Journal of Nanomedicine & Nanotechnology

Abstract

Nanoimaging of ssRNA: Genome Architecture of the Hepatitis C Virus Revealed by Atomic Force Microscopy

Jamie L Gilmore, Hideki Aizaki, Aiko Yoshida, Katashi Deguchi, Masahiro Kumeta, Julia Junghof, Takaji Wakita and Kunio Takeyasu

The complex structures that RNA molecules fold into play important roles in their ability to perform various functions in the cell. The structure and composition of viral RNA influences the ability of the virus to implement the various stages of the viral lifecycle and can influence the severity of the virus effects on the host. Although many individual secondary structures and some tertiary interactions of the Hepatitis C virus genome have previously been identified, the global 3D architecture of the full 9678 nucleotide genome still remains uncertain. One promising technique for the determination of the overall 3D structure of large RNA molecules is nanoimaging with Atomic Force Microscopy. In order to get an idea of the structure of the HCV genome, we imaged the RNA prepared in the presence of Mg2+, which allowed us to observe the compact folded tertiary structure of the viral genome. In addition, to identify individual structural elements
of the genome, we imaged the RNA prepared in the absence of Mg2+, which allowed us to visualize the unfolded secondary structure of the genome. We were able to identify a recurring single stranded region of the genome in many of the RNA molecules which was about 58 nm long. This method opens up a whole new avenue for the study of the secondary and tertiary structure of long RNA molecules. This ability to ascertain RNA structure can aid in drawing associations between the structure and the function of the RNA in cells which is vital to the development of potential antiviral therapies.