Evolving methods for rational de novo design of functional RNA molecules

Partial RNA design

MOTIVATION

RNA design is a key technique to achieve new functionality in fields like synthetic biology or biotechnology. Computational tools could help to find such RNA sequences but they are often limited in their formulation of the search space.

RESULTS

In this work, we propose partial RNA design, a novel RNA design paradigm that addresses the limitations of current RNA design formulations. Partial RNA design describes the problem of designing RNAs from arbitrary RNA sequences and structure motifs with multiple design goals. By separating the design space from the objectives, our formulation enables the design of RNAs with variable lengths and desired properties, while still allowing precise control over sequence and structure constraints at individual positions. Based on this formulation, we introduce a new algorithm, libLEARNA, capable of efficiently solving different constraint RNA design tasks. A comprehensive analysis of various problems, including a realistic riboswitch design task, reveals the outstanding performance of libLEARNA and its robustness.

AVAILABILITY AND IMPLEMENTATION

libLEARNA is open-source and publicly available at: https://github.com/automl/learna_tools.

Developing Complex RNA Design Applications in the Infrared Framework

Applications in biotechnology and bio-medical research call for effective strategies to design novel RNAs with very specific properties. Such advanced design tasks require support by computational tools but at the same time put high demands on their flexibility and expressivity to model the application-specific requirements. To address such demands, we present the computational framework Infrared. It supports developing advanced customized design tools, which generate RNA sequences with specific properties, often in a few lines of Python code. This text guides the reader in tutorial format through the development of complex design applications. Thanks to the declarative, compositional approach of Infrared, we can describe this development as a step-by-step extension of an elementary design task. Thus, we start with generating sequences that are compatible with a single RNA structure and go all the way to RNA design targeting complex positive and negative design objectives with respect to single or even multiple target structures. Finally, we present a "real-world" application of computational design to create an RNA device for biotechnology: we use Infrared to generate design candidates of an artificial "AND" riboswitch, which activates gene expression in the simultaneous presence of two different small metabolites. In these applications, we exploit that the system can generate, in an efficient (fixed-parameter tractable) way, multiple diverse designs that satisfy a number of constraints and have high quality w.r.t. to an objective (by sampling from a Boltzmann distribution).

Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch

We describe a synthetic riboswitch element that implements a regulatory principle which directly addresses an essential tRNA maturation step. Constructed using a rational in silico design approach, this riboswitch regulates RNase P-catalyzed tRNA 5′-processing by either sequestering or exposing the single-stranded 5′-leader region of the tRNA precursor in response to a ligand. A single base pair in the 5′-leader defines the regulatory potential of the riboswitch both in vitro and in vivo. Our data provide proof for prior postulates on the importance of the structure of the leader region for tRNA maturation. We demonstrate that computational predictions of ligand-dependent structural rearrangements can address individual maturation steps of stable non-coding RNAs, thus making them amenable as promising target for regulatory devices that can be used as functional building blocks in synthetic biology.