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The nonamer r(GCUUCGGC)dBrU, where dBrU is 5-bromo-2'-deoxyuridine, contains the tetraloop sequence UUCG. It crystallizes in the presence of Rh(NH3)6Cl3. In solution the oligomer is expected to form a hairpin loop but the x-ray structure analysis, to a resolution of 1.6 A, indicates an eight-base-pair A-RNA duplex containing a central block of two G.U and two C.U pairs. Self-pairs which approximate to Watson-Crick geometry are also formed in the extended crystal structure between symmetry-related BrU residues and are part of infinite double-helical stacks. The G.U pair is a wobble base pair analogous to the G.T pair found in DNA fragments. The C.U mismatch involves one hydrogen-bonded contact between the bases and a bridging water molecule which ensures a good fit of the base pair in the RNA helix. The BrU.BrU pair is held by two hydrogen bonds in an orientation which is compatible with duplex geometry. The structure observed within the crystal has some parallels with the structure of globular RNAs, and the presence of stable, noncanonical base pairs has implications for the prediction of RNA secondary structure.

An improved procedure for the transformation of 5′-0-monomethoxytrityl- 2′-0-acetyl-3′-phosphates of uridine la inosine lb and 6-N-benzoyladenosine lc into corresponding 3′/2,2,2-trichloroethyl, 2-cyanoethyl/-phosphates lla-c is reported. 1H NMR characterization of nucleoside 3′-phosphotriesters is presented. New conditions i. e. anhydrous triethylamine-pyridine treatment have been found for the selective removal of 2-cyanoethyl group from nucleoside 3′-phosphotriesters in the presence of neighbouring 2′-0-acetyl one.

Zinc/acetylacetone/pyridine treatment has been designed as a very efficient method for removal of 2,2,2-trichloroethyl group from phosphoesters. Internucleotide and terminal 2,2,2-trichloroethyl phosphotriesters were transformed to corresponding diesters quantitatively. Much less reactive 2,2,2-trichloroethyl phosphodiesters produced monoesters with Ca. 90% yield. 31P NMR spectroscopy has been proposed as a new tool for analysis of removal of internucleotide phosphate protecting groups - a crucial step in oligonucleotides synthesis via phosphotriester approach.

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In this work, the first example of chemical synthesis of oligoribonucleotide containing the hypermodified nucleoside N6-/N-threonylcarbonyl/-adenosine/t6A/ is presented. Synthesis of the heptamer C-C-C-A-U-t6A-A IX, the sequence of which is related to the anticodon loop of the initiator tRNA from yellow lupine, was achieved by: /i/ phosphotriester block synthesis of suitably protected heptamer VI containing an adenosine unit with a free exo-NH2 group, /ii/ highly effective “one-flask” procedure for the transformation of the free exo-NH2 group of adenosine unit of heptamer VI into a N,N′-disubstituted urea system of t6A of heptamer VII /hypermodification/, and /iii/ final deprotection of VIII /32% total yield/ with the use of a new approach for simultaneous hydrogenolysis /Pd0-hydrogen-pyridine/ of the p-nitrobenzyl group and 2,2,2-trichloroethyl groups from carboxyl function of t6A and internucleotide phosphates respectively.