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Honors Project On-Campus Access Only

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Honors Advisor: Marcos Ortega

Abstract

To package their genomes into an empty capsid, double stranded DNA viruses utilize molecular motors consisting of a portal protein through which DNA is translocated, a large terminase subunit with ATPase and nuclease activity, and the small terminase subunit responsible for the recognition of viral DNA. The sequence homology for the components of the molecular motor may be very low between different dsDNA viruses, yet they are structurally very similar. As a result, dsDNA bacteriophages are used as a model to understand the DNA packaging mechanisms of dsDNA viruses with eukaryotic hosts. Although all dsDNA bacteriophages are thought to package DNA through very similar mechanisms, the molecular motors of relatively few phages have been studied in detail. The research outlined in this thesis aims to fill in this gap in scientific knowledge by analyzing the small terminase subunit of phage N15, known as gp1. Sequence analysis of gp1 in comparison with gpNu1, the small terminase subunit of the well-studied λ phage shows high sequence homology except in the winged-helix-turn-helix (WHTH) motif responsible for the binding of viral DNA. Gel mobility assays show gp1 binds viral DNA into a stable complex better then gpNu1. We theorize the low glycine content in the WHTH motif of the DNA binding domain (DBD) of gp1 provides greater stability and is responsible for gp1’s greater efficiency binding viral DNA.

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