The role of phosphate groups in the VS ribozyme-substrate interaction

摘要: The VS ribozyme trans-cleavage substrate interacts with the catalytic RNA via tertiary interactions. To study role of phosphate groups in ribozyme-substrate interaction, 18 modified substrates were synthesized, where an epimeric phosphorothioate replaces one diester linkages. Sites stem-loop substitution impaired reaction cluster two regions. first site is scissile linkage and nucleotides downstream this second within loop region. addition manganese ions caused recovery rate for substitutions between A621 A622 U631 C632, suggesting that these may serve as ligands metal ions. In contrast, significant rescue was not observed implying electrophilic catalysis by unlikely to contribute catalysis. addition, increase unmodified when a mixture magnesium acted cofactor. One possible explanation effect cleavage limited dependent docking on ribozyme.