Structural Analysis of Kaposi\u27s Sarcoma Associated Herpesvirus PAN RNA

Kaposi’s sarcoma-associated herpesvirus (KSHV) is a herpesvirus linked to Kaposi’s sarcoma and two forms of lymph node cancer. KSHV infects cells with its DNA and uses it to create a molecule called RNA that generally creates proteins that help take control and destroy the infected cell. However one RNA called polyadenylated nuclear RNA (PAN RNA) has been shown to promote important functions of KSHV, such as gene expression, replication, and immune modulation despite PAN RNA’s lack of direct protein translation. Analysis of the structure of the PAN RNA molecule gives perspective on how the molecule performs its many important functions. The selective 2’-hydroxyl acylation analyzed by primer extension with mutational profiling (SHAPE-MaP) method chemically modifies the molecule, converts it into cDNA wherein modified nucleotides generate mutations. By sequencing the molecule, the shape of the molecule can be inferred through algorithmic analysis. Using the exceptionally accurate SHAPE-MaP method to analyze PAN structure will refine the current understanding of the secondary structure of the molecule