Tertiary structure and computer modeling of plant 5S ribosomal RNA

A new model of secondary and tertiary structure of higher plant 5S rRNA is proposed. It consists of three domains. Domain alpha includes stem I and loop A; domain beta contains stems II and III and loops B and C; domain gamma consists of stems IV and V and loops D and E. We propose that the domains beta and gamma adopt RNA-A like structure due to irregularities caused by the different in size internal loops B and E and the bulges occurring in the model. A suggested bending of RNA could bring single stranded fragments of domains beta and gamma close enough to each other to allow tertiary interactions. The new model of plant 5S rRNA differs from those suggested previously for eukaryotic 5S rRNA, by arrangement of the domains beta and gamma and the base pairing scheme of domain gamma. The model is based on our results of partial digestion obtained with single and double strand specific nucleases. The experimental results were confirmed by computer aided secondary structure prediction analysis of all higher plant 5S rRNAs and computer modeling using energy minimalization approach. Further support of our model have been provided by experiments including alpha sarcin, ribonuclease H and chemical modifications.