Viral nanomotors for packaging of dsDNA and dsRNA

Abstract

While capsid proteins are assembled around single-stranded genomic DNA or RNA in rod-shaped viruses, the lengthy double-stranded genome of other viruses is packaged forcefully within a preformed protein shell. This entropically unfavourable DNA or RNA packaging is accomplished by an ATP-driven viral nanomotor, which is mainly composed of two components, the oligomerized channel and the packaging enzymes. This intriguing DNA or RNA packaging process has provoked interest among virologists, bacteriologists, biochemists, biophysicists, chemists, structural biologists and computational scientists alike, especially those interested in nanotechnology, nanomedicine, AAA+ family proteins, energy conversion, cell membrane transport, DNA or RNA replication and antiviral therapy. This review mainly focuses on the motors of double-stranded DNA viruses, but double-stranded RNA viral motors are also discussed due to interesting similarities. The novel and ingenious configuration of these nanomotors has inspired the development of biomimetics for nanodevices. Advances in structural and functional studies have increased our understanding of the molecular basis of biological movement to the point where we can begin thinking about possible applications of the viral DNA packaging motor in nanotechnology and medical applications.

Fig. 1

Viral DNA packaging motors. A. The portal or the connector structure of bacteriophage ε15 (a) (Jiang et al., 2006), T3 (b) (Valpuesta et al., 2000), T7 (c) (Agirrezabala et al., 2005) and P22 (d) (Lander et al., 2006). B. The assembly pathway of λ terminase and the structure of the related DNA substrate (Maluf et al., 2006; Ortega and Catalano, 2006). C. Similarity between two models; the phi29 DNA packaging motor (a) and PCNA/clamp-loader complex (b) (Lee and Guo, 2006). Figures were adapted with permission from the authors and from Elsevier, American Association for the Advancement of Science, and American Chemical Society to the respective citation.

Fig. 2

Single molecule studies on bacteriophage phi29 DNA packaging motor (adapted from (Shu et al., 2007) with permission from the European Molecular Biology Organization). A–C. Single molecule dual-view imaging for pRNA counting on the motor. (A) Experimental design. (B) Single molecule counting of Cy3 (green) or Cy5 (red)-labelled pRNA via step photobleaching. Each step represents the presence of single Cy3 or Cy5 on pRNA. (C) Single molecule dual imaging of procapsid containing Cy3-pRNA (green spots), Cy5-pRNA (red spots) or both Cy3 and Cy5-pRNA (yellow spots). The histograms of procapsid with Cy3 photobleaching steps were compared with the theoretical histogram predicted to have three Cy3 pRNA with a labelling efficiency of 70%. The stoichiometry of ferritin-conjugated pRNA on procapsid also revealed by EM. D. Direct observation of phi29 DNA translocation with gradual reduction of swinging range (distance) of the fluorescence microsphere at real time. The experimental design and the frames of the image are also shown.