Characterizing The Binding Of The Hiv-1 Nc Protein To Hairpins Formed By Cag Repeats

Trinucleotide repeats (TNRs) occur throughout the genome and their expansion affects varied cellular processes such as gene expression, mRNA processing, and protein folding. TNR expansion is facilitated by formation of stable non-canonical secondary structures and has been linked to several neurodegenerative diseases, such as Huntington's Disease (HD). HD occurs when the CAG repeats in exon 1 of the huntingtin gene expands. When the repeats become single stranded, either during DNA replication or through long-patch base excision repair, they form a hairpin containing a four base loop and a stem containing A•A mismatches. While hairpin formation is the causative mechanism of HD, hairpins are also useful regulatory system. In the HIV-1 genome, hairpin formation by the trans-activation response (TAR) element is a key part of regulating reverse transcription of the genome. The nucleocapsid (NC) protein binds to the loop of the TAR hairpin and destabilizes the stem, allowing reverse transcription to proceed. Interestingly, there is a noticeable similarity between the structure of the TAR hairpin and the hairpin formed by the CAG repeats in the huntingtin gene. Thus, we are interested in determining if the NC protein can recognize the hairpin formed by CAG repeats. Using a crude purification of recombinant NC protein, we demonstrated putative binding of a (CAG)10 hairpin by the NC protein, and now provide more detailed characterization of the NC/CAG hairpin binding.