New Method Helps Separation of DNA Fragments in Hydrogels

A Texas A&M University chemical engineer has provided an important advancement to DNA analysis by revealing a new method of separating DNA fragments more effectively, which has the potential to benefit the fields of genetic engineering, biomedical research and forensics.

Victor M. Ugaz, an associate professor in the university's Artie McFerrin Department of Chemical Engineering, along with Nan Shi, a graduate student, have been working with a gelatin called hydrogel in order to develop and observe the certain types of conditions that "result in the optimum gel pore structure for separation of a wide range of DNA fragment sizes." The way DNA fragments moved through the hydrogel was key to their findings.

Ugaz and Shi's research consisted of using a process called electrophoresis, where negatively charged DNA is inserted into a porous hydrogel. Then, an electric field is applied in order to make DNA fragments move though the hydrogel's pores. Smaller chains are able to move through pores easier and faster, where longer chains have to "unthread" and separate in order to pass through pores that are either the same size or smaller than the coiled DNA fragment. This separation process is called entropic trapping. Longer DNA chains separate and squeeze quickly through smaller pores and return to its coiled shape in larger pores.

"It changes the way you think about the entire process because these findings demonstrate a rational way to connect the pore structure of the gel quantitatively to the mechanism by which the DNA moves through the gel," said Ugaz. "Researchers can now actually design gels to specifically harness certain effects, and they will need this information we have found to do that."

What makes Ugaz and Shi's work an important advancement is the use of entropic trapping for separation within a hydrogel because up until this point, scientists were unsure as to how the DNA fragment's transport system was linked to the hydrogel's structure of pores. Choosing the correct hydrogel for these types of processes was difficult because hydrogels have specific properties, and there was no way of knowing which hydrogel possessed the right properties for this type of research. But entropic trapping within the gel has proved to be an efficient way for DNA fragments to travel through the pores.

"You want to be able to detect the smallest possible difference in size between DNA fragments," said Ugaz. "The size of the fragments may be very close, and you may need to detect a difference of one unit in size. To do this, you would want to be able to specifically construct a hydrogel with the necessary pore structure to achieve this.

"We have a better picture of how to do this than what has existed. We know what the gel needs to look like and how it needs to be prepared. We're able to understand how to construct a gel that would allow DNA to move via an entropic trapping method that enhances separation performance and in turn leads to more effective analysis. This finding could have enormous implications by helping remove current barriers to separation efficiency."

Via : dailytech.com

Synthetic Life Now A Fact

EVERYONE grumbles from time to time about doctors “playing God,” but now scientists have finally managed to create a cell that has fully synthetic DNA. In the most literal sense, we are now in the business of creating life.

It used to be the stuff of science fiction (what isn’t these days?), but it’s true, and it’s happening today.

Combining advanced computer modeling techniques with genetic engineering, researchers have managed to recode the DNA of a bacterium, more or less at will. Keep in mind, the bacteria hasn’t been created “from scratch,” rather, the individual DNA sequences were synthesized from a “blueprint” on a computer.

At present, the implementation of the technique is more of a “micro-transplant” than anything else. A DNA synthesizer generates the customized sequences, which are then added to specialized yeast cultures. The yeast’s built-in genetic mechanisms tie together the new sequences in their proper order. After this has been done, the completed genomes are extracted, and then planted into donor cells. The donor cells will then reproduce according to the instructions printed on the synthetic DNA.

So what’s the upshot of all of this technical mumbo-jumbo? Initially, not much. They can encode some junk strands with strings of letters, or inject genes that will cause the cells to produce a specific protein. In the near term, applications are broad, ranging from new types of oil-eating bacteria to improved antibiotics.

In the long term, the implications are staggering. If we can recode the genomes of individual bacterial cells, we’ll soon be able to do the same for more complex creatures, like tardigrades (small animals that can survive in extreme weather), capybaras, or humans. With this technique, we’re a big leap closer to being able to correct genetic conditions, for example. But of course, there’s a catch (in bioscience, there’s always a catch to any new advancement).

If we can inject DNA into bacteria that makes it produce an antibiotic or other useful compound, the same techniques could be used to make an engineered organism more resistant to antibiotics, or better suited to biological warfare.

So, while scientists will herald this and other advancements as a great leap forward, whistleblowers, doomsday theorists and other naysayers will see this as yet another skid down a steep slippery slope. Religious groups will no doubt take offense to humans tinkering with our own genetic blueprints.

My perspective on it – the real breakthrough here is the ability to easily model and design genes. The rest of the technology, as described, is simply a refinement of pre-existing techniques. Ethical concerns aside, these techniques are here to stay, and they’ll only improve with time.

Via : timesleader.com