Secondary structure of very large RNAs via high-throughput oligonucleotide-binding microarrays

Nucleic acid hybridization underlies an extraordinary range of in vitro biological research (e.g. CRISPR, FISH, DNA origami) as well as in vivo biological regulation (e.g. miRNA, lncRNA). In principle, hybridization is straightforward: if two nucleic acids are complementary, they will hybridize. In practice, intramolecular nucleic acid structure must be disrupted in order for hybridization to proceed, and the energetic barriers involved can preclude hybridization from occurring on realistic timescales. I will describe how we use the non-equilibrium nature of RNA hybridization as a lens to examine the equilibrium structures of large RNA molecules. We designed microarrays containing DNA oligonucleotides (oligos) perfectly complementary to different regions of structured RNA. Oligos corresponding to regions with lower secondary structure are expected to typically bind at a higher frequency, but this behavior is complicated by the fact that each hybridization involves the interaction of many nucleotides. To address this challenge, we employ high dimensional gradient descent through automatic differentiation to find the best-fit structure to the data. I will describe results of this methodology on both short RNA molecules (<100 nucleotides) as well as long RNA (>1000 nucleotides).