Determining Nucleocapsid Protein Recognition Of Non-Canonical Substrate Hairpins

The nucleocapsid (NC) protein of HIV binds to and destabilizes the TAR hairpin in the HIV genome. Studies have shown that G-containing base pairs next to a distortion in the duplex are prime sites for NC induced destabilization. Indeed, the NMR structure of the NC protein bound at the G/C base pair at the stem-loop interface, and flipping out the bases in the loop. While the NC protein primarily binds to RNA, it can also recognize DNA hairpins. Here, we present basic characterization of NC protein binding to various DNA hairpins previously shown to form in the eukaryotic genome.