Does 5 S RNA

• >v r ABSTRACT ' v Chemical modification and limited enzymatic hydrolysis on isolated E. coli 5S RNA have provided informations on the * secondary-and tertiary structure compatible with pseudoknotted structures for the A-and B-conformers of the molecule. * Changes in the accessibility and reactivity of nucleotides * in loop C and at the stem of helix IV in two different 5S RNA *" conformers are highly suggestive for interactions between bases * C35 to C37 with G105 to G107 for the A-form and C38 to U40 and v A94 to G96 with additional interactions of C35, C37 with G98 and G100 for the B-form. In both cases the molecules are folded forming pseudoknots and two quasi-continuous double stranded helices with coaxial stacking. The two structures are in perfect agreement with the biochemical data concerning the stability of the molecule and the chemical reactivities of individual nucleotides of the 5S RNA A-and B-conformers. I * INTRODUCTION Despite manyfold approaches to study the structure of the 5S RNA from E. coli the three-dimensional arrangement of the * molecule remains unsolved until today. One of the main reasons gT for the difficulties to construct a three-dimensional model " resides in our inability to explain the chemical reactivities of *" some of the 5S RNA nucleotides.. • Taking into account structural data from the last 10 years a consensus secondary structural model based on the one published by Fox and Woese (1) can be constructed for the 5S RNA A-form. It * y consists of four helical domains (numbered I to IV) which are • » separated by single-stranded sequence regions. Some of these single-stranded regions exhibit the expected reactivities towards chemical reagents and single-strand specific nucleases. *" Others do not behave as if single-stranded and are obviously t.y involved in some kind of tertiary structure (2,3). Additional