STUDY OF PROTEIN-DNA INTERACTIONS WITH BIOSENSORS

Mithil Chokshi

VTPP 434

Section 501

Proteins and DNA are two most important biomolecules. Scientists have been working on the research pertaining to all the different interactions of these biomolecules since a long time. These interactions are most important tools for studying the fundamental cellular processes such as transcription, DNA damage and repair and apoptosis. This article is about the protein-DNA interactions (in particular) and a feat of biomedical engineering in it.

Paul Hergenrother and Brian Cunningham at the University of Illinois have developed a new class of disposable, microplate-based optical biosensors capable of detecting protein-DNA interactions. These biosensors can be used for the identification of the protein-nucleic acid and protein-protein interactions. You might have heard about the biosensors that break down the blood glucose with the help of an enzyme called glucose oxidase. The concept of the biosensors for the protein-DNA interactions is the same but obviously a different type of an application. Screening for compounds that inhibit particular kinds of protein-DNA binding is a very important step in drug development. The researchers say that apart from the protein-DNA interactions for which this biosensor is designed for, analogous experiments could also be conducted with the protein-protein and protein-RNA interactions.

These photonic crystal biosensors works as following: they consist of a low-refractive-index polymer grating coated with a film of high-refractive-index titanium oxide, attached to the bottom of a standard 384-well microplate. So, a researcher inserts the biomolecule that is been studied at the bottom of the so-called well of the device and then with the help of a technique called through-put screening mode, the researcher can detect the inhibition of the protein-DNA binding. The high through-put screening is a method of scientific experimentation which allows a researcher to quickly conduct millions of biochemical, genetic or pharmacological tests. Through this process one can rapidly identify active compounds, antibodies or genes that modulate a particular biomolecular pathway. Basically, one can find out how a metabolic pathway dependent on the protein-DNA interaction is inhibited and can help us find out a way around it.

These biosensors were demonstrated using two very different protein-DNA interactions. The first was the bacterial toxin-antitoxin system MazEF, which binds to DNA in a sequence-specific manner and is thought to be responsible for the maintenance of resistance-encoding plasmids in certain infectious bacteria. The second was the human apoptosis-inducing factor (AIF), a protein that binds to chromosomal DNA in a DNA-sequence-independent manner. They further utilized it in a screen for inhibitors of the AIF-DNA interaction, where approximately 1000 different compounds were screened and they identified that aurin tricarboxylic acid was the first in vitro inhibitor of AIF. It displayed an amazing 80% of inhibition of the AIF-DNA binding.

Every new technology is essentially invented to replace the current with a more cost efficient, less time consuming, mass reproducible, and a one that can lead to a more accurate biological assay. Well, guess what, you can do the same with this technology of biosensors. These photonic biosensors are mass-producible. The different biochemical interactions of potential pharmaceutical compounds can be screened against a wide range of proteins which could be a critical step towards drug discoveries. The benefit of this would be that the costly failures of the drugs by trying it on animals and humans could be avoided.

In conclusion, I think that these novel biosensors are an efficiect way to study the protein-nucleic acid and protein-protein interactions and could possibly become a reason for a breakthrough in designing various drugs and curing fatal diseases.

I thought that since we just studied in-detail structures of proteins and nucleic acids and also cellular activities like apotosis, this article should interest everyone in protein-nucleic acid and protein-protein interactions and research them to understand them better.

URL:

http://www.sciencedaily.com/releases/2008/09/080923121954.htm