A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction

AbstractSplit inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of extein junction sequences. To address this, we augment a mini-Mu transposon-based screening approach and devise the intein-assisted bisection mapping (IBM) method. IBM robustly reveals clusters of split sites on five proteins, converting them into AND or NAND logic gates. We further show that the use of inteins expands functional sequence space for splitting a protein. We also demonstrate the utility of our approach over rational inference of split sites from secondary structure alignment of homologous proteins, and that basal activities of highly active proteins can be mitigated by splitting them. Our work offers a generalizable and systematic route towards creating split protein-intein fusions for synthetic biology.

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Intein-assisted bisection mapping systematically splits proteins for Boolean logic and inducibility engineering

10.1101/2020.11.30.381921 ◽

2020 ◽

Author(s):

Trevor Y. H. Ho ◽

Alexander Shao ◽

Zeyu Lu ◽

Harri Savilahti ◽

Filippo Menolascina ◽

...

Keyword(s):

Protein Function ◽

Logic Gates ◽

Identification Problem ◽

Boolean Logic ◽

Host Protein ◽

Structure Alignment ◽

Protein Activity ◽

Homologous Proteins ◽

Split Protein ◽

Rational Inference

AbstractSplit inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of extein junction sequences. To address this, we augmented a mini-Mu transposon-based screening approach and devised the intein-assisted bisection mapping (IBM) method. IBM robustly revealed clusters of split sites on five proteins, converting them into AND or NAND logic gates. We further showed that the use of inteins expands functional sequence space for splitting a protein. We also demonstrated the utility of our approach over rational inference of split sites from secondary structure alignment of homologous proteins. Furthermore, the intein inserted at an identified site could be engineered by the transposon again to become partially chemically inducible, and to some extent enabled post-translational tuning on host protein function. Our work offers a generalizable and systematic route towards creating split protein-intein fusions and conditional inteins for protein activity control.

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High Speed All-Optical Logic Gate Using QD-SOA and its Application

10.20944/preprints201706.0101.v1 ◽

2017 ◽

Author(s):

Shuai Zhao ◽

Hongyu Hu

Keyword(s):

High Speed ◽

Logic Gate ◽

Logic Gates ◽

Boolean Logic ◽

Hole Burning ◽

Spectral Hole Burning ◽

Optical Logic ◽

Carrier Heating ◽

Optical Logic Gates ◽

All Optical

The scheme to realize high speed (~250Gb/s) all-optical Boolean logic gates using semiconductor optica amplifiers with quantum-dot (QD-SOA) is introduced and analyzed in this review. Numerical simulation method was presented by solving the rate equation and taking into account nonlinear dynamics including carrier heating and spectral hole-burning. Binary phase shift keyed (BPSK) signal and on-off keyed signal are used to generate high speed all-optical logic gates. The applications based on all-optical logic gates such as, all-optical latches, pseudo random bit sequence (PRBS) generation and all-optical encryption, are also discussed in this review. Results show that the scheme based on QD-SOA is a promising method for the realization of high speed all-optical communication system in the future.

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Engineering the Stability of Nanozyme-Catalyzed Product for Colorimetric Logic Gate Operations

Molecules ◽

10.3390/molecules26216494 ◽

2021 ◽

Vol 26 (21) ◽

pp. 6494

Author(s):

Lianlian Fu ◽

Deshuai Yu ◽

Dijuan Zou ◽

Hao Qian ◽

Youhui Lin

Keyword(s):

Glucose Oxidase ◽

Xanthine Oxidase ◽

Color Change ◽

Logic Gate ◽

Logic Gates ◽

Boolean Logic ◽

Blue Color ◽

Push Forward ◽

Logic Operations ◽

The Stability

Recently, the design and development of nanozyme-based logic gates have received much attention. In this work, by engineering the stability of the nanozyme-catalyzed product, we demonstrated that the chromogenic system of 3, 3′, 5, 5′-tetramethylbenzidine (TMB) can act as a visual output signal for constructing various Boolean logic operations. Specifically, cerium oxide or ferroferric oxide-based nanozymes can catalyze the oxidation of colorless TMB to a blue color product (oxTMB). The blue-colored solution of oxTMB could become colorless by some reductants, including the reduced transition state of glucose oxidase and xanthine oxidase. As a result, by combining biocatalytic reactions, the color change of oxTMB could be controlled logically. In our logic systems, glucose oxidase, β-galactosidase, and xanthine oxidase acted as inputs, and the state of oxTMB solution was used as an output. The logic operation produced a colored solution as the readout signal, which was easily distinguished with the naked eye. More importantly, the study of such a decolorization process allows the transformation of previously designed AND and OR logic gates into NAND and NOR gates. We propose that this work may push forward the design of novel nanozyme-based biological gates and help us further understand complex physiological pathways in living systems.

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Contextual dependencies expand the re-usability of genetic inverters

10.1101/2020.07.15.204651 ◽

2020 ◽

Author(s):

Huseyin Tas ◽

Lewis Grozinger ◽

Ruud Stoof ◽

Victor de Lorenzo ◽

Angel Goñi-Moreno

Keyword(s):

Synthetic Biology ◽

Computational Analysis ◽

Logic Gate ◽

Logic Gates ◽

Boolean Logic ◽

Regulatory Proteins ◽

Genetic Circuits ◽

Genetic Construct ◽

Genetic Components ◽

Logic Functions

The design and implementation of Boolean logic functions in living cells has become a very active field within synthetic biology. By controlling networks of regulatory proteins, novel genetic circuits are engineered to generate predefined output responses. Although many current implementations focus solely on the genetic components of the circuit, the host context in which the circuit performs is crucial for its outcome. Here, we characterise 20 genetic NOT logic gates (inverters) in up to 7 bacterial-based contexts each, to finally generate 135 different functions. The contexts we focus on are particular combinations of four plasmid backbones and three hosts, two Escherichia coli and one Pseudomonas putida strains. Each NOT logic gate shows seven different logic behaviours, depending on the context. That is, gates can be reconfigured to fit response requirements by changing only contextual parameters. Computational analysis shows that this range of behaviours improves the compatibility between gates, because there are considerably more possibilities for combination than when considering a unique function per genetic construct. Finally, we address the issue of interoperability and portability by measuring, scoring, and comparing gate performance across contexts. Rather than being a limitation, we argue that the effect of the genetic background on synthetic constructs expand the scope of the functions that can be engineered in complex cellular environments, and advocate for considering context as a fundamental design parameter for synthetic biology.

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Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria

eLife ◽

10.7554/elife.33908 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 22

Author(s):

Madeline E Sherlock ◽

Narasimhan Sudarsan ◽

Shira Stav ◽

Ronald R Breaker

Keyword(s):

De Novo ◽

Rna World ◽

Logic Gate ◽

Logic Gates ◽

Boolean Logic ◽

Control Synthesis ◽

Messenger Rnas ◽

Phosphoribosyl Pyrophosphate ◽

Rna Molecules ◽

Regulatory Systems

Gene control systems sometimes interpret multiple signals to set the expression levels of the genes they regulate. In rare instances, ligand-binding riboswitch aptamers form tandem arrangements to approximate the function of specific two-input Boolean logic gates. Here, we report the discovery of riboswitch aptamers for phosphoribosyl pyrophosphate (PRPP) that naturally exist either in singlet arrangements, or occur in tandem with guanine aptamers. Tandem guanine-PRPP aptamers can bind the target ligands, either independently or in combination, to approximate the function expected for an IMPLY Boolean logic gate to regulate transcription of messenger RNAs for de novo purine biosynthesis in bacteria. The existence of sophisticated all-RNA regulatory systems that sense two ancient ribonucleotide derivatives to control synthesis of RNA molecules supports the hypothesis that RNA World organisms could have managed a complex metabolic state without the assistance of protein regulatory factors.

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Nano-bio-computing lipid nanotablet

Science Advances ◽

10.1126/sciadv.aau2124 ◽

2019 ◽

Vol 5 (2) ◽

pp. eaau2124 ◽

Cited By ~ 10

Author(s):

Jinyoung Seo ◽

Sungi Kim ◽

Ha H. Park ◽

Da Yeon Choi ◽

Jwa-Min Nam

Keyword(s):

Lipid Bilayer ◽

Logic Gate ◽

Logic Gates ◽

Boolean Logic ◽

Circuit Board ◽

Particle Assembly ◽

Supported Lipid Bilayer ◽

Particle Level ◽

Logic Operations ◽

And Control

Using nanoparticles as substrates for computation enables algorithmic and autonomous controls of their unique and beneficial properties. However, scalable architecture for nanoparticle-based computing systems is lacking. Here, we report a platform for constructing nanoparticle logic gates and circuits at the single-particle level on a supported lipid bilayer. Our “lipid nanotablet” platform, inspired by cellular membranes that are exploited to compartmentalize and control signaling networks, uses a lipid bilayer as a chemical circuit board and nanoparticles as computational units. On a lipid nanotablet, a single-nanoparticle logic gate senses molecules in solution as inputs and triggers particle assembly or disassembly as an output. We demonstrate a set of Boolean logic operations, fan-in/fan-out of logic gates, and a combinational logic circuit such as a multiplexer. We envisage that our approach to modularly implement nanoparticle circuits on a lipid bilayer will create new paradigms and opportunities in molecular computing, nanoparticle circuits, and systems nanoscience.

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ORGANIC MEMRISTOR DEVICES FOR LOGIC ELEMENTS WITH MEMORY

International Journal of Bifurcation and Chaos ◽

10.1142/s0218127412502835 ◽

2012 ◽

Vol 22 (11) ◽

pp. 1250283 ◽

Cited By ~ 31

Author(s):

VICTOR EROKHIN ◽

GERARD DAVID HOWARD ◽

ANDREW ADAMATZKY

Keyword(s):

Low Power ◽

Logic Gate ◽

Logic Gates ◽

Full Adder ◽

Experimental Results ◽

Boolean Logic ◽

Next Generation ◽

Nanoscale Fabrication ◽

Thresholding Function ◽

With Memory

Memristors are promising next-generation memory candidates that are nonvolatile, possess low power requirements and are capable of nanoscale fabrication. In this article, we physically realize and describe the use of organic memristors in designing stateful boolean logic gates for the AND OR and NOT operations. The output of these gates is analog and dependent on the length of time that suitable charge is applied to the inputs, displaying a learning property. Results may be also interpreted in a traditional binary manner through the use of a suitable thresholding function at the output. The memristive property of the gate allows for the production of analog outputs that vary based on the charge-dependent nonvolatile state of the memristor. We provide experimental results of physical fabrication of three types of logic gate. A simulation of a one-bit full adder comprised of memristive logic gates is also included, displaying varying response to two distinct input patterns.

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An error-resilient non-volatile magneto-elastic universal logic gate with ultralow energy-delay product

Scientific Reports ◽

10.1038/srep07553 ◽

2014 ◽

Vol 4 (1) ◽

Cited By ~ 16

Author(s):

Ayan K. Biswas ◽

Jayasimha Atulasimha ◽

Supriyo Bandyopadhyay

Keyword(s):

Logic Gate ◽

Error Resilience ◽

Logic Gates ◽

Error Rates ◽

Boolean Logic ◽

Digital Information ◽

Universal Logic ◽

Nanomagnetic Logic ◽

Ultralow Energy ◽

Energy Delay Product

Abstract A long-standing goal of computer technology is to process and store digital information with the same device in order to implement new architectures. One way to accomplish this is to use nanomagnetic logic gates that can perform Boolean operations and then store the output data in the magnetization states of nanomagnets, thereby doubling as both logic and memory. Unfortunately, many of these nanomagnetic devices do not possess the seven essential characteristics of a Boolean logic gate : concatenability, non-linearity, isolation between input and output, gain, universal logic implementation, scalability and error resilience. More importantly, their energy-delay products and error rates tend to vastly exceed that of conventional transistor-based logic gates, which is unacceptable. Here, we propose a non-volatile voltage-controlled nanomagnetic logic gate that possesses all the necessary characteristics of a logic gate and whose energy-delay product is two orders of magnitude less than that of other nanomagnetic (non-volatile) logic gates. The error rate is also superior.

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Digital logic gates in soft, conductive mechanical metamaterials

Nature Communications ◽

10.1038/s41467-021-21920-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Charles El Helou ◽

Philip R. Buskohl ◽

Christopher E. Tabor ◽

Ryan L. Harne

Keyword(s):

Integrated Circuits ◽

Electronic Materials ◽

Polymer Networks ◽

Conductive Polymer ◽

Network Connectivity ◽

Logic Gates ◽

Boolean Logic ◽

Digital Logic ◽

Mechanical Metamaterials ◽

Logic Operations

AbstractIntegrated circuits utilize networked logic gates to compute Boolean logic operations that are the foundation of modern computation and electronics. With the emergence of flexible electronic materials and devices, an opportunity exists to formulate digital logic from compliant, conductive materials. Here, we introduce a general method of leveraging cellular, mechanical metamaterials composed of conductive polymers to realize all digital logic gates and gate assemblies. We establish a method for applying conductive polymer networks to metamaterial constituents and correlate mechanical buckling modes with network connectivity. With this foundation, each of the conventional logic gates is realized in an equivalent mechanical metamaterial, leading to soft, conductive matter that thinks about applied mechanical stress. These findings may advance the growing fields of soft robotics and smart mechanical matter, and may be leveraged across length scales and physics.

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Glutathione disulfide-sensitive Janus nanomachine controlled by an enzymatic AND logic gate for smart delivery

Nanoscale ◽

10.1039/d0nr08282a ◽

2021 ◽

Author(s):

Beatriz Mayol ◽

Paula Diez ◽

Alfredo Sánchez ◽

Cristina De La Torre Paredes ◽

Anabel Villalonga ◽

...

Keyword(s):

Mesoporous Silica ◽

Logic Gate ◽

Boolean Logic ◽

Glutathione Disulfide ◽

Janus Nanoparticles

This work describes the assembly of a novel enzyme-controlled nanomachine operated through an AND Boolean logic gate for on-command delivery. The nanodevice was constructed on Au-mesoporous silica Janus nanoparticles capped...

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