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Sc2.0 | Synthetic Yeast 2.0

This is the site where you will learn about our ongoing project to synthesize the genome – from oligos to chromosomes, and the design features of the new version of Saccharomyces cerevisiae which we fondly refer to as Sc2.0.

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Homegrown labware made with 3D printer

by Helen Shen

"Armed with a three-dimensional (3D) printer and the type of silicone-based sealant typically used for bathrooms, researchers have demonstrated a novel way to control chemical reactions: by making the reaction vessel an integral part of the experiment itself. The results, published 15 April in Nature Chemistry1, could open the door to a new generation of custom labware made to suit individual researchers’ needs...."

http://bit.ly/HCtxW1

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Molecular "Wankel Engine" Driven By Photons - Technology Review

Molecular "Wankel Engine" Driven By Photons - Technology Review | SynBioFromLeukipposInstitute | Scoop.it

"One of the great discoveries of biology is that the engines of life are molecular motors--tiny machines that create, transport and assemble all living things.

That's triggered more than a little green-eyed jealousy from physicists and engineers who would like to have molecular machines at their own beck and call. So there's no small interest in developing molecular devices that can be easily harnessed to do the job.

Today, Jin Zhang at the University of California Los Angeles and a few pals say they've identified a machine that fits the bill.

A couple of year ago, chemists discovered that groups of 13 or 19 boron molecules form into concentric rings that can rotate independently, rather like the piston in a rotary Wankel engine. Because of this, they quickly picked up the moniker "molecular Wankel engines". The only question was how to power them..."

 
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The future of metabolic engineering and synthetic biology: Towards a systematic practice

by: Vikramaditya G. Yadav, Marjan De Mey, Chin Giaw Lim, Parayil Kumaran Ajikumar, Gregory Stephanopoulos

"Industrial biotechnology promises to revolutionize conventional chemical manufacturing in the years ahead, largely owing to the excellent progress in our ability to re-engineer cellular metabolism. However, most successes of metabolic engineering have been confined to over-producing natively synthesized metabolites in E. coli and S. cerevisiae. A major reason for this development has been the descent of metabolic engineering, particularly secondary metabolic engineering, to a collection of demonstrations rather than a systematic practice with generalizable tools. Synthetic biology, a more recent development, faces similar criticisms. Herein, we attempt to lay down a framework around which bioreaction engineering can systematize itself just like chemical reaction engineering. Central to this undertaking is a new approach to engineering secondary metabolism known as ‘multivariate modular metabolic engineering’ (MMME), whose novelty lies in its assessment and elimination of regulatory and pathway bottlenecks by re-defining the metabolic network as a collection of distinct modules. After introducing the core principles of MMME, we shall then present a number of recent developments in secondary metabolic engineering that could potentially serve as its facilitators. It is hoped that the ever-declining costs of de novo gene synthesis; the improved use of bioinformatic tools to mine, sort and analyze biological data; and the increasing sensitivity and sophistication of investigational tools will make the maturation of microbial metabolic engineering an autocatalytic process. Encouraged by these advances, research groups across the world would take up the challenge of secondary metabolite production in simple hosts with renewed vigor, thereby adding to the range of products synthesized using metabolic engineering."

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Will 3-D printing launch a new industrial revolution?

Will 3-D printing launch a new industrial revolution? | SynBioFromLeukipposInstitute | Scoop.it
Peter Schmitt, an MIT doctoral student, printed a clock in 2009. He didn't print an image of a clock on a piece of paper.
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Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal Tissues

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Yoshiyuki Shibata, Pankaj Kumar1, Ryan Layer, Smaranda Willcox, Jeffrey R. Gagan, Jack D. Griffith, Anindya Dutta

 

We have identified tens of thousands of short extrachromosomal circular DNAs (microDNA) in mouse tissues as well as mouse and human cell lines. These microDNAs are 200 to 400 base pairs long, are derived from unique nonrepetitive sequence, and are enriched in the 5′-untranslated regions of genes, exons, and CpG islands. Chromosomal loci that are enriched sources of microDNA in the adult brain are somatically mosaic for microdeletions that appear to arise from the excision of microDNAs. Germline microdeletions identified by the “Thousand Genomes” project may also arise from the excision of microDNAs in the germline lineage. We have thus identified a previously unknown DNA entity in mammalian cells and provide evidence that their generation leaves behind deletions in different genomic loci."

 

 

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PLoS ONE: A Biobrick Library for Cloning Custom Eukaryotic Plasmids

PLoS ONE: A Biobrick Library for Cloning Custom Eukaryotic Plasmids | SynBioFromLeukipposInstitute | Scoop.it

A biobrick library for cloning custom eukaryotic plasmids

by
Marco Constante, Raik Grünberg, Mark Isalan

"Researchers often require customised variations of plasmids that are not commercially available. Here we demonstrate the applicability and versatility of standard synthetic biological parts (biobricks) to build custom plasmids. For this purpose we have built a collection of 52 parts that include multiple cloning sites (MCS) and common protein tags, protein reporters and selection markers, amongst others. Importantly, most of the parts are designed in a format to allow fusions that maintain the reading frame. We illustrate the collection by building several model contructs, including concatemers of protein binding-site motifs, and a variety of plasmids for eukaryotic stable cloning and chromosomal insertion. For example, in 3 biobrick iterations, we make a cerulean-reporter plasmid for cloning fluorescent protein fusions. Furthermore, we use the collection to implement a recombinase-mediated DNA insertion (RMDI), allowing chromosomal site-directed exchange of genes. By making one recipient stable cell line, many standardised cell lines can subsequently be generated, by fluorescent fusion-gene exchange. We propose that this biobrick collection may be distributed peer-to-peer as a stand-alone library, in addition to its distribution through the Registry of Standard Biological Parts (http://partsregistry.org/)."
http://bit.ly/IJAFT3

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Synthesis, properties, and applications of olig... [Acc Chem Res. 2011] - PubMed - NCBI

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Li NS, Frederiksen JK, Piccirilli JA.
"RNA represents a prominent class of biomolecules. Present in all living systems, RNA plays many essential roles in gene expression, regulation, and development. Accordingly, many biological processes depend on the accurate enzymatic processing, modification, and cleavage of RNA. Understanding the catalytic mechanisms of these enzymes therefore represents an important goal in defining living systems at the molecular level. In this context, RNA molecules bearing 3'- or 5'-S-phosphorothiolate linkages comprise what are arguably among the most incisive mechanistic probes available. They have been instrumental in showing that RNA splicing systems are metalloenzymes and in mapping the ligands that reside within RNA active sites. The resulting models have in turn verified the functional relevance of crystal structures. In other cases, phosphorothiolates have offered an experimental strategy to circumvent the classic problem of kinetic ambiguity; mechanistic enzymologists have used this tool to assign precise roles to catalytic groups as general acids or bases. These insights into macromolecular function are enabled by the synthesis of nucleic acids bearing phosphorothiolate linkages and the unique chemical properties they impart. In this Account, we review the synthesis, properties, and applications of oligonucleotides and oligodeoxynucleotides containing an RNA dinucleotide phosphorothiolate linkage. Phosphorothioate linkages are structurally very similar to phosphorothiolate linkages, as reflected in the single letter of difference in nomenclature. Phosphorothioate substitutions, in which sulfur replaces one or both nonbridging oxygens within a phosphodiester linkage, are now widely available and are used routinely in numerous biochemical and medicinal applications. Indeed, synthetic phosphorothioate linkages can be introduced readily via a sulfurization step programmed into automated solid-phase oligonucleotide synthesizers. In contrast, phosphorothiolate oligonucleotides, in which sulfur replaces a specific 3'- or 5'-bridging oxygen, have presented a more difficult synthetic challenge, requiring chemical alterations to the attached sugar moiety. Here we begin by outlining the synthetic strategies used to access these phosphorothiolate RNA analogues. The Arbuzov reaction and phosphoramidite chemistry are often brought to bear in creating either 3'- or 5'-S-phosphorothiolate dinucleotides. We then summarize the responses of the phosphorothiolate derivatives to chemical and enzymatic cleavage agents, as well as mechanistic insights their use has engendered. They demonstrate particular utility as probes of metal-ion-dependent phosphotransesterification, general acid-base-catalyzed phosphotransesterification, and rate-limiting chemistry. The 3'- and 5'-S-phosphorothiolates have proven invaluable in elucidating the mechanisms of enzymatic and nonenzymatic phosphoryl transfer reactions. Considering that RNA cleavage represents a fundamental step in the maturation, degradation, and regulation of this important macromolecule, the significant synthetic challenges that remain offer rich research opportunities."
http://1.usa.gov/IN2DK0

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Information on Synthetic Biology and the Lab’s Safety Approach « Today at Berkeley Lab

Information on Synthetic Biology and the Lab’s Safety Approach « Today at Berkeley Lab | SynBioFromLeukipposInstitute | Scoop.it

Prepared by the Lab’s Synthetic Biology Working Group, formed under the direction of Sam Chapman, manager of State & Community Relations and including representatives from Public Affairs, Federal Government Relations, the Joint Genome Institute, Joint BioEnergy Institute, Environmental Health & Safety, UC Berkeley and others.

What is synthetic biology?

Synthetic biology combines modern principles of science and engineering to develop novel biological functions and systems.

This includes the design and construction of new biological devices, such as molecules, genetic circuits or cells, and the re-designing and engineering of existing biological systems, such as microorganisms. The goal is to engineer microorganisms to produce valuable chemical products from simple, inexpensive and renewable starting materials, such as sugars, in a sustainable manner.

Is synthetic biology an entirely new and untested field of science?

No. Through selective breeding, humans have been altering the genetic code of plants and animals for more than a thousand years. Synthetic biology today is an extension of the genetic engineering research that began about 40 years ago. Also known as recombinant DNA technology, genetic engineering has produced valuable chemical products such as human insulin and growth hormones, hormones for treating infertility, monoclonal antibodies and the hepatitis B vaccine. Through better understanding of biological systems and metabolic pathways, coupled with enormous advances in computing, synthetic biology moves beyond these earlier efforts to make the design and production of biological parts and systems more predictable and reliable. Berkeley Lab scientists will apply synthetic biology to the production of advanced biofuels that can replace gasoline, diesel and jet fuel in today’s engines and can be transported via existing pipeline infrastructures. Spinoffs from this research will include medical drugs, biodegradable and green chemistry replacements for other petrochemical products, such as plastics, and environmental restoration through decontamination of hazardous pollutants.

How safe is synthetic biology?

Out of four potential biosafety levels (BLs) of containment detailed in national and international standards, (BL1=least dangerous to BL4) Berkeley Lab operates at only the two lowest and most common biosafety levels, BL1 and BL2.

Synthetic biology research at JBEI typically operates at the BL1 level, which is defined as being: “Suitable for work involving agents of unknown or minimal potential hazard to laboratory personnel and the environment, or work with defined and characterized strains of viable microorganisms not known to consistently cause disease in healthy adult humans.”

Through the Integrated Safety Management (ISM) program the Lab meets or exceeds standards for biosafety, worker safety and health, and environmental protection set by the National Institutes of Health (NIH) and Centers for Disease Control and Prevention (CDC) for the biosafety of recombinant and other research; California Department of Public Health (CDPH) for biohazardous waste; Occupational Safety and Health Administration (OSHA) for bloodborne pathogens; U.S. Department of Agriculture (USDA) for protection of animal and plant resources; and other agencies.

Biosafety of research is also reviewed by a Lab Institutional Biosafety Committee (IBC) comprised of peer researchers, safety and health experts, and members of the public. IBC reviews include assessment and documentation of any risks and required controls.

Berkeley Lab maintains a robust incident and emergency reporting and response program in which staff and management are trained and encouraged to report incidents. The California Department of Public Health inspects the Lab for compliance with medical waste storage and disposal requirements and has consistently found the Lab’s program in compliance.

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The singularity is coming: 3 chips that meld man and machine | GAFnews

The singularity is coming: 3 chips that meld man and machine | GAFnews | SynBioFromLeukipposInstitute | Scoop.it

Cramming biology on silicon is not a new effort, and it’s one that has helped advance the science of genomics and led to the $1,000 genome. But in the last few weeks, I’ve noticed some pretty sweet combinations of biology and chip research. They will first end up helping biological research and test new drug compounds, but in the future might become something out of Ray Kurzweil’s The Singularity, the melding of man and machine.

A gut chip for a gut check: You and I might not want a chip that mimics the entire process of a human digestive system including peristalsis and living bacteria, but folks trying to test out drugs do. And now, thanks to researchers at Harvard University they have one. The lab-on-chip uses two thin channels coated in a biological growth medium and human intestinal cells to create a mini-intestine that apparently can sustain actual gut bacteria for about a week. Who needs an ant farm anymore?...

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Meet Microryza: Crowd funding for scientific research

Meet Microryza: Crowd funding for scientific research | SynBioFromLeukipposInstitute | Scoop.it
This is awesome. Launching today is Microryza, a Seattle-based firm that is taking the popular crowd-based fundraising model and is applying it to a critical component of the modern economy: scientific research.

Yes, you just might be able to help fund your own Sheldon Cooper now. The platform allows for direct donation to researchers that are working on the things that you care about, allowing you to put your money where your nerdy hunches and passions are. I would fund people looking to figure out if there was ever life on Mars. That’s just me.

 
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PLoS ONE: A GFP-lacZ Bicistronic Reporter System for Promoter Analysis in Environmental Gram-Negative Bacteria

PLoS ONE: A GFP-lacZ Bicistronic Reporter System for Promoter Analysis in Environmental Gram-Negative Bacteria | SynBioFromLeukipposInstitute | Scoop.it

by

Rafael Silva-Rocha, Victor de Lorenzo
"Here, we describe a bicistronic reporter system for the analysis of promoter activity in a variety of Gram-negative bacteria at both the population and single-cell levels. This synthetic genetic tool utilizes an artificial operon comprising the gfp and lacZ genes that are assembled in a suicide vector, which is integrated at specific sites within the chromosome of the target bacterium, thereby creating a monocopy reporter system. This tool was instrumental for the complete in vivo characterization of two promoters, Pb and Pc, that drive the expression of the benzoate and catechol degradation pathways, respectively, of the soil bacterium Pseudomonas putida KT2440. The parameterization of these promoters in a population (using β-galactosidase assays) and in single cells (using flow cytometry) was necessary to examine the basic numerical features of these systems, such as the basal and maximal levels and the induction kinetics in response to an inducer (benzoate). Remarkably, GFP afforded a view of the process at a much higher resolution compared with standard lacZ tests; changes in fluorescence faithfully reflected variations in the transcriptional regimes of individual bacteria. The broad host range of the vector/reporter platform is an asset for the characterization of promoters in different bacteria, thereby expanding the diversity of genomic chasses amenable to Synthetic Biology methods."
http://bit.ly/HzC5My

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Leukippos

Leukippos | SynBioFromLeukipposInstitute | Scoop.it

Synthetic Biology Lab in the Cloud

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Crowd-Sourcing Brain Research Leads to Breakthrough

Crowd-Sourcing Brain Research Leads to Breakthrough | SynBioFromLeukipposInstitute | Scoop.it

By BENEDICT CAREY

 "In the largest collaborative study of the brain to date, scientists using imaging technology at more than 100 centers worldwide have for the first time zeroed in on genes that they agree play a role in intelligence and memory. Scientists working to understand the biology of brain function — and especially those using brain imaging, a blunt tool — have been badly stalled. But the new work, involving more than 200 scientists, lays out a strategy for breaking the logjam. The findings appear in a series of papers published online Sunday in the journal Nature Genetics..." Crowd-Sourcing will also be powerful in other areas of science!
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Pills That Text You When You Forget to Take Them

Pills That Text You When You Forget to Take Them | SynBioFromLeukipposInstitute | Scoop.it

There are several of such devices, which can monitor your body on the horizon. One area of synthetic biology is about to build such sensor out of biological material. This concept has also clear ethical implications and ethical engineering of this kind of devices is important to do in parallel with the physical engineering. In medicine it is very important to have a pure focus on the individual patient. Thus it is very important that data obtained remain under full control of the patient. There is misuse potential.

For details see this post by ANJELIKA PARANJPE

 "We've all been there. The weekend was simply too fun or the day at work totally got away from you, and you forgot to take your daily medication. No matter how many times you set that iPhone alarm, you always seem to miss it. Well, forgetful folks, your days of missing crucial doses are behind you thanks to… The Cyberpill....."

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Web freedom faces greatest threat ever, warns Google's Sergey Brin

Web freedom faces greatest threat ever, warns Google's Sergey Brin | SynBioFromLeukipposInstitute | Scoop.it

A free and open internet is key for modern data driven science, such as systems biology and it's practical application synthetic biology. Thus I support a battle for a free internet. Scientists need their data collected in an open free accessible common data pool. Internet censorship will destroy modern science, and thus future companies and jobs.

For details see this article by Ian Katz in the Guardian

"The principles of openness and universal access that underpinned the creation of the internet three decades ago are under greater threat than ever, according to Google co-founder Sergey Brin.

In an interview with the Guardian, Brin warned there were "very powerful forces that have lined up against the open internet on all sides and around the world". "I am more worried than I have been in the past," he said. "It's scary."

The threat to the freedom of the internet comes, he claims, from a combination of governments increasingly trying to control access and communication by their citizens, the entertainment industry's attempts to crack down on piracy, and the rise of "restrictive" walled gardens...."

A free and open internet is key for modern data driven science. Thus I support a battle for a free internet.

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Application of Synthetic Biology to Regenerative Medicine

"Synthetic biology uses interchangeable and standardized “bio-parts” to construct complex genetic networks that include sensing-, information processing- and effector-modules: these allow robust and tunable transgene expression in response to a change in signal input. The rise of this field has coincided closely with the emergence of regenerative medicine as a distinct discipline. Unlike synthetic biology, regenerative medicine uses the natural abilities of cells to make trophic factors and to produce new tissues as they would in normal development and tissue maintenance. In this article, we argue that bringing these young fields together, so that synthetic biology techniques are applied to the problem of regeneration, has the potential to significantly enhance our ability to help those in clinical need. We first review the synthetic tool kit available for engineered mammalian networks, then examine the main areas in which synthetic biology techniques might be applied to promote regeneration: (i) biosynthesis and controlled release of therapeutic molecules, (ii) synthesis of scaffold material, (iii) regulation of stem cells, and (iv) programming cells to organize themselves into novel tissues. We finally consider the long-term potential of synthetic biology for regenerative medicine, and the risks and challenges ahead."

 
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Synthetic chemists print labware to order - the next step in 3D printing

"The time may soon come for chemists to throw away all their old glass reaction vessels. UK and Norwegian scientists have now shown that far better and more effective vessels can be fabricated on a 3D printer.

Not only do 3D printers offer the possibility of producing vessels with much more complex architectures, but the vessels can be designed to influence the course of the reaction or even to take part in it. And if that's not enough, 3D printers also offer a convenient way to introduce reactant chemicals into the vessels.

'I have always been interested in new ways of doing complex chemistry and exploring new reaction spaces,' explains lead researcher Lee Cronin at the University of Glasgow. 'I had never used a 3D printer before but met a researcher interested in designing new objects for 3D printed architecture and got to asking them about combining it with chemistry.'..."

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Systematic identification of edited microRNAs in the human brain

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Shahar Alon, Eyal Mor, Francois Vigneault, George Church, Franco Locatelli, Federica Galeano, Angela Gallo, Noam Shomron and Eli Eisenberg

"A-to-I editing modifies RNA transcripts from their genomic blueprint. A prerequisite for this process is a double-stranded RNA (dsRNA) structure. Such dsRNAs are formed as part of the microRNA (miRNA) maturation process, and it is therefore expected that miRNAs are affected by A-to-I editing. Editing of miRNAs has the potential to add another layer of complexity to gene regulation pathways, especially if editing occurs within the miRNA-mRNA recognition site. Thus, it is of interest to study the extent of this phenomenon. Current reports in the literature disagree on its extent; while some reports claim that it may be widespread others deem the reported events as rare. Utilizing a next-generation sequencing (NGS) approach supplemented by an extensive bioinformatic analysis, we were able to systematically identify A-to-I editing events in mature miRNAs derived from human brain tissues. Our algorithm successfully identified many of the known editing sites in mature miRNAs, and revealed 17 novel human sites, 12 of which are in the recognition sites of the miRNAs. We confirmed most of the editing events using in-vitro ADAR over-expression assays. The editing efficiency of most sites identified is very low. Similar results are obtained for publicly available datasets of mouse brain-regions tissues. Thus, we find that A-to-I editing does alter several miRNAs but it is not widespread."
http://bit.ly/ITHN0m

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Top Financial Site PennyStockDetectives.Com Points Out Great Opportunities in Synthetic Biology

Top Financial Site PennyStockDetectives.Com Points Out Great Opportunities in Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it

"In a recent Penny Stock Detectives article, editor Danny Esposito reports on opportunities in synthetic biology, a revolutionary biotechnology that engineers and so rebuilds natural systems, imitating nature. Esposito reveals that there are biotech companies creating an artificial gene, with the only function of absorbing oil that has been spilled in the ocean, or creating a synthetic gene with the sole purpose of absorbing the harmful pollution that is emitted right from the manufacturer’s site. According to the editor, these are just few examples of the profits that can be made with synthetic biology."

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A Method for Fast, High-Precision Characterization of Synthetic Biology Devices

A Method for Fast, High-Precision Characterization of Synthetic Biology Devices

by
Jacob Beal1, Ron Weiss2, Fusun Yaman1, Noah Davidsohn2, and Aaron Adler1
1Raytheon BBN Technologies and 2MIT

"Engineering biological systems with predictable behavior is a founda- tional goal of synthetic biology. To accomplish this, it is important to accurately characterize the behavior of biological devices. Prior charac- terization efforts, however, have generally not yielded enough high-quality information to enable compositional design. In the TASBE (A Tool-Chain to Accelerate Synthetic Biological Engineering) project we have developed a new characterization technique capable of producing such data. This document describes the techniques we have developed, along with exam- ples of their application, so that the techniques can be accurately used by others."

free PDF can be found here:
http://bit.ly/HzJcnC

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Expressing bacterial operons in plants | The 4th Domain

Expressing bacterial operons in plants | The 4th Domain | SynBioFromLeukipposInstitute | Scoop.it

Posted by Thomas Howard
One of the advantages of working with bacteria is that genes can be clustered together under control of a single promoter (known as an operon). Multiple protein products can therefore be generated from a single messenger RNA strand (the mRNA is said to be polycistronic (Fig. 1)). As a result entire metabolic pathways can be created using a single promoter.

In eukaryotic systems this is generally not the case. mRNA in eukaryotes is typically monocistronic (there are a few exceptions but these undergo post-transcriptional processing and are not viewed as truly polycistronic e.g. lower box Fig. 1). This limitation means more DNA cloning/synthesis, repeated rounds of transformation and increased difficulty in controlling the expression levels of different genes – which can be important for metabolic engineering, for example.

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Combinatorial targeting of ribbon–helix–helix artificial transcription factors to chimeric recognition sites

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Massimiliano Zampini and Finbarr Hayes
"Artificial transcription factors (ATFs) are potent synthetic biology tools for modulating endogenous gene expression and precision genome editing. The ribbon–helix–helix (RHH) superfamily of transcription factors are widespread in bacteria and archaea. The principal DNA binding determinant in this family comprises a two-stranded antiparallel β-sheet (ribbons) in which a pair of eight-residue motifs insert into the major groove. Here, we demonstrate that ribbons of divergent RHH proteins are compact and portable elements that can be grafted into a common α-helical scaffold producing active ATFs. Hybrid proteins cooperatively recognize DNA sites possessing core tetramer boxes whose functional spacing is dictated by interactions between the α-helical backbones. These interactions also promote combinatorial binding of chimeras with different transplanted ribbons, but identical backbones, to synthetic sites bearing cognate boxes for each protein either in vitro or in vivo. The composite assembly of interacting hybrid proteins offers potential advantages associated with combinatorial approaches to DNA recognition compared with ATFs that involve binding of a single protein. Moreover, the new class of RHH ATFs may be utilized to re-engineer transcriptional circuits, or may be enhanced with affinity tags, fluorescent moieties or other elements for targeted genome marking and manipulation in bacteria and archaea."

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Open biohacking - DIY genetic engineering, synbio (synthetic biology), join the fight against disease and death

DIY genetic engineering, synbio, bio-experimentalism -- join the fight against disease and death today.

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