Scientists later realized that the unique sequences in between the DNA repeats matched the DNA of viruses—specifically those that could potentially infect bacteria. The conclusion holds that CRISPR is one part of the bacteria’s immune system, which keeps bits of dangerous viruses it its system, so that it can recognize and defend against those viruses in future attacks. The second part of the defense mechanism is a set of enzymes called Cas (CRISPR-associated proteins), which can precisely snip DNA and slice the invading viruses. Cas-9, which is the best known of the associated proteins, is an RNA-guided endonuclease that catalyzes site-specific cleavage of double stranded DNA.
Instead of trying to build genomes from scratch, George Church and researchers at the Wyss Institute have developed MAGE, a machine that harnesses the natural principles of evolution to simplify genome design and automates these steps to shorten the time scale that would typically be needed. Billions of different mutant genomes can now be generated per day. Mutants of interest are kept, and mutants that do not have the desired properties are discarded. This is rapid prototyping on a massive scale.The MAGE device can perform up to 50 different genomic alterations at nearly the same time, and is capable of taking a population of cells and adding, deleting, and replacing DNA sequences at very specific target locations within the cell’s genome.
Genome Editing
Gene Editing with CRISPR
In the last few years, human ability to edit genomes has advanced at a shockingly rapid pace. In fact, it has developed so quickly that one of the easiest and most popular tools for genome editing, known as CRISPR-Cas9, is only four years old. CRISPR was never “invented”; it is actually a naturally-occurring defense mechanism found in a wide range of bacteria. Since the 1980s, scientists observed a strange pattern in several bacterial genomes. A certain DNA sequence would be repeated over and over again, with unique sequences in between the repeats. They called this odd occurrence “clustered regularly interspaced short palindromic repeats,” or CRISPR.
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See how CRISPR works by watcing this video, brought to you by the McGovern Brain Research Institute!
When asked what CRISPR-Cas9 can potentially do for synthetic biology , Christopher Voigt answers:
“The big promise is orthogonality. You can create an almost limitless number of DNA binding proteins with Cas9 guided by different promoters. The challenge in building genetic circuits is getting enough regulatory proteins that don’t interfere with each other. CRISPR is so orthogonal and programmable that you can make a very large number of regulators. That basically means larger genetic circuits that could conceivably be as large as natural regulatory networks.”
In Synthetic Biology, Another new technology is Gene Drive, developed by Kevin Esvelt, who recently joined MIT Media Lab. Gene Drive uses CRISPR to engineer genes and ensure the changes get passed on to all future generations. For example, modifying mosquitos that do not pass on malaria, or potentially eliminating the recent outbreak in ZIKA Virus.
To quell societal fears about the potential of genome editing, Synthetic Biologist Josiah Zayner is even trying to establish CRISPR-Cas9 as a Do-It-Yourself Science. Imagine editing genomes for only 100 dollars at the comfort of your own home.The CRISPR at-home DIY kits include all the basics for a budding biohacker, not only the DNA coding for the Cas9 protein, guide RNAs, and donor template DNA to introduce genes, but also a micropipette, media, tubes, plates, and even video protocols he's developed to turn someone with no lab experience into a genetic engineer within the course of a week. Step one, Zayner says, is to learn how to use a pipette (4.11, 4.12, 4.13, 4.14).
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Multiplex Automated Genomic Engineering
MAGE is both a process and a device. In its process form, it takes advantage of recent developments in genome engineering that include a wide variety of environmentally friendly chemicals, fuels, and drugs. In its device state, MAGE automates much of the work involved in gene manipulation by taking advantage of recent innovations and, consequently, allows making genome changes at lower cost. For example, Church and Wyss researchers were able to make the bacteria Escherichia coli (E. coli) synthesize five times the normal quantity of lycopene, (an antioxidant found naturally in humans and in red fruits in vegetables), in a matter of days and just $1,000 in substances for use in chemical analysis or other reactions involved in the genome manipulation; however, if these Wyss researchers were to use the traditional method of genome manipulation, the work would have taken a biotech company months, or possibly even years to complete.
The speed and ease with which Multiplex Automated Genome Engineering (MAGE) can alter genomes will transform how scientists, researchers and innovators approach the manufacturing and production optimization of industrially significant compounds in the bioenergy, pharmaceutical, agricultural, and chemical industries (4.1, 4.2, 4.3, 4.4).
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Also, MAGE can efficiently edit multiple DNA sequences simultaneously, instead of targeting one gene at a time. This allows for the creation of cell populations that have greater genetic diversity. MAGE can be thought of as an instrument of accelerated directed evolution -- it is able to harness the power of natural selection to evolve properties not found in nature.
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