Insight into the structural organization of the omega leader of TMV RNA: The role of various regions of the sequence in the formation of a compact structure of the omega RNA

► Polyribonucleotides containing altered omega sequences of TMV RNA are synthesized. ► Synthetic RNAs are studied by sedimentation and thermal melting technique. ► The modified RNAs are less stable and less compact than the original omega RNA. ► Central (CAA)n and 3′-end parts form together stable tertiary structure of omega RNA. The 5′-untranslated sequence of tobacco mosaic virus RNA – the so called omega leader – is a well-known translational enhancer. The structure of the omega RNA has unusual features. Despite the absence of extensive secondary structure of the Watson–Crick type, the omega RNA possesses a stable compact conformation. The central part of the omega sequence contains many CAA repeats and is flanked by U-rich regions. In this work we synthesized the polyribonucleotides containing modified omega sequences, and studied them using analytical ultracentrifugation and thermal melting techniques. It was demonstrated that changes made in both the central and the 3′-proximal part of the sequence led to a strong destabilization of the omega RNA structure. We conclude that the regular (CAA)n core region and the 3′-proximal AU-rich region of the omega RNA interact with each other and contribute together to the formation of a stable tertiary structure.