Researchers at Northwestern University, US, have developed a nanoparticle-based test that assesses the binding strength of triplex DNA binders. The technique could lead to high-throughput screening methods for developing drugs to treat genetic diseases.
"Pharmaceutical companies are targeting DNA for different therapies and they need to identify DNA or small molecules that selectively bind to DNA to turn on or off the gene expression related to a particular disease," said Chad Mirkin of Northwestern. "Our method, which is simpler, faster and more convenient than conventional methods, should help researchers zero in on potential anti-cancer agents from their large libraries of candidates more quickly."
DNA generally has a duplex structure in which a pair of DNA strands link up and form a double helix. But occasionally three strands will bind together. This triplex DNA, also known as triple helix DNA, is only stable in the presence of a small molecule triplex binder.
To test whether a molecule acts a triplex binder, the team add it to a solution containing two types of DNA strand functionalized with 13 nm-diameter gold nanoparticles, as well as free DNA strands complementary to one of the other two types.
If the introduced test molecule does not act as a triplex binder, the complementary DNA will form a double helix and the other functionalized DNA will remain unbound.
But if a triplex binder is added, the three types of DNA form a stable triplex structure. As a result, the nanoparticles aggregate together and their plasmon resonance undergoes a red-shift. This causes a red-to-blue colour change that's easy and quick for researchers to identify.
The process is reversible by heating the solution, which breaks up the triplex structures. The temperature at which the break-up - and associated colour change back to red - occurs indicates the strength with which the triplex binder links to the DNA. The higher the temperature needed to break the bonds, the stronger they were.
Mirkin and colleagues demonstrated the technique using the known triplex binding agents benzo[e]pyridoindole (BePI) and coralyne (CORA). The strong binder BePI required higher temperatures to break up the triplex structures than the weaker binder CORA did.
"It's impossible to do a full-blown study on every triplex binder or small molecule," said Mirkin. "You need to narrow down the possible candidates. This method allows researchers to identify the types of triplex binders or molecules that are effective for a given DNA sequence. Most diseases have a unique genetic code associated with them, and by manipulating the genes with the right triplex binders or small molecules you can develop new therapies."
Now Mirkin and colleagues hope to test libraries of triplex binders and small molecules provided by the research community.
"Source"[http://nanotechweb.org/articles/news/5/4/2?alert=1].
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