Synthetic biology is an approach to engineer biology. Core to the discipline is genetic engineering, which is made more akin to engineering by adding the levels of standardization, automation, and abstraction.

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Why isn't there a standard unit of promoter strength?

Sometimes in synthetic biology, we need to know rates of transcription of one promoter in relation to others (particularly inducible vs constitutive) in order to perform tasks like balancing ...
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1answer
31 views

Why does pETDuet-1 only have one T7 terminator but two T7 promoters?

Why does pETDuet-1 only have one T7 terminator but two T7 promoters (vector map below)? Is there any advantage of having only one terminator? There are going to be two mRNAs transcribed from this ...
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What is the highest number of genes expressed under one T7 promoter?

What is the highest number of genes expressed under one T7 promoter? Also, what is the longest polycistronic mRNA? I am interested in the context of heterologously expressing biosynthetic gene ...
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Synthetic biology: examples of cell orientation driven by genes or genetic modification

First of all, forgive for the naive question. I know that genes can drive the shape of cells, as the sickle-shaped red blood cells. On the spirit of synthetic biology or tissue engineering, does ...
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Barcode exchange between neighbouring cells

I am currently interested in equipping animal cells in a tissue with individual barcodes. These barcodes should get amplified in the cells (not to a cell degrading extent, of course), and also ...
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24 views

How do genetic logic gates work?

Recently researchers at MIT have developed genetic logic gates which can be built into programs. How do these "genetic logic gates" work? "The language is based on Verilog, which is commonly used to ...
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44 views

In theory how fast could nerve signals travel if the nerve fibre was perfectly insulated?

My question is purely theoretical and my main aim is to find out the maximum speed that a nerve signal can travel within a nervous system and and whether this speed represents the physical limit of ...
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45 views

What prevent us from synthesizing a cell from “scratch”?

In this recent article "Design and synthesis of a minimal bacterial genome", they created a minimal cell with only 473 genes. However, they didn't synthesize all of the necessary components of the ...
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46 views

A career in synthetic biology [closed]

So I am thinking about a career in synthetic biology, but I am not sure what route should/needs to be taken. I don't want to do technician work--I want to be involved in the planning. Y'know, the ...
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Balanced vs Maximized Codon Optimization

I have worked with the optimization of several viral proteins, from different viruses/families, with different results. When Menzella, 2011 was published I tried that method. I found quite the ...
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21 views

XNAs as a Genetic material [closed]

I heard there is a new genetic material called XNAs.I wanted to know more about this.Does anyone about XNAs as genetic material?
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1answer
127 views

Do DNA supply houses maintain a watch list for dangerous oligos (Anthrax, Smallpox, etc.)?

The recent work by DeLoache, et al. on a synthetic opiate-precursor production pathway in yeast has generated a lot of scare stories in the media about people homebrewing heroin as easily as they ...
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How hard would it be to synthesize a virus in 1960? [closed]

Assuming 1960 technology, how hard would it be to synthesize a virus? Im curious as to how developed technology was back then and the amount of cost and effort it would take given the fairly basic ...
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1answer
18 views

Colormetric assay for a phenol product?

I am working on an assay for phenol products created by a colony of bacteria. I have searched up a paper that involves gibbs reageant but the protocol is kind of unclear. Does any of you know where I ...
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30 views

“Antibiotic resistance” equivalent in archaea for selection during cloning

I'm beginning to work with halophilic archaea and I'm trying to figure out a good way to select for cells that have taken up a plasmid. Obviously, one can't use antibiotic resistance since they are ...
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1answer
1k views

How to secrete a recombinant protein from E. coli?

What are some secretory pathways that can be used to secrete a recombinant bacterial enzyme from E. coli? I have a recombinant protein (29kDa) that I will express in E. coli BL21 cells. For now I ...
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1answer
144 views

What is the spacing between stop codon and transcription terminator?

When one tries to express a protein from a synthetic plasmid in E. coli, how many base pairs should there be between stop codon and the transcription terminator site?
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6answers
493 views

Introductory literature for synthetic / systems biology?

I'm a computer engineer (MsC Computer Engineering) who's looking to switch into the field of synthetic / systems biology. I've got a comprehensive layman's understanding of evolution, genetics, ...
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5answers
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Difference between genetic engineering and synthetic biology

I've recently seen the term synthetic biology being used to describe research involving genetic modification of organisms. What is the difference between synthetic biology and genetic engineering? Is ...
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1answer
76 views

T7 Tagging in Synthetic Biology

What is a T7 tag and can if be used to purify synthesized proteins? Is it charge based like a His tag?
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His Tag location in gene circuit

I am part of an undergraduate research group and we are trying to produce a protease in an E.coli gene circuit. We are not sure where to place the His tag in our circuit. The sequence is ...
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1answer
21 views

Will tagging a protease with HlyA for secretion inactivate the protease?

We are looking to secrete the protease proline iminopeptidase by attaching the secretion signal HlyA to the protease in a gene circuit. Since the natural HlyA secretion sequence in Escherichia coli ...
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1answer
48 views

Proline Iminopeptidase v Proline Aminopeptidase

We're an undergraduate independent research team and we are having trouble purchasing commercial proline iminopeptidase as it is unavailable on Sigma Aldrich and very expensive on other websites. We ...
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2answers
31 views

T7 Tagging Next to Met

Will a T7 tag still work if it is placed next to a start codon? Meaning, will it still work with a Met attached to it in the amino acid sequence? Thank you!
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Some kind of better oxygen-transport protein or something… Can you help me find it?

I remember reading about artificial or man-made, oxygen-transport protein that is somehow an improvement on hemoglobin, and that it is possibly immune to sickle-cell anemia, or something... But I ...
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How predictably will RNA polymerase not transcribe repetitive sequences?

I am working on an (expensive) synthetic construct, which happens to have many "repetitive" sequences within it that are integral to its function. Primarily, the two sequences that are worrying me ...
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1answer
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Is it possible to insert DNA without cutting the recognition site with CRISPR/Cas9?

We are looking for a way to insert DNA into a genome, but we would like to do it in a way that the recognition site stay intact to be able to add again DNA at the same location. Do you know if it is ...
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How can CI repressor both activate and repress $P_{RM}$ promoter found in $\lambda$ phage?

I'm reading a paper where the authors constructed a toggle switch that uses bidirectional $P_R/P_{RM}$ promoter found in the $\lambda$ phage. There are 3 binding sites - $O_{R1}$, $O_{R2}$, $O_{R3}$ - ...
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How would you affect bulk DNA gene therapy for a human?

Let's imagine that we understood DNA programming and our genome very well and realized that there were some significant flaws (we die, we need sleep, etc.) And let's imagine that we understand how to ...
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382 views

Can genetic engineering be performed without a laboratory setting? [closed]

I'm becoming more interested in genetic engineering as I learn more about it, and it's becoming more and more apparent that there's very few resources on genetic engineering at home. A similar ...
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42 views

How do I get recombinant proteins into the nucleus of mammal cells?

I know that there are Nuclear Localisation Sequencenes (NLS). They can be taken from endogenous or viral proteins and fused to the N or C terminus of my recombinant protein. Which is the best one? ...
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182 views

How significant is RNA degradation with removal of cap/polyA's in eukaryotes, or UTR's in prokaryotes?

Question is rather self-explanatory, but segmented into two parts. I'm attempting to make use of a repression system that employs cleaving RNA at specific areas with ribozymes with the intent of ...
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1answer
304 views

Ribosomal Turing Machines, DNA/RNA computation

I'm a computer science guy, recently crossing over to do some research in computational biology on RNA secondary structure prediction. While looking through the materials I got a crazy idea, what if ...
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1answer
36 views

Do the phage repressors CI and Mnt exhibit crosstalk?

I am interested in using the CI and Mnt proteins as well as their respective promoters (pR and Pmnt) within the same synthetic system, but am concerned as to their similarity and potential crosstalk. ...
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What are the rules for plasmid names?

What are best practices for naming newly created plasmids? For example, a common format is pABC123. What is the exact specification? Must there be 3 letters? What ...
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1answer
59 views

Forum on synthetic biology and hypothetical biology?

I am interested in synthetic biology, but not a scientist, and would like some advice on where to look for an online forum on synthetic biology and creating fictional species and animals or if someone ...
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Has anyone tried Gibson Assembly Optimizations?

Has anyone tried the chew back-anneal in vitro DNA assembly method (known as Gibson Assembly) for difficult sequences, like GC-rich sequences? How big constructs could you efficiently assemble? Did ...
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2answers
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Are there known downsides to removing UV mutation hotspots to prevent some skin cancers (Genetic sunblock)?

Khavari et al. recently demonstrated that a significant fraction of one of the major forms of skin cancer (cutaneous squamous cell carcinomas) are associated with a mutated KNSTRN gene (a protein ...
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Assembling DNA fragments with ~10kb overlap in vitro

Let's say I have two fragments of bacterial DNA (~50kb in length each) that overlap on the ends by roughly ~10kb; the overlap sequences are unknown. I would like to assemble these into longer ...
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1answer
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Activity of glucokinase

From Solomon et al, 2013 ACC Synthetic biology and from this video : Here, there are 2 competing reactions for glucose - one with glk as enzyme and other with gdh as enzyme. In the graph, y axis ...
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1answer
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Can two hammerhead ribozymes simultaneously cleave each other?

I am working on a project in which an XOR gate is being built by having two hammerhead ribozymes simultaneously cleave each other when both are expressed, but have these ribozymes cleave a target ...
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Can spider silk be synthesized for 3D printing with spider silk?

With the recent rise in 3D printing, I keep hearing about more novel ways to use the technology: cell 3D printing, liquid aluminum or plastic 3D printing. For example, this Ted talk deals with ...
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1answer
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What is the relation between plasmid concentration and mRNA levels?

Suppose a simple synthetic construct, consisting of a constitutive promoter and a single gene: One of the simplest ways to model GFP transcription is to use an ODE: $\frac{d [GFP_{mRNA}]}{dt} = a - ...
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2answers
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What can cause incompatible sticky ends to be ligated?

Actual question I have reason to believe (details see below) that in a ligation I carried out, an EcoRI sticky end (EcoRI: G'AATT_C) and an XmaI sticky end (XmaI: C'CCGG_G) were somehow ligated ...
2
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1answer
123 views

Can a plant be programmed to produce any arbitrary object?

I'm wondering if a plant can be programmed (by modifying its genes) to grow into any shape that it's programming instructs. I understand that a plants genes are its instructions of how to convert the ...
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1answer
721 views

Is there an optimal composition and length for protein linkers in FRET?

I'm designing a protein that I'd like to use in FRET reporting. General idea on the shape is: FRETprotein1--Linker--CleavageSite--Linker--FRETprotein2. I would like to know what AA are best for the ...
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1answer
184 views

Synthetic construct with multiple ORFs not expressing

I designed a synthetic construct on paper and got it synthesized from a company. The objective was to make a vector which can be used to study both transcriptional and post-transcriptional regulation ...
5
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2answers
572 views

What are common causes of unexpected ligation products?

I digested two plasmids, one with EcoRI and AgeI and the other with EcoRI and XmaI. Digests looked as expected, so I purified the respective fragments and set up the T4 DNA ligation (AgeI and XmaI ...
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1answer
326 views

Has synthetic biology created new plants or animals as of 2013?

I've seen a Ted.com talk where the speaker suggests that modern science can create new micro organisms, like bacteria with a pre- defined new set of traits. But has anyone create a new species of ...
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How can I accurately predict proper transgenic protein function/structure from different species?

I am currently building a synthetic system in E.coli, and am often faced with the need to use genes from other distant prokaryotes. I know that myself and most of my colleagues resort to an educated ...