通过组合约束规范进行基因设计

Genetic Design via Combinatorial Constraint Specification.

作者信息

Bhatia Swapnil P, Smanski Michael J, Voigt Christopher A, Densmore Douglas M

机构信息

Biological Design Center, Department of Electrical and Computer Engineering, Boston University , Boston, Massachusetts 02215, United States.

Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota , St Paul, Minnesota 55108, United States.

出版信息

ACS Synth Biol. 2017 Nov 17;6(11):2130-2135. doi: 10.1021/acssynbio.7b00154. Epub 2017 Oct 4.

DOI:10.1021/acssynbio.7b00154

PMID:28874044

Abstract

We present a formal language for specifying via constraints a "design space" of DNA constructs composed of genetic parts, and an algorithm for automatically and correctly creating a novel representation of the space of satisfying designs. The language is simple, captures a large class of design spaces, and possesses algorithms for common operations on design spaces. The flexibility of this approach is demonstrated using a 16-gene nitrogen fixation pathway and genetic logic circuits.

摘要

我们提出了一种形式语言，用于通过约束来指定由基因元件组成的DNA构建体的“设计空间”，以及一种用于自动且正确地创建满足设计空间的新颖表示的算法。该语言简单，涵盖了一大类设计空间，并拥有用于设计空间常见操作的算法。使用16基因固氮途径和遗传逻辑电路展示了这种方法的灵活性。