In this project, we implement three basic RNA nanotechnology approaches to construct functional and robust RNA nanoparticles. (i) Computational approach includes in silico (computer-aided) design of RNA nanoobjects (2D and 3D geometries) using naturally occurring RNA building blocks. (ii) Experimental approach includes RNA synthesis, self-assembly, and structural characterization of the designed RNA nanoparticles. Lastly (iii), depending on the choice of application, these nanoparticles can be functionalized with various of biologically active compounds, used as a nanocontainers, utilized in construction of patterned arrays etc.
Bio-computing using Fluorogenic “Light-Up” RNA aptamers
The driving core of the fully operational computer system lies at the basis of Boolean logic gates and, therefore, to create a bio-computer one has to first generate biomolecular device possessing logic gate functons. Fluorogenic RNA and DNA aptamers are attractive candidates to fulfill this task due to their various light emitting properties and structural diversity.
In our lab, we implement secondary structure prediction algorithms to design and construct RNA and RNA/DNA complexes that are able to perform basic AND, OR, NOR, NAND logistic operations. Our goal is to achieve a nucleic acid based combinatorial logic system with unbiased emission output from a set of short oligonucleotide inputs.
Thermodynamics of RNA non-canonical interactions
Structures of large RNA molecules, such as the ribosomal RNAs (rRNA), have revealed that no more than ~70% of all basepairs are cis Watson-Crick (cWW) AU, GC, or GU pairs. The rest are non-WC basepairs, and together with base-stacking and base-backbone interactions, they form single-stranded regions of hairpin loops, internal loops, and multi-helix junctions, many of which are recurrent.
Multiple nucleotides are isosteric, indicating that basepairs can potentially substitute for each other while preserving the 3D structure of the overall motif. However, only limited information is available about the relative effects of isosteric vs. non-isosteric base substitutions on the thermodynamic stabilities of well-structured RNA 3D motifs. This project addresses fundamental questions regarding the thermodynamic and structural stability of native RNA molecules.
We want to thank our sponsors for funding our research projects:
Awards numbers R15EB031388-01 and R03EB027910
NSF MRI award number 2214573
BSU ASPiRE ADVANCE and Juniour Faculty Research programs
IAS award # 461-15