scholarly journals Transcriptional interference in toehold switch-based RNA circuits

2021 ◽  
Author(s):  
Elisabeth Falgenhauer ◽  
Andrea Mückl ◽  
Matthaeus Schwarz-Schilling ◽  
Friedrich C Simmel
Keyword(s):  
Antisense Transcription ◽  
Genetic Circuit ◽  
Transcriptional Interference ◽  
Reporter Protein ◽  
Xor Gate ◽  
Inducible Promoters ◽  
Regulatory Circuits ◽  
Close Proximity ◽  
Exclusive Or ◽  
Design Options

Gene regulation based on regulatory RNA is an important mechanism in cells and is increasingly used for regulatory circuits in synthetic biology. Toehold switches are rationally designed post-transcriptional riboregulators placed in the 5' untranslated region of mRNA molecules. In the inactive state of a toehold switch, the ribosome-binding site is inaccessible for the ribosome. In the presence of a trigger RNA molecule protein production is turned on. Using antisense RNA against trigger molecules (anti-trigger RNA), gene expression can also be switched off again. We here study the utility and regulatory effect of antisense transcription in this context, which enables a particularly compact circuit design. Our circuits utilize two inducible promoters that separately regulate trigger and anti-trigger transcription, whereas their cognate toehold switch, regulating expression of a reporter protein, is transcribed from a constitutive promoter. We explore various design options for the arrangement of the promoters and demonstrate that the resulting dynamic behavior is strongly influenced by transcriptional interference (TI) effects, leading to more than four-fold differences in expression levels. Our experimental results are consistent with previous findings that enhanced local RNA polymerase concentrations due to active promoters in close proximity lead to an increase in transcriptional activity of the strongest promoter in the circuits. Based on this insight, we selected optimum promoter designs and arrangements for the realization of a genetic circuit comprised of two toehold switches, two triggers and two anti-triggers that function as a post-transcriptional RNA regulatory exclusive OR (XOR) gate.

scholarly journals A New XOR Structure Based on Resonant-Tunneling High Electron Mobility Transistor

VLSI Design ◽  
2009 ◽  
Vol 2009 ◽  
pp. 1-9 ◽  
Author(s):  
Mohammad Javad Sharifi ◽  
Davoud Bahrepour
Keyword(s):  
Electron Mobility ◽  
Resonant Tunneling ◽  
High Performance ◽  
High Electron Mobility Transistor ◽  
High Electron ◽  
Xor Gate ◽  
High Electron Mobility ◽  
Existing Structures ◽  
Input And Output ◽  
Exclusive Or

A new structure for an exclusive-OR (XOR) gate based on the resonant-tunneling high electron mobility transistor (RTHEMT) is introduced which comprises only an RTHEMT and two FETs. Calculations are done by utilizing a new subcircuit model for simulating the RTHEMT in the SPICE simulator. Details of the design, input, and output values and margins, delay of each transition, maximum operating frequency, static and dynamic power dissipations of the new structure are discussed and calculated and the performance is compared with other XOR gates which confirm that the presented structure has a high performance. Furthermore, to the best of authors' knowledge, it has the least component count in comparison to the existing structures.

scholarly journals Antisense lncRNA transcription drives stochastic Protocadherin α promoter choice

2018 ◽  
Author(s):  
Daniele Canzio ◽  
Chiamaka L. Nwakeze ◽  
Adan Horta ◽  
Sandy M. Rajkumar ◽  
Eliot L. Coffey ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Neural Circuit ◽  
Antisense Transcription ◽  
Dna Demethylation ◽  
Ctcf Binding ◽  
Gene Promoters ◽  
Protein Coding ◽  
Close Proximity ◽  
A Cell

SUMMARYStochastic and combinatorial activation of clustered Protocadherin (Pcdh) α, β, and γ gene promoters generates a cell-surface identity code in individual neurons that functions in neural circuit assembly. Here we show that Pcdhα promoter choice requires transcription of a long noncoding RNA (lncRNA) initiated from newly identified promoters located in the protein coding sequence of each Pcdhα exon. Antisense transcription of the lncRNA through the sense promoter results in its activation and in DNA demethylation of the binding sites for the CCCTC-binding protein, CTCF, located in close proximity to both sense and antisense promoters. Increased CTCF binding promotes the assembly of long-range DNA contacts between the activated promoter and a neuron-specific enhancer, thus locking in the epigenetic state of the stochastically chosen Pcdhα promoter. Examination of this hierarchical molecular mechanism in differentiating olfactory sensory neurons, suggests that antisense Pcdhα transcription is a key prerequisite for stochastic Pcdhα promoter choice in vivo.

InGaAsP/InP optoelectronic exclusive-OR (XOR) gate operating with optical inputs and outputs

1991 ◽  
Vol 3 (11) ◽  
pp. 1013-1015 ◽  
Author(s):  
H. Adachi ◽  
K. Matsuda ◽  
T. Chino ◽  
J. Shibata
Keyword(s):  
Xor Gate ◽  
Exclusive Or ◽  
Inputs And Outputs

scholarly journals Design and evaluation of an incoherent feed-forward loop for an arsenic biosensor based on standard iGEM parts

2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Federico Barone ◽  
Francisco Dorr ◽  
Luciano E Marasco ◽  
Sebastián Mildiner ◽  
Inés L Patop ◽  
...  
Keyword(s):  
Inorganic Arsenic ◽  
Output Pulse ◽  
Genetic Circuit ◽  
Reporter Protein ◽  
Independent Manner ◽  
Feed Forward ◽  
Feed Forward Loop ◽  
Worldwide Distribution ◽  
Scientific Results ◽  
System Designs

Abstract The diversity and flexibility of life offers a wide variety of molecules and systems useful for biosensing. A biosensor device should be robust, specific and reliable. Inorganic arsenic is a highly toxic water contaminant with worldwide distribution that poses a threat to public health. With the goal of developing an arsenic biosensor, we designed an incoherent feed-forward loop (I-FFL) genetic circuit to correlate its output pulse with the input signal in a relatively time-independent manner. The system was conceived exclusively based on the available BioBricks in the iGEM Registry of Standard Biological Parts. The expected behavior in silico was achieved; upon arsenic addition, the system generates a short-delayed reporter protein pulse that is dose dependent to the contaminant levels. This work is an example of the power and variety of the iGEM Registry of Standard Biological Parts, which can be reused in different sophisticated system designs like I-FFLs. Besides the scientific results, one of the main impacts of this synthetic biology project is the influence it had on team’s members training and career choices which are summarized at the end of this article.

scholarly journals Transcription mediated insulation and interference direct gene cluster expression switches

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Tania Nguyen ◽  
Harry Fischl ◽  
Françoise S Howe ◽  
Ronja Woloszczuk ◽  
Ana Serra Barros ◽  
...  
Keyword(s):  
Carbon Sources ◽  
Gene Clusters ◽  
Antisense Transcription ◽  
Regulation Of Transcription ◽  
Transcript Analysis ◽  
Transcriptional Interference ◽  
State Switching ◽  
Direct Gene ◽  
Reciprocal Expression ◽  
Metabolic Cycle

In yeast, many tandemly arranged genes show peak expression in different phases of the metabolic cycle (YMC) or in different carbon sources, indicative of regulation by a bi-modal switch, but it is not clear how these switches are controlled. Using native elongating transcript analysis (NET-seq), we show that transcription itself is a component of bi-modal switches, facilitating reciprocal expression in gene clusters. HMS2, encoding a growth-regulated transcription factor, switches between sense- or antisense-dominant states that also coordinate up- and down-regulation of transcription at neighbouring genes. Engineering HMS2 reveals alternative mono-, di- or tri-cistronic and antisense transcription units (TUs), using different promoter and terminator combinations, that underlie state-switching. Promoters or terminators are excluded from functional TUs by read-through transcriptional interference, while antisense TUs insulate downstream genes from interference. We propose that the balance of transcriptional insulation and interference at gene clusters facilitates gene expression switches during intracellular and extracellular environmental change.

Design of reversible Feynman and double Feynman gates in quantum-dot cellular automata nanotechnology

Circuit World ◽  
2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Sadat Riyaz ◽  
Vijay Kumar Sharma
Keyword(s):  
Cellular Automata ◽  
Quantum Dot ◽  
Cell Count ◽  
High Speed ◽  
Xor Gate ◽  
Content Type ◽  
Quantum Dot Cellular Automata ◽  
Logical Operations ◽  
Feynman Gate ◽  
Exclusive Or

Purpose This paper aims to propose the reversible Feynman and double Feynman gates using quantum-dot cellular automata (QCA) nanotechnology with minimum QCA cells and latency which minimizes the circuit area with the more energy efficiency. Design/methodology/approach The core aim of the QCA nanotechnology is to build the high-speed, energy efficient and as much smaller devices as possible. This brings a challenge for the designers to construct the designs that fulfill the requirements as demanded. This paper proposed a new exclusive-OR (XOR) gate which is then used to implement the logical operations of the reversible Feynman and double Feynman gates using QCA nanotechnology. Findings QCA designer-E has been used for the QCA designs and the simulation results. The proposed QCA designs have less latency, occupy less area and have lesser cell count as compared to the existing ones. Originality/value The latencies of the proposed gates are 0.25 which are improved by 50% as compared to the best available design as reported in the literature. The cell count in the proposed XOR gate is 11, while it is 14 in Feynman gate and 27 in double Feynman gate. The cell count for the proposed designs is minimum as compared to the best available designs.

scholarly journals New Proposal for MCML Based Three-Input Logic Implementation

VLSI Design ◽  
2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Neeta Pandey ◽  
Kirti Gupta ◽  
Bharat Choudhary
Keyword(s):  
Current Mode ◽  
Cmos Technology ◽  
Theoretical Concept ◽  
Logic Function ◽  
Circuit Element ◽  
Worst Case ◽  
Xor Gate ◽  
Static Power ◽  
Digital System Design ◽  
Exclusive Or

This paper presents a new proposal for three-input logic function implementation in MOS current mode logic (MCML) style. The conventional realization of such logic employs three levels of stacked source-coupled transistor pairs. It puts restriction on minimum power supply requirement and results in increased static power. The new proposal presents a circuit element named as quad-tail cell which reduces number of stacked source-coupled transistor levels by two. A three-input exclusive-OR (XOR) gate, a vital element in digital system design, is chosen to elaborate the approach. Its behavior is analyzed and SPICE simulations using TSMC 180 nm CMOS technology parameters are included to support the theoretical concept. The performance of the proposed circuit is compared with its counterparts based on CMOS complementary pass transistor logic, conventional MCML, and cascading of existing two input tripple-tail XOR cells and applying triple-tail concept in conventional MCML topology. It is found that the proposed XOR gate performs best in terms of most of the performance parameters. The sensitivity of the proposed XOR gate towards process variation shows a variation of 1.54 between the best and worst case. As an extension, a realization of 4 : 1 multiplexer has also been included.

Optoelectronic exclusive-OR (XOR) gate

1993 ◽  
Vol 5 (6) ◽  
pp. 686-688 ◽  
Author(s):  
F.R. Beyette ◽  
K.M. Geib ◽  
S.A. Feld ◽  
M.J. Hafich ◽  
X. An ◽  
...  
Keyword(s):  
Xor Gate ◽  
Exclusive Or

scholarly journals Characterizing Genetic Circuit Components in E. coli towards a Campylobacter jejuni Biosensor

2018 ◽  
Author(s):  
Natalia Brzozowska ◽  
Jane Gourlay ◽  
Ailish O’Sullivan ◽  
Frazer Buchanan ◽  
Ross Hannah ◽  
...  
Keyword(s):  
Campylobacter Jejuni ◽  
Regulatory Protein ◽  
Food Poisoning ◽  
Saturation Mutagenesis ◽  
Genetic Circuit ◽  
Reporter System ◽  
E Coli ◽  
Regulatory Circuits ◽  
Small Molecule Ligands ◽  
Circuit Components

AbstractCampylobacter jejuni is responsible for most cases of bacterial gastroenteritis (food poisoning) in the United Kingdom. The most common routes of transmission are by contact with raw poultry. Current detection systems for the pathogen are time-consuming, expensive or inaccessible for everyday users. In this article we propose a cheaper and faster system for detection of C. jejuni using a synthetic biology approach. We aimed to detect C. jejuni by the presence of xylulose, an uncommon bacterial capsular saccharide. We characterized two sugar-based regulatory systems that displayed potential to act as tools for detection of xylulose. Using a two-plasmid reporter system in Escherichia coli, we investigated the regulatory protein component (MtlR) of the mannitol operon from Pseudomonas fluorescens. Our findings suggest that the promoter of mtlE is activated by MtlR in the presence of a variety of sugar inducer molecules, and may exhibit cross-activity with a native regulator of E. coli. Additionally, we engineered the L-arabinose transcriptional activator (AraC) of E. coli for altered ligand specificity. We performed site-specific saturation mutagenesis to generate AraC variants with altered effector specificity, with an aim to generate a mutant activated by xylulose. We characterized several mutant AraC variants which have lost the ability to respond specifically to the native L-arabinose effector. We promote this technique as a powerful tool for future iGEM teams to create regulatory circuits activated by novel small molecule ligands.

scholarly journals The Design of Low-Power High-Speed Two-Level Three Input XOR gate

2020 ◽  
Vol 9 (5) ◽  
pp. 1813-1818
Keyword(s):  
Low Power ◽  
High Speed ◽  
High Performance ◽  
Supply Voltage ◽  
Propagation Delay ◽  
Signal Frequency ◽  
Xor Gate ◽  
Input Signal Frequency ◽  
Transmission Gates ◽  
Exclusive Or

The Large Fan-In and high performance gates are essential to make portable electronic devices. In this paper an efficient realization of three input two level XOR(Exclusive-OR) is presented. The design of low power and high speed proposed XOR gate involves the combination of pass and transmission gates. The main objective to achieve this is based on the selection of input signals to propagate and maintain the good logic swing. Two methods were used to design proposed XOR, one (i.e. Pass_gate) is purely based on pass transistors with 8 MOSFET’s and second method(Modified_Pass_gate) uses transmission gates with 12 transistors. The Modified_Pass_gate offers 86.14% and 6.66% of power dissipation reduction compared to static and Pass_gate XOR respectively and 77.18% and 50.94% less propagation delay compared to static and Pass_gate XOR respectively, at the supply voltage of 0.7v with input signal frequency of 3GHz. The simulation is performed based on 32nm technology node(PTM-models) using Hspice Synopsis simulation tool.

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