The 5S rRNA system within Xenopus oocytes includes transcription of the 5S rRNA gene, storage of the 75 RNP, conversion to 5S RNP, assembly of the SOS ribosomal subunit and proposed mediation of translocation with the ribosome. Transcription Factor IIIA (ThIIIA) participates in binding to both the DNA of the 5S rRNA gene and the RNA of the 5S rRNA transcript which is exported to the cytoplasm for storage as 75 RNP. TFIIIA shares a nuclear export signal (NES) with Rev protein, which exploits the 5S rRNA transport system for export of viral mRNA from human immunodeficiency virus type 1. TFIIIA is able to discriminate between DNA and RNA, using a nine repeats of the zinc finger motif. The first three fingers have been specialized for high affinity binding to the 5S rRNA gene, whereas the middle three fingers specifically recognize the 5S rRNA transcript equally high affinity. Changes in the amino acid sequence, the zinc ligand spacing and the inter-finger linker composition dictate the structural and dynamic determinants of nucleic acid binding. Other closely related zinc finger proteins are capable of protein-protein recognition. Understanding the parameters which define molecular recognition in zinc fingers has potential applications in molecular biology and gene therapy with the rational design of zinc finger proteins to recognize nucleic acid sequences from oncogenic and retroviral disease systems. The research proposed herein aims to determine the structure and dynamics of TFIIIA fingers 4-6 free and bound to a subdomain of 5S rRNA comprising Loop A, Helix IV and Loop E. Further studies aim to study the complex of TFIIIA zf4-6 and intermediate element DNA of the 5S rRNA gene.
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