Oligonucleotide conformations. III. Comparative optical and thermodynamic studies of uridylyl‐3′‐5′‐nucleosides containing ribose, deoxyribose, or 2′‐deoxy‐2′‐fluororibose in the uridine moiety

The synthesis of uridylyl‐3′‐5′‐nucleosides containing ribose, deoxyribose, or 2′‐fluoro‐2′‐deoxyribose in the uridine‐3′‐bound moiety and adenosine, guanosine, cytidine or uridine in the 5′‐nucleoside is reported. The temperature dependence of the circular dichroism of these dinucleoside phosphates in 0.06 M phosphate buffer at pH 7 was analyzed by the two‐state model and the oscillating dimer model. From the former, apparent thermodynamic parameters were determined by means of an iterative computer method. The comparison between the three different dinucleoside phosphates in each series indicated that the fluororiboside and the riboside resembled each other and were more stacked than the analogue containing deoxyribose. It further appeared that the similarity between the fluororiboside and the riboside is influenced by the nature of the neighboring 5′‐bound base. The interaction between the 3′‐bound sugar moiety and the 5′‐bound base is evoked as a possible stabilization mechanism.