Accelerated RNA Secondary Structure Design Using Pre-Selected Sequences for Helices and Loops

Abstract

Nanoscale nucleic acids can be designed to be nano-machines, pharmaceuticals, or probes for detecting pathogens and other molecules. RNA secondary structures can form the basis of self-assembling nanostructures. There are only four natural RNA bases, therefore it can be difficult to design sequences that fold to a single, specified structure because many other structures are often possible for a given sequence. One approach taken by state-of-the-art sequence design methods is to select sequences that fold to the specified input structure using stochastic, iterative refinement. The goal of this work is to accelerate design. Many existing iterative methods select and refine sequences one base pair and one unpaired nucleotide at a time. Here, the hypothesis that sequences can be preselected in order to accelerate design was tested. To this aim, a database was built of RNA helix sequences that demonstrate thermodynamic features found in natural sequences and that also have little tendency to cross-hybridize. The natural RNA sequences were observed to be composed of helices within an observed folding free energy range, with high probability of folding to the helix and also with low ensemble defect of helix formation. Additionally, a database was assembled of RNA loop sequences with low helix-formation propensity and little tendency to cross-hybridize with either the helices or other loops. These databases of pre-selected sequences accelerate the selection of sequences that fold with minimal ensemble defect [J Comput Chem. 2011. 32: 439] by replacing some of the trial and error of current refinement approaches. When using the database of pre-selected sequences as compared to randomly chosen sequences, sequences for natural structures are designed about 36 times faster, and random structures are designed about 6 times faster. The sequences selected with the aid of the database have similar ensemble defect as those sequences selected at random. The sequence database is part of RNAstructure package and can be downloaded from http://rna.urmc.rochester.edu/RNAstructure.html.