination of AMBER* modeling and simulated annealing with NMR-derived distance and torsion-angle restraints resulting in a Watson-Crick base-paired right-handed antiparallel helix showing large roll angles, especially between the centre base pairs, leading to a bent helix axis.

The A*[s]U(*) dinucleosides 1 and 2 form thermoreversible gels in organic solvents. The basis of the gelation is the formation of linear aggregates by base pairing following desolvation of the nucleobases. This is evidenced by the absence of gel formation by the C(6)-deaminated analogue 3 of 1, the correlation of gelation with the anti-conformation, as preferred for 1, and the temperature-, concentration-, and time-dependent CD spectra. The gels were also characterized by the minimum gelation concentration, the gel–sol transition (melting) temperature, and rheological properties.

The thiomethylene-linked U*[s]U(*) dimers 9–14 were synthesized by substitution of the 6-[(mesyloxy)methyl]uridine 6 by the thiolate derived from the uridine-5′-thioacetates 7 and 8 followed by O-deprotection. Similarly, the thiomethylene-linked A*[s]A(*) dimers 9–14 were obtained from the 8-(bromomethyl)adenosine 15 and the adenosine-5′-thioacetates 16 and 17. The concentration dependence of both HN(3) of the U*[s]U(*) dimers 9–14 evidences the formation of linear and cyclic duplexes, and of linear higher associates, C(8 or 6)CH2OH and/or C(5′/II)OH groups favouring the formation of cyclic duplexes. The concentration dependence of the chemical shift for both H2NC(6) of the A*[s]A(*) dimers 18–23 evidences the formation of mainly linear associates. The heteroassociation of U*[s]U(*) to A*[s]A(*) dimers is stronger than the homoassociation of U*[s]U(*) dimers, as evidenced by diluting equimolar mixtures of 11/20 and 13/22. A 1 : 1 stoichiometry of the heteroassociation is evidenced by a Job's plot for 11/20, and by mole ratio plots for 9/18, 10/19, 12/21, 13/22, and 14/23.

The formation of cyclic duplexes (pairing) of known oxymethylene-linked self-complementary U*[o]A(*) dinucleosides contrasts with the absence of pairing of the ethylene-linked U*[ca]A(*) analogues. The origin of this difference, and the expected association of U*[x]A(*) and A*[x]U(*) dinucleosides with x=CH2, O, or S was analysed. According to this analysis, pairing occurs via constitutionally isomeric Watson–Crick, reverse Watson–Crick, Hoogsteen, or reverse Hoogsteen H-bonded linear duplexes. Each one of them may give rise to three diastereoisomeric cyclic duplexes, and each one of them can adopt three main conformations. The relative stability of all conformers with x=CH2, O, or S were analysed. U*[x]A(*) dinucleosides with x=CH2 do not form stable cyclic duplexes, dinucleosides with x=O may form cyclic duplexes with a gg-conformation about the C(4′)C(5′) bond, and dinucleosides with x=S may form cyclic duplexes with a gt-conformation about this bond. The temperature dependence of the chemical shift of HN(3) of the self-complementary, oxymethylene-linked U*[o]A(*) dinucleosides 1–6 in CDCl3 in the concentration range of 0.4–50 mM evidences equilibria between the monoplex, mainly linear duplexes, and higher associates for 3, between the monoplex and cyclic duplexes for 6, and between the monoplex, linear, and cyclic duplexes as well as higher associates for 1, 2, 4, and 5. The self-complementary, thiomethylene-linked U*[s]A(*) dinucleosides 27–32 and the sequence isomeric A*[s]U(*) analogues 33–38 were prepared by S-alkylation of the 6-(mesyloxymethyl)uridine 12 and the 8-(bromomethyl)adenosine 22. The required thiolates were prepared in situ from the C(5′)-acetylthio derivatives 9, 15, 19, and 25. The association in CHCl3 of the thiomethylene-linked dinucleoside analogues was studied by 1H-NMR and CD spectroscopy, and by vapour-pressure osmometric determination of the apparent molecular mass. The U*[s]A(*) alcohols 28, 30, and 31 form cyclic duplexes connected by Watson–Crick H-bonds, while the fully protected dimers 27 and 29 form mainly linear duplexes and higher associates. The diol 32 forms mainly cyclic duplexes in solution and corrugated ribbons in the solid state. The nucleobases of crystalline 32 form reverse Hoogsteen H-bonds, and the resulting ribbons are cross-linked by H-bonds between HOCH2C(8/I) and N(3/I). Among the A*[s]U(*) dimers, only the C(8/I)-hydroxymethylated 37 forms (mainly) a cyclic duplex, characterized by reverse Hoogsteen base pairing. The dimers 34–36 form mainly linear duplexes and higher associates. Dimers 34 and particularly 38 gelate CHCl3. Temperature-dependent CD spectra of 28, 30, 31, and 37 evidence π-stacking in the cyclic duplexes. Base stacking in the particularly strongly associating diol 32 in CHCl3 solution is evidenced by a melting temperature of ca. 2°.