Thermodynamic and first-principles biomolecular simulations applied to synthetic biology: promoter and aptamer designs

Abstract

A major challenge in the field of metabolic engineering and synthetic biology is the design of DNA elements, most often promoters, that achieve precisely targeted levels of expression of a given protein. The most widely applied strategy for addressing this challenge includes making libraries of thousands of mutants, then screening and selecting each mutant in the hopes of finding a favorable change to the DNA of interest which yields the desired expression level. Even with rational approaches to the design of these mutants, this process is slow and labor-intensive and requires improvements in high throughput screening methods to improve discovery rates. Biomolecular models (designed from a combination of first-principles thermodynamics and empirical data) and solution of these models through simulation, bypass these approaches, enabling nucleotide and amino acid level resolution by carrying out screening processes in silico or allowing for a more rational method of design. This review examines recent advances in biomolecular simulations and methods of subsequent data analysis in their role of designing functional DNA, RNA, and protein elements. We provide an orienting introduction to design choices in biomolecular simulations then discuss major recent developments in simulation technology with a more intensive focus on promoter and aptamer design. We then conclude with both a forward-looking prospectus on the field as well as pitfalls and areas for further study.