Domain-Specific Programming Languages for Computational Nucleic Acid Systems

Abstract

The construction of models of system behavior is of great importance throughout science and engineering. In bioengineering and bionanotechnology, these often take the form of dynamic models that specify the evolution of different species over time. To ensure that scientific observations and conclusions are consistent and that systems can be reliably engineered on the basis of model predictions, it is important that models of biomolecular systems can be constructed in a reliable, principled, and efficient manner. This review focuses on efforts to address this need by using domain-specific programming languages as the basis for custom design tools for researchers working on computational nucleic acid devices, where a domain-specific language is simply a programming language tailored to a particular application domain. The underlying thesis of our review is that there is a continuum of practical implementation strategies for computational nucleic acid systems, which can all benefit from appropriate domain-specific languages and software design tools. We emphasize the need for specialized yet flexible tools that can be realized using domain-specific languages that compile to more general-purpose representations.

Evaluating the effect of ionic strength on PNA:DNA duplex formation kinetics

“…This has led to uses in many applications ranging from therapeutics and diagnostics to materials and programming. [1][2][3][4] However, these applications remain limited by the propensity of naturally occurring DNA and RNA for chemical and biological degradation, for example by nucleases present in biological systems. To mitigate this issue, researchers have attempted to improve the stability of natural nucleic acids through substitutions or modifications of the native phosphodiester and sugar backbone.…”

Chemical Reaction Networks’ Programming for Solving Equations

“…An important issue is abstracting the basic reaction module [4] and controlling the calculation order [5][6][7]. Excellent work has been performed in the realization of computing and programmability [8][9][10][11][12][13]. Based on the characteristics of different molecules, people have developed a system that can realize logic operations [14][15][16][17] and a calculation model with reprogrammable execution algorithms [18].…”

Amphiphilic DNA nanostructures for bottom-up synthetic biology

“…By affording unprecedented control over the shape 11 , interactions 12,13 , and mechanical properties of nanostructures 14 , the DNA origami technology has opened further new avenues for the field, with concrete applications to biomolecular scaffolding [15][16][17] , single-molecule analysis 18,19 , biosensing 20 , nanomedicine 21 , imaging 22 , and the construction of advanced materials 23,24 . In parallel to structural control, our growing understanding of nucleic acid kinetics and thermodynamics has resulted in the ability to program dynamic responses 25 , marking the advent of DNA-based molecular computing [26][27][28] and the development of proof-of-concept actuable nanodevices 29,30 , biosensors 31,32 , and technologies for optical imaging [33][34][35][36][37] .…”