Recent advances and opportunities in synthetic logic gates engineering in living cells

Abstract

Recently, a number of synthetic biologic gates including AND, OR, NOR, NOT, XOR and NAND have been engineered and characterized in a wide range of hosts. The hope in the emerging synthetic biology community is to construct an inventory of well-characterized parts and install distinct gene and circuit behaviours that are externally controllable. Though the field is still growing and major successes are yet to emerge, the payoffs are predicted to be significant. In this review, we highlight specific examples of logic gates engineering with applications towards fundamental understanding of network complexity and generating a novel socially useful applications.

Designing miRNA-Based Synthetic Cell Classifier Circuits Using Answer Set Programming

“…Here, mathematical modeling is highly valuable for the design process because it allows the formalization of demands and the computation of optimal solutions within the design space (Teo et al, 2015 ; Mohammadi et al, 2017 ). Since many of the biological building blocks for synthetic circuits, and in particular classifiers, are geared toward steep response profiles to ensure robust performance and assembled as logic gates (Singh, 2014 ; Siuti et al, 2015 ), Boolean modeling approaches are well-suited for this task. However, the logical formalization often remains implicit and the computational capabilities within the Boolean framework remain largely unused (Xie et al, 2011 ; Moon et al, 2012 ; Mohammadi et al, 2017 ).…”

Exploring the Potential of Small Regulatory RNA towards Microbial Engineering

“…It is a good choice due to its ease of culture, short life cycle, well-known genetics and accessible tools. In recent years, a number of synthetic parts that include promoters [5,6], regulatory proteins and RNAs [7][8][9], devices and circuits such as riboregulators [7], riboswitches [10,11], biologic gates [12,13], and oscillators [14][15][16] have been designed and characterized in a wide range of hosts. These synthetic networks have been implemented for rewiring [17][18][19][20], the coupling [21] of intracellular networks, or manipulating the cellular functions at certain scales that can be further useful for tight, tunable or periodic biological production.…”

Challenges and Opportunities for Synthetic Biology in India

“…Later, Registry of Standard Biological Parts-MIT, USA (partsregistry.org) has established and standardized the genetic parts which are freely available to scientific community. In recent years, a number of synthetic genetic parts, device and circuit including promoter [4,5], regulatory proteins and RNAs [6][7][8][9][10], scaffolds [11], oscillators [2,[12][13][14], riboregulators [15][16][17][18], riboswitches [19,20], toggle switch [3] and biologic gates [21][22][23][24][25] that have been successfully engineered and characterized in a wide range of hosts including mammalians.…”