title: Develop reusable and combinable designs for transcriptional logic gates.
abstract: One limit on developing complex synthetic gene circuits is the lack of basic components such as transcriptional logic gates that can process combinatorial inputs. Here, we propose a strategy to construct such components based on reusable designs and convergent reengineering of well-studied natural systems. We demonstrated the strategy using variants of the transcription factor (TF) LacI and operator Olac that form specifically interacting pairs. Guided by a mathematical model derived from existing quantitative knowledge, rational designs of transcriptional NAND, NOR and NOT gates have been realized. The NAND gates have been designed based on direct protein-protein interactions in coupling with DNA looping. We demonstrated that the designs are reusable: a multiplex of logic devices can be readily created using the same designs but different combinations of sequence variants. The designed logic gates are combinable to form compound circuits: a demonstration logic circuit containing all three types of designed logic gates has been synthesized, and the circuit truthfully reproduces the pre-designed input-output logic relations.
authors.affiliation: School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Zhan
authors.forename: Bo
authors.initials: B
authors.lastname: Ding
authors.forename: Rui
authors.initials: R
authors.lastname: Ma
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Ma
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Su
authors.forename: Yun
authors.initials: Y
authors.lastname: Zhao
authors.forename: Ziqing
authors.initials: Z
authors.lastname: Liu
authors.forename: Jiarui
authors.initials: J
authors.lastname: Wu
authors.forename: Haiyan
authors.initials: H
authors.lastname: Liu
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D017076:Computer-Aided Design; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004581:Electronics / Q000295:instrumentation; D004926:Escherichia coli; D053263:Gene Regulatory Networks; D007763:Lac Operon / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009875:Operator Regions, Genetic; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D049490:Systems Biology / Q000379:methods*; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
chemical_list: D011506:Proteins; D014157:Transcription Factors; D004247:DNA