Prohead RNA Sequence Variation

Abstract

Department of Chemistry and Biochemistry and Botany and MicrobiologyUniversity of Oklahoma.Prohead RNA (pRNA) is an essential component of the self-assembling phi29 bacteriophage DNA packaging motor. Although different species of bacteriophage share only 12 % similarity in pRNA sequences, the secondary structure for prohead RNA is conserved. The NMR structure of the most conserved loop sequence, the E loop hairpin, reveals a UU pair, a U-turn, and a syn guanosine. Comparison of the pRNA E loop hairpin to ribosomal RNA hairpins and predictions from MC-SYM provides benchmarks for improving RNA structure prediction. All the different pRNA sequences self-assemble in dimers, trimers, and higher order multimers. The energetics for dimer and trimer formation in different pRNA sequences are similar despite very different sequences in the loop-loop interactions. The architecture surrounding the interlocking loops contributes to the stability of the pRNA quaternary interactions, and sequence variation outside the interlocking loops may counterbalance the changes in the loop sequences. Thus, the evolutionary divergence of pRNA sequences maintains not only function and secondary structure, but also the stabilities of quaternary interactions. The self-assembly of the different pRNA sequences can be fine-tuned with variations in salt, temperature, and concentration. The ability to control pRNA self-assembly holds promise for the development of nanoparticle therapeutic applications and further biophysical studies of the structure and function of pRNA in the packaging motor.