THE STRUCTURE OF THE ISOLATED, CENTRAL HAIRPIN OF THE HDV ANTIGENOMICRIBOZYME - NOVEL STRUCTURAL FEATURES AND SIMILARITY OF THE LOOP IN THE RIBOZYME AND FREE IN SOLUTION

The structure of an RNA hairpin containing a seven-nucleotide loop tha t is present in the self-cleaving sequence of hepatitis delta virus an tigenomic RNA was determined by high resolution NMR spectroscopy. The loop, which is composed of only one purine and six pyrimidines, has a surprisingly stable structure, mainly supported by sugar hydroxyl hydr ogen bonds and base-base and base-phosphate stacking interactions. Com pared with the structurally well-determined, seven-membered anticodon loop in tRNA, the sharp turn which affects the required 180 degrees ch ange in direction of the sugar-phosphate backbone in the loop is shift ed one nucleotide in the 3' direction. This change in direction can be characterized as a reversed U-turn. It is expected that the reversed U-turn may be found frequently in other molecules as well. There is ev idence for a new non-Watson-Crick UC base pair formed between the firs t and the last residue in the loop, while most of the other bases in t he loop are pointing outwards making them accessible to solvent. From chemical modification, mutational and photocrosslinking studies, a sim ilar picture develops for the structure of the hairpin in the active r ibozyme indicating that the loop structure in the isolated hairpin and in the ribozyme is very similar.