title: RNA nanotechnology for computer design and in vivo computation.
abstract: Molecular-scale computing has been explored since 1989 owing to the foreseeable limitation of Moore's law for silicon-based computation devices. With the potential of massive parallelism, low energy consumption and capability of working in vivo, molecular-scale computing promises a new computational paradigm. Inspired by the concepts from the electronic computer, DNA computing has realized basic Boolean functions and has progressed into multi-layered circuits. Recently, RNA nanotechnology has emerged as an alternative approach. Owing to the newly discovered thermodynamic stability of a special RNA motif (Shu et al. 2011 Nat. Nanotechnol. 6, 658-667 (doi:10.1038/nnano.2011.105)), RNA nanoparticles are emerging as another promising medium for nanodevice and nanomedicine as well as molecular-scale computing. Like DNA, RNA sequences can be designed to form desired secondary structures in a straightforward manner, but RNA is structurally more versatile and more thermodynamically stable owing to its non-canonical base-pairing, tertiary interactions and base-stacking property. A 90-nucleotide RNA can exhibit 4⁹⁰ nanostructures, and its loops and tertiary architecture can serve as a mounting dovetail that eliminates the need for external linking dowels. Its enzymatic and fluorogenic activity creates diversity in computational design. Varieties of small RNA can work cooperatively, synergistically or antagonistically to carry out computational logic circuits. The riboswitch and enzymatic ribozyme activities and its special in vivo attributes offer a great potential for in vivo computation. Unique features in transcription, termination, self-assembly, self-processing and acid resistance enable in vivo production of RNA nanoparticles that harbour various regulators for intracellular manipulation. With all these advantages, RNA computation is promising, but it is still in its infancy. Many challenges still exist. Collaborations between RNA nanotechnologists and computer scientists are necessary to advance this nascent technology.
authors.affiliation: Department of Computer Engineering, San Jose State University, , San Jose, CA 95192, USA.
authors.forename: Meikang
authors.initials: M
authors.lastname: Qiu
authors.forename: Emil
authors.initials: E
authors.lastname: Khisamutdinov
authors.forename: Zhengyi
authors.initials: Z
authors.lastname: Zhao
authors.forename: Cheryl
authors.initials: C
authors.lastname: Pan
authors.forename: Jeong-Woo
authors.initials: JW
authors.lastname: Choi
authors.forename: Neocles B
authors.initials: NB
authors.lastname: Leontis
authors.forename: Peixuan
authors.initials: P
authors.lastname: Guo
mesh_terms: D039301:Computers, Molecular / Q000639:trends*; D005812:Genes, Switch / Q000235:genetics*; D036103:Nanotechnology / Q000639:trends*; D012313:RNA / Q000737:chemistry* / Q000235:genetics*; D012815:Signal Processing, Computer-Assisted
chemical_list: D012313:RNA
keywords: RNA computation; RNA nanoparticles; RNA nanostructure; computer; molecular-scale computing; nanobiotechnology