Poster abstracts
Poster number 70 submitted by Geneva LaForce
In-silico design and experimental validation of Boolean logic gates based on a fluorogenic RNA aptamer
Geneva R. LaForce (Department of Chemistry, Ball State University), Victoria R. Goldsworthy (Department of Chemistry, Ball State University), Dayna A. M. Arnett (Department of Chemistry, Ball State University), Emil F. Khisamutdinov (Department of Chemistry, Ball State University)
Abstract:
RNA aptamers that bind a non-fluorescent dye and activate its fluorescence are highly sensitive, non-perturbing, and convenient probes in the field of synthetic biology. These artificial aptamers operate as molecular nanoswitches that experience altered folding and function in response to ligand binding. We demonstrate a computational approach for designing smart RNA nanodevices based on a malachite green (MG) binding RNA aptamer in which fluorescent output is controlled by the binding of DNA oligonucleotide inputs. Four types of RNA switches, possessing AND, OR, XOR, and NAND Boolean logic functions, were created in modular form, allowing MG dye binding affinity to be changed without altering the RNA aptamer core sequence. All computationally designed RNA devices were synthesized and experimentally tested in vitro. The ability to design smart nanodevices based on RNA binding aptamers offers new ways to engineer ligand-sensing regulatory circuits, nucleic acid detection systems, gene control elements, and a promising complement to silicon technology.
Keywords: Boolean logic, RNA aptamers, nanodevice