RNA Nanomotor Based Active Devices for Biology and Medicine

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DESCRIPTION (provided by applicant): Nanotechnology is truly revolutionizing our ability to manufacture and design active devices and systems that are small, cheap, and ultra-sensitive. The need to produce small medical devices for rapid and parallel detection or health monitoring is intensifying. Moreover, as the micro-fabricated devices get smaller and smaller with each new development in materials science and engineering, the need to design and fabricate biologically inspired nanoscale devices and sensors and ultra-compact power sources to drive these devices and sensors are emerging. Nature can provide the tools to address the above needs. Molecular motors, such as ATPase [Noji et al., 1997], bacterial flagellar [Sowa et al., 2005], or viral DNA packaging motors [Guo, 2002; Shu et al., 2003] can be utilized to synthesize power at the nano-scale. Some of these motors can generate force up to tens or hundreds of pico Newtons. Some of them can use energy and generate force, via ATP hydrolysis, or use the force and generate energy in the form of ATP, via electrolocomotive force or pH gradients, with efficiencies in the range of 80-100% [Yasuda et al., 2001; Aksimentiev et al., 2004]. Some of these motors can have rotational speeds of 100-1000 rpm [Sowa et al., 2005]. In the recent years, nanofabrication capabilities have progressed to a point where sub 20nm nanopores, nanowires, and nanotubes can be grown at specific locations on a silicon wafer such that these structures can possibly be interfaced with biological motors for applications such as nanomechanics, filtration, locomotion, and energy generation and harvesting. In this project, we propose to develop active nanostructures and systems based on biological nanomotors. Our focus here would be the use of the bacteriophage phi29 DNA packaging nanomotor that is driven and geared by small RNA molecules termed packaging RNA or "pRNA". This nanomotor has been shown to play a novel and essential role in transporting phi29 genomic DNA into procapsids. As more progress is made in understanding the structure and mechanisms of these novel systems, it is time to evaluate these structures using bionanotechnology-based approaches and to explore the interface between these nanomotors and synthetic structures using top down and bottoms up fabrication technology to form active nanostructures and nanosystems. Our core platform will consist of the pRNA-driving motors anchored on nanoporous membranes on micromachined silicon or Alumina based membrane via a 2-dimensional self- assembled DNA crystal. The use of the DNA self assembled layer will ensure the integrity and functionality of the nanomotor. The development and characterization of this basic platform is a significant challenge in itself and requires a cohesive interdisciplinary approach. We will integrate the nanomotor in a hybrid silicon based device and demonstrate its operation, and then integrate the nanomotor without the capsid and demonstrate the translocation of dsDNA through the motor. Once these tasks are accomplished, it will be possible to investigate various technology modules such as active pumping surfaces within microfluidic channels, active sieving and filtration, and many other applications directly relevant to biology and medicine.