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Questions tagged [synthetic-biology]

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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Strong activation of MAPK signaling pathway

I am reading a paper named "Mathematical models of protein kinase signal transduction". In that paper, I encountered a condition called "strongly activated pathways". In that ...
이영규's user avatar
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1 answer
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How do molecular biologists typically get their oligos?

What's the typical route taken to obtain synthetic DNA/RNA samples in practice? Are they pretty much always custom ordered from a place that prints them using sold-phase synthesis, or can you cobble ...
Gumpf's user avatar
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Is there a name for this type of diagram?

Is there any commonly used name for this type of diagram / symbology? I have not been able to find them referred to by any name.
tsj's user avatar
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Production method of custom seed mir451? How to edit middle of a fragment?

I am trying to create a plasmid that produces mir451 targeting a new gene, so I need to alter the seed sequence. The seed sequence is 7 bp long, so I think that is too long for PCR mutagenesis. How do ...
TinyVampire's user avatar
4 votes
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Adh2 promoter in saccharomyces cerevisiae

I'm looking at expressing a protein in saccharomyces cerevisiae using the Adh2 promoter. My understanding is that the gene will be repressed by the presence of glucose, but when glucose runs out it ...
Shreyas Patel's user avatar
-1 votes
1 answer
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How would it be possible to engineer cows to have more offspring?

Cows usually only give birth to one calf per year and only several in their lifetime. What would we have to genetically alter so they can have more offspring, more frequently. I read that their is a ...
Max's user avatar
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4 votes
1 answer
369 views

DNA Design for Multi-Site Restriction Enzymes

I have to use the SacII restriction enzyme, which requires multiple recognition sites to efficiently cut DNA, for a DNA assembly. From my understanding, multiple copies of DNA holding only a single ...
JEJS's user avatar
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5 votes
1 answer
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For a biological AND Gate to work, do the two inputs need to arrive at the same time?

I understand that AND gates require the two inputs to be present for the output to be produced. However, if one input arrives faster than the other input does the output still get produced? For ...
Marc Amil's user avatar
1 vote
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What is the structure of PduK in the Pdu BMC?

My lab is creating 1,2-propanediol utilization bacterial microcompartments (Pdu BMCs) with an operon containing genes for PduA, PduB, PduJ, PduK, PduN, PduU, and PduT. According to Mayer et al., all ...
David Bass's user avatar
6 votes
1 answer
123 views

Which genetic oscillator should I use to generate oscillations in range of 2-20 mins?

I'm looking to phase-separate the expression of two enzymes and hence am looking for a multi-component genetic oscillator. However, repressilators and metabolators have a large period of around 45 ...
Siddharth Fitwe's user avatar
2 votes
1 answer
194 views

Using PCR to add the overhangs to gBlocks for NEB HiFi

Does adding the overhangs to gBlocks for NEB Hifi using PCR pose a big problem? The IDT website suggests that one should design the gBlocks with the overhangs. However, if I did not do this, will it ...
Confused Student's user avatar
3 votes
1 answer
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T-vector creation

I'm working on TA cloning for the first time and I need to turn some existing plasmid backbones into T-vectors. I'm using a Klenow fragment (3' -> 5' exo-) to dA-tail my inserts. Is there any ...
Kat's user avatar
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2 votes
2 answers
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Identifying Promoters in Non-homologous Sequences within the Same Organism

In this paper, the authors cloned a GPD promoter for use in driving a GFP gene from Lentinula edodes using a set of provided primers. The primers were derived from the following accession GQ457137.1 ...
doremi's user avatar
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5 votes
1 answer
158 views

How to replace intron region in a plasmid?

I'm considering working with the plasmid pRFHUE-eGFP and would like to replace the gpdA intron (which is the eGFP promoter region) with a promoter from another organism. What would be a good strategy ...
doremi's user avatar
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4 votes
3 answers
188 views

Production of plant derivatives using genetic engineered micro-organisms

I saw a Thought Emporium video where spider silk was produced by genetically modifying yeast. I have also read about companies making vanillin (vanilla flavour) using this technique. I am curious to ...
Solar Flare's user avatar
4 votes
1 answer
98 views

Impact of Terminator Efficiency in Genetic Constructs

I was looking at the iGEM Bioregistry of Terminator parts which offer varying degrees of termination efficiency. I am wondering why studies into combinatorial synthesis of genetic circuits for ...
JEJS's user avatar
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0 answers
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What is the life of cell-free genetic circuits?

Can genetic circuits be tested in a cell-free environment? What would be their life if we keep them at room temperature? The circuits which are composed of DNA-based components are commonly referred ...
Hasan Baig's user avatar
8 votes
1 answer
801 views

Does gene orientation relative to origin of replication matter on small plasmids?

The recent question about forward vs. reverse strand got me thinking about directionality conventions in synthetic biology. As noted in the answer to that question, if we consider only DNA in ...
jakebeal's user avatar
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4 votes
1 answer
2k views

Forward or Reverse Strand: Is there a difference when encoding genetic devices?

Background: In synthetic biology, and also in nature, there are lots of examples of genes in both the forward and reverse orientation. It seems in synthetic biology/bioengineering, most genetic ...
Brad0440's user avatar
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6 votes
2 answers
517 views

Compatibility between spytag/spycatcher versions

Background SpyTag and SpyCatcher are peptides which can associate via a spontaneous amide bond. Because of this, they can be fused to proteins of interest as tags to cause the proteins to bind. There ...
Brad0440's user avatar
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6 votes
2 answers
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Can we dilute PureExpress Cell Free Mix to increase number of reactions?

Since the PureExpress Cell Free mix is so expensive, I was wondering if it might be possible to just dilute the mix to increase the number of reactions we need to use. From this image I found: It ...
rkrishnasanka's user avatar
9 votes
2 answers
150 views

How would you use readthrough as part of a genetic circuit design?

Traditionally, in synthetic biology, researchers tried to avoid some transcription phenomena (like roadblocking of tandem promoters or readthrough of weak terminators) since they are not in line with ...
Pedro Fontanarrosa's user avatar
4 votes
2 answers
264 views

What genes are required to make E. coli photosynthetic?

"All" of the genes for bacterial photosynthesis were discovered in a gene cluster almost 40 years ago. Marrs, J.Bact. What more is needed to make E. coli photosynthetic?
Youvan's user avatar
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6 votes
1 answer
115 views

How large an expression boost is typical from codon optimization?

There are lots of different codon optimization approaches out there, and a lot of different qualitative reasons to want optimization (e.g., organism codon bias, GC content, avoiding secondary ...
jakebeal's user avatar
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9 votes
3 answers
251 views

Assembling small DNA parts using Golden Gate

Background I've always been told that DNA assembly can be tricky when using very small DNA parts due to low efficiency. I've also seen this when using 3A biobrick assembly to assemble promoters and ...
Brad0440's user avatar
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8 votes
1 answer
461 views

Why is electroporation not the prefered choice transforming for Mammalian Cells (HEK)?

I see a lot of folks using different techniques for transforming mammalian cell (specifically HEK) instead of doing electroporation like I see with E.Coli (bacteria). Is there a reason for this ?
rkrishnasanka's user avatar
12 votes
2 answers
512 views

Is there a favoured mathematical model of bacterial growth?

One of the most regularly measured phenotypes in bacterial synthetic biology is growth. Anyone who does wet lab microbiology or synthetic biology will have performed a growth curve measurement. ...
ajhfedorec's user avatar
11 votes
2 answers
327 views

Can I use multiple bicistronic RBS sequences in a synthetic biological circuit?

The bicistroninc RBS sequences (BCDs) developed by Mutalik et al. [1] aim to remove context sensitivity from translation and therefore ensure more predictable gene expression. However, I have been ...
ajhfedorec's user avatar
7 votes
4 answers
930 views

Measuring luminescence in a fluorescence plate reader

We're considering organizing some interlaboratory work on calibrating luminescence reporters (e.g., luciferase), and one of the key questions I don't know the answer to is whether most plate readers ...
jakebeal's user avatar
  • 6,987
6 votes
1 answer
818 views

How can I convert plate reader measurements of Pichia pastoris OD to cells per ml?

I am performing experiments with the yeast Pichia pastoris where it will be beneficial to calculate product yield per cell. I plan to use a plate reader to measure OD600 of my cultures and then ...
Noah Sprent's user avatar
4 votes
1 answer
177 views

How long would you expect a designed plasmid to remain in a population of E. coli after transformation?

When transforming E. coli with a genetically-modified plasmid, how quickly/often is this plasmid "lost" because of mutation, or horizontal-transfer, or "dilution" over reproduction ...
Pedro Fontanarrosa's user avatar
3 votes
1 answer
1k views

Are 2A cleavage sites functional in bacteria?

In mammalian cell lines, 2A self-cleaving peptides are frequently used to for expression of multiple genes from a single transcript. They've got some issues, e.g., leaving some proteins as fusions, ...
jakebeal's user avatar
  • 6,987
7 votes
3 answers
163 views

Is there any problem with using a single stop codon with a single CDS in prokaryotes?

All protein coding sequences in the iGEM Registry are supposed to end with a double stop codon. Presumably, this is to decrease the potential for read-through, which could be problematic if one is ...
jakebeal's user avatar
  • 6,987
2 votes
2 answers
2k views

Why is the start of my coding sequence ATG and not TAC?

I am engineering a set of genetic sequences and have come across a surprisingly basic point of confusion that seems to have fallen through the cracks regarding coding sequences. The standard start ...
jakebeal's user avatar
  • 6,987
2 votes
1 answer
99 views

Is synthesizing DNA in-house feasible?

I've been reading up about DNA writing, and it seems there are machines available around the five-figure US dollar mark for DNA synthesis, and I'm considering picking one up for my lab. We normally ...
TheEnvironmentalist's user avatar
-1 votes
2 answers
100 views

What is the energy required for storing and performing computations in synthetic computational biological cells?

I want to know the energy costs of various computations performed through synthetic biological circuits in terms of ATP. I am primarily interested in storing of bits, addition, and multiplication ...
Userhanu's user avatar
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0 votes
1 answer
166 views

How can I get started in molecular biology? [closed]

I have a background in computer science and math and am interested in learning molecular / synthetic biology - what resources do people recommend?
Andrew's user avatar
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1 vote
1 answer
69 views

How to estimate mRNA counts from Relative Promoter Units (RPU) or RNAP per second (PoPS) in E. coli?

I need a rough estimate on how to translate RPU or Polymerases Per Second (PoPS) to mRNA count (or even better protein count) in E. coli. I understand that any number we come up with will be a very ...
Pedro Fontanarrosa's user avatar
2 votes
1 answer
173 views

Source for 'EVERY living organism uses ATP as energy carrier', and can we make a synthetic one that doesn't?

I have read it repeatedly that 'all living organisms use ATP as an energy currency etc' and 'some use GTP in addition'. However I am yet to find a reliable resource, rather than just quora/reddit/...
Meep's user avatar
  • 2,969
4 votes
1 answer
174 views

Replacing, instead of repairing, DNA

I've been doing some light reading on DNA damage theory of aging. One of the main ideas from that theory that I got is that the accumulation of damage in our DNA is one of the biggest causes of why we ...
TheLast Cipher's user avatar
0 votes
1 answer
29 views

What are low-accumulating genotypes? [closed]

What are low-accumulating genotypes? And how does it differ from high-accumulating genotypes?
Line's user avatar
  • 15
4 votes
2 answers
445 views

Will new proteins incorporating new amino acids trigger an immune response?

This article reported that scientists have succeeded in adding two new bases to the quartet of A, C, G and T, resulting in non-canonical amino acid. Additionally, the bacteria in which this was done ...
Daud's user avatar
  • 473
1 vote
1 answer
1k views

What is the purpose of the AraC gene in pGLO?

The AraC gene activates in pGLO from my understanding in the presence of arabinose. Arabinose is present as a metabolite from other metabolic in the e.coli cell. Is it that there's no termination ...
Sargun Dhillon's user avatar
1 vote
0 answers
40 views

Papers where protein oligomerization has been engineered away

I have a protein that acts as a monomer, but appears to have a relatively high self-affinity in vivo (measured using transient transfection of a plasmid coding for the protein), which is annoying ...
Mike Flynn's user avatar
0 votes
2 answers
374 views

A synthetic sieve organ known as kliver?

in this video at 5:28, the narrator talks about a "vat-grown all-purpose sieve organ" called Kliver that would do away with both liver and kidney transplant. But i don't seem to find online resources ...
raaaay's user avatar
  • 135
0 votes
1 answer
234 views

MIT's Programming Language for Cells

I have read a lot about the programming language, Cello, that MIT created to program DNA; however, I cannot seem to find any sources online that shows you how to program with Cello. Are there any good ...
Kile Maze's user avatar
1 vote
1 answer
245 views

Could the protein dystrophin be artificially synthesised?

Could the protein dystrophin be artificially synthesised and if so could patients with DMD (Duchenne Muscular Dystrophy) benefit from it? //Now I don't have much scientific background other than a ...
Dylan's user avatar
  • 11
3 votes
2 answers
133 views

Dealing with Repetitive Bases in DNA?

I have been given a project involving a plasmid that contains long stretches of Adenine (60 or 120 bases each). These PolyA stretches are interrupted by the occasional G or C. I understand that ...
user137's user avatar
  • 5,348
1 vote
0 answers
32 views

Assay for Glycosyltransferase

I want to do an assay to see, if an ordered enzyme is active or not. It's a glucosyltransferase from S. mutans which hydrolyses sucrose into fructose and glucose. It then connects the glucose-monomers ...
Simon Pflug's user avatar
37 votes
3 answers
5k views

What does it mean to "write an image and GIF into the DNA of bacteria"?

BBC News recently published an article saying that: An image and short film has been encoded in DNA, using the units of inheritance as a medium for storing information ... The team sequenced the ...
PiratePi's user avatar
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