Porous hydrogel structure  (Source: Harvard University)
Entropic Trapping helps DNA fragments travel through the hydrogel's porous structure

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."

This study was published in the September 3 issue of Physical Review Letters.

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