Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch (original) (raw)

Foundations for the design and implementation of synthetic genetic circuits

Nature Reviews Genetics, 2012

Synthetic gene circuits are designed to program new biological behaviour, dynamics and logic control. For all but the simplest synthetic phenotypes, this requires a structured approach to map the desired functionality to available molecular and cellular parts and processes. In other engineering disciplines, a formalized design process has greatly enhanced the scope and rate of success of projects. When engineering biological systems, a desired function must be achieved in a context that is incompletely known, is influenced by stochastic fluctuations and is capable of rich nonlinear interactions with the engineered circuitry. Here, we review progress in the provision and engineering of libraries of parts and devices, their composition into large systems and the emergence of a formal design process for synthetic biology.

Implementation of a genetic logic circuit: bio-register

Systems and synthetic biology, 2015

We introduce an idea of synthesizing a class of genetic registers based on the existing sequential biological circuits, which are composed of fundamental biological gates. In the renowned literature, biological gates and genetic oscillator have been unveiled and experimentally realized in recent years. These biological circuits have formed a basis for realizing a primitive biocomputer. In the traditional computer architecture, there is an intermediate load-store section, i.e. a register, which serves as a part of the digital processor. With which, the processor can load data from a larger memory into it and proceed to conduct necessary arithmetic or logic operations. Then, manipulated data are stored back to the memory by instruction via the register. We propose here a class of bio-registers for the biocomputer. Four types of register structures are presented. In silicon experiments illustrate results of the proposed design.

Engineering in the biological substrate: information processing in genetic circuits

Proceedings of the IEEE, 2000

We review the rapidly evolving efforts to analyze, model, simulate, and engineer genetic and biochemical information processing systems within living cells. We begin by showing that the fundamental elements of information processing in electronic and genetic systems are strikingly similar, and follow this theme through a review of efforts to create synthetic genetic circuits. In particular, we describe and review the "silicon mimetic" approach, where genetic circuits are engineered to mimic the functionality of semiconductor devices such as logic gates, latched circuits, and oscillators. This is followed with a review of the analysis, modeling, and simulation of natural and synthetic genetic circuits, which often proceed in a manner similar to that used for electronic systems. We conclude by presenting examples of naturally occurring genetic and biochemical systems that recently have been conceptualized in terms familiar to systems engineers. Our review of these newly forming fields of research demonstrates that the expertise and skills contained within electrical and computer engineering disciplines apply not only to design within biological systems, but also to the development of a deeper understanding of biological functionality. This review of these efforts points to the emergence of both engineering and basic science disciplines following parallel paths.

Realizing logic gates with time-delayed synthetic genetic networks

Nonlinear Dynamics, 2014

We demonstrate the realization of fundamental logic operations, as well as a memory element, with engineered delayed synthetic gene networks. Further, we investigate the effect of time delay in different kinds of processes, on the operational range of this biological logic gate. We show that this delay can either enhance or diminish logic behavior, depending on its functional form. Lastly, we show that the desired response to inputs can be induced, even in the absence of noise, by time delay alone.

Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology

Nature Communications, 2011

modular and orthogonal genetic logic gates are essential for building robust biologically based digital devices to customize cell signalling in synthetic biology. Here we constructed an orthogonal AnD gate in Escherichia coli using a novel hetero-regulation module from Pseudomonas syringae. The device comprises two co-activating genes hrpR and hrpS controlled by separate promoter inputs, and a σ 54 -dependent hrpL promoter driving the output. The hrpL promoter is activated only when both genes are expressed, generating digital-like AnD integration behaviour. The AnD gate is demonstrated to be modular by applying new regulated promoters to the inputs, and connecting the output to a noT gate module to produce a combinatorial nAnD gate. The circuits were assembled using a parts-based engineering approach of quantitative characterization, modelling, followed by construction and testing. The results show that new genetic logic devices can be engineered predictably from novel native orthogonal biological control elements using quantitatively in-context characterized parts.

Design of Asynchronous Genetic Circuits

Proceedings of the IEEE, 2019

Most digital electronic circuits utilize a timing reference to synchronize the progression of signals and enable sequential memory elements. These designs may not be realizable in biological substrates due to the lack of a reliable high frequency clock signal. Asynchronous designs eliminate the need for a clock with data encodings and request/acknowledge handshake protocols. This paper proposes a workflow to automate the design of asynchronous genetic circuits. This workflow extends genetic design tools by leveraging asynchronous logic design methods customized for this technology. This workflow is demonstrated on a genetic sensor that uses filtering and cellular communication to improve its reliability.

Engineering Gene Circuits: Foundations and Applications

Nanotechnology in Biology and Medicine, 2007

Synthetic biology has emerged as a useful approach to decoding fundamental laws underlying biological control. Recent efforts have produced many exciting systems and generated substantial insights. These progresses highlight the potential of synthetic biology to impact diverse areas including biology, computation, engineering, and medicine. 20.1 Introduction Biological systems often function reliably in diverse environments despite internal or external perturbations. This behavior is often characterized as ''robustness.'' Based on extensive studies over the last several decades, much of this robustness can be attributed to the control of gene expression through complex cellular networks [1-4]. These networks are known to consist of various regulatory modules, including feedback [5] and feed-forward [6] regulation and cell-cell communication [7]. With these basic regulatory modules and motifs, researchers are now constructing artificial networks that mimic nature to gain fundamental biological insight and understanding [8]. In addition, other artificial networks that are engineered with novel functions will serve as building blocks for future practical applications. These efforts form the foundation of the recent emergence of synthetic biology [3,9,10]. These artificial networks are interchangeably called ''synthetic gene circuits'' or ''engineered gene circuits.'' Recent accomplishments in synthetic biology include engineered switches [11-14], oscillators [15,16], logic gates [17-19], metabolic control [20], reengineered translational machinery [21], population control [22] and pattern formation [23] using natural or synthetic [24] cell-cell communication, reengineered viral genome [25], and hierarchically complex circuits built upon smaller, well-characterized

Genetic regulatory circuits: Advances toward a genetic circuit engineering

Genetic circuits can now be engineered that perform moderately complicated switching functions or exhibit predictable dynamical behavior. These "forward engineering" techniques may have to be combined with directed evolution techniques to produce robustness comparable with naturally occurring circuits or to meet perfo rmance specifications.

Design principles of transcriptional logic circuits

Using a set of genetic logic gates (AND, OR and XOR), we constructed a binary full-adder. The optimality analysis of the full-adder showed that, based on the position of the regulation threshold, the system displays different optimal configurations for speed and accuracy under fixed metabolic cost. In addition, the analysis identified an optimal trade-off curve bounded by these two optimal configurations. Any configuration outside this optimal trade-off curve is sub-optimal in both speed and accuracy. This type of analysis represents a useful tool for synthetic biologists to engineer faster, more accurate and cheaper genes.

Building blocks of a biochemical CPU based on DNA transcription logic

2004

In this paper we study the design of transcriptional logic based on quantitative models of cis-regulatory networks. Recent efforts in the area of synthetic biology have shown that logic gates can be implemented using the DNA transcriptional machinery of the cell. We show how to extend these previous results to the design of combinational and sequential circuits. The extension of our method to the design of sequential circuits is particularly attractive because they represent the most general class of circuits. As representative examples here we demonstrate the construction of a memory element and of a 1-bit ALU, two basic building blocks of a transcription-based biochemical CPU.