Tag: genetic

First Ever Organism with “Alien” DNA

alien-dna-640x353Normal DNA, which is characterized by the double helix and its the four bases that bond it together – known as T, G, A, and C – is at the heart of all living organisms. While permutations and differences exist between species, this basic structure has existed unchanged for billions of years. That is, until now. This past May, researchers announced that they had created the first ever organism with synthetic DNA that has two new bases – X and Y. Mary Shelley and H.G. Wells must be turning over in their graves, as scientists are officially playing God now!

This landmark study, 15 years in the making, was carried out by scientists at the Scripps Research Institute and published in Nature today under the title “A semi-synthetic organism with an expanded genetic alphabet”. In normal DNA, the four bases combine in predictable ways. A always bonds with T, and C always bonds with G, creating a fairly simple “language” of base pairs — ATCGAAATGCC, etc. Combine a few dozen base pairs together in a long strand of DNA and you then have a gene, which tells the organism how to produce a certain protein.

DNA-MicroarrayIf you know the sequence of letters down one strand of the helix, you always know what other letter is. This “complementarity” is the fundamental reason why a DNA helix can be split down the middle, and then have the other half perfectly recreated. In this new study, the Scripps scientists found a method of inserting a new base pair into the DNA of an e. coli bacterium. These two new bases are represented by the letters X and Y, but the actual chemicals are described as “d5SICS” and “dNaM.”

A previous in vitro (test tube) study had shown that these two chemicals were compatible with the enzymes that split and copy DNA. For the purposes of this study, the scientists began by genetically engineering an e. coli bacterium to allow the new chemicals (d5SICS and dNaM) through the cell membrane. Then they inserted a DNA plasmid (a small loop of DNA) that contained a single XY base pair into the bacterium.

dnaheadAs long as the new chemicals were available, the bacterium continued to reproduce normally, copying and passing on the new DNA, alien plasmid and all, and continued to carry on flawlessly for almost a week. For now, the XY base pair does nothing; it just sits there in the DNA, waiting to be copied. In this form, it could be used as biological data storage which, as a new form of biocomputing, could result in hundreds of terabytes of data being stored in a single gram of synthetic, alien DNA. 

Floyd Romesberg, who led the research, has much grander plans:

If you read a book that was written with four letters, you’re not going to be able to tell many interesting stories. If you’re given more letters, you can invent new words, you can find new ways to use those words and you can probably tell more interesting stories.

Now his target is to find a way of getting the alien DNA to actually do something, such as producing amino acids (and thus proteins) that aren’t found in nature. If Romesberg and his colleagues can crack that nut, then it will suddenly become possible to engineer cells that produce proteins that target cancer cells, or special amino acids that help with fluorescent microscopy, or new drugs/gene therapies that do weird and wonderful things.

dna_cancerUltimately it may even be possible to create a wholly synthetic organism with DNA that contains dozens (or hundreds) of different base pairs that can produce an almost infinitely complex library of amino acids and proteins. At that point, we’d basically be rewriting some four billion years of evolution. The organisms and creatures that would arise would be unrecognizable, and be capable of just about anything that a researcher (or mad scientist) could dream up.

In the future, this breakthrough should allow for the creation of highly customized organisms – bacteria, animals, humans – that behave in weird and wonderful ways that mundane four-base DNA would never allow. At the same time, it raises ethical dilemmas and fears that may be well founded. But such is the nature of breakthroughs. The potential for harm and good are always presumably equal when they are firts conceived.

Source: extremetech.com

Happy DNA Day!

dna_cancerThough I am a week late in expressing this sentiment, I feel I must acknowledge this rather interesting of events. As it stands, this past April 22nd was the sixty-first anniversary of the molecular structure of DNA being revealed to the world. What began as a publication in the magazine Nature has now become emblematic of the programming language of life, and our understanding of DNA has grown by leaps and bounds over the past six decades.

To commemorate such an important landmark in the history of humanity, a look back at some of the more recent developments in the field of genetic research would seem to be in order. For example, it was on April 22nd of this year that a rather interesting study was published in the Proceedings of the National Academy of Sciences. The lead on this study was none other than Svante Pääbo – the world’s foremost expert in Neanderthal genetics.

humanEvolutionBased on the genomes of three neanderthals that were found in disparate locations in Eurasia, Pääbo and his colleagues have concluded that the genetic diversity in Neanderthals is significantly less when compared to present-day Homo sapiens. It also appears as if the Neanderthal populations were relatively isolated and tiny, so gene flow was extremely limited for these groups. In short, our homonid cousins didn’t get around and interbreed quite as much as we’ve done, which may shed some light on their disappearance.

On the very same day, an article was published in the Proceedings of the Royal Society B that proposed that skin cancer from the sun’s damaging UV rays was actually a driving force in the national selection for dark skin in early humans. In the article, Mel Greaves delivers a compelling argument that the deadliness of skin cancer in young albino children in Africa and Central America demonstrates just how vital it was for early humans to develop dark skin.

GenoChipAnd on April 25th, National Geographic and Family Tree DNA teamed up to announce the release of a brand new version of the human Y-DNA tree. This new tree of Y chromosome mutations has over 1,200 branches — almost double the number of branches that the Genographic Project was displaying before. With this much refinement, it’s now even easier to track the historical migrations of your distant ancestors.

To celebrate this monumental roll-out, Family Tree DNA offered a 20% discount on the 37-marker Y-DNA test and all individual Y-DNA SNP (single-nucleotide polymorphism) tests, an offer which sadly expired on April 27th. However, interested parties can still have this cutting-edge anthropological genetic test performed for $200. And it’s something to keep in mind for next year certainly. What better way to celebrate DNA day than to have a full genetic profile of yourself made?

encodeAnd let’s not forget, 2012 was also the year that the Encyclopedia of DNA Elements (ENCODE) Consortium – an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI) – released the world’s most complete report on the human genome to date. Unlike the Human Genome Project, which released the first catalog of human DNA back in 2003, ENCODE was not only able to catalog the human genome’s various parts, but also what those components actually do.

Among the initiative’s many findings was that so-called “junk DNA” – outlier DNA sequences that do not encode for protein sequences – are not junk at all, and are in fact responsible for such things as gene regulation, disease onset, and even human height. As I’ve said before, these findings will go a long way towards developing gene therapy, biotechnology that seeks to create artificial DNA and self-assembling structures, and even cloning.

Tree-600x405Yes, it’s an exciting time for the field of DNA research, and not just because of the many doors its likely to open. Beyond medical and bioresearch, it helps us to understand of ourselves as a species, our collective origins, and may perhaps help us to see just how interconnected we all truly are. For centuries now, a great many evils and prejudices have been committed in the name of “racial superiority” or racial differences.

Armed with this new knowledge, we might just come to realize that this great organism known as humanity is all fruit of the same tree.

Sources: extremetech.com, genome.ucsc.edu, newswatch.nationalgeographic.com