The detection system, called colorimetric screening, can be used to detect a variety of targets, such as DNA, small molecules and proteins, that bind to DNA, and the strength of the bond is indicated by a simple color change.
In a paper reported online today (March 28) by the Journal of the American Chemical Society (JACS), the research team used the colorimetric method to screen for molecules that can facilitate the formation of a special form of DNA called a triple helix. Triple helix DNA involves three strands rather than the two associated with normal DNA. However, unlike double helix DNA, the triple helix is unstable alone and requires a small molecule triplex binder to increase its stability. This research builds on work reported March 6 in the German journal Angewandte Chemie in which the same method was used to screen small molecules for their binding affinity to duplex DNA.
"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 A. Mirkin, George B. Rathmann Professor of Chemistry, professor of medicine and professor of materials science and engineering, who led both studies. "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."
In the JACS paper, the researchers demonstrated that when a triplex binder binds to a given DNA triple helix in solution the strength of that binding event can be detected by the naked eye. The color of the solution changes from blue to red when heated, and the temperature at which this occurs indicates the strength of the triplex binder’s bond.
Much like tiny bits of gold produce the vibrant red in stained glass windows, the Northwestern team also takes advantage of gold’s intense color when the metal is measured on the scale of atoms. The researchers start with gold nanoparticles, each just 13 nanometers in diameter, held together by DNA in a triple helix conformation. Because they are held together within a certain critical distance, the gold nanoparticles -- and the solution they are in -- are blue. When the solution is heated, the DNA breaks apart, and the gold nanoparticles, no longer in close proximity to each other, are now bright red.
When a triplex binder binds to DNA it creates a stronger bond that requires a higher temperature to break apart the DNA strands. By adding different triplex binders to a solution with a specific DNA sequence between the gold nanoparticles, the colorimetric method can distinguish molecules that are strong binders, medium binders and weak binders. (Current methods using fluorescence can only indicate whether or not a bond has formed.) When heated, the solution with a triplex binder that is a weak binder turns red at a lower temperature than the solution with a strong binder. This color change from blue to red allows the researchers by simple visual inspection to see which triplex binders bind to the DNA and how strongly they bind.
"It’s impossible to do a full-blown study on every triplex binder or small molecule," said Mirkin, who is director of Northwestern’s Center for Cancer Nanotechnology Excellence. "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."
A certain DNA sequence might be linked to colon cancer, for example, and the proteins expressed by that DNA produce cancer cells. By identifying a triplex binder or small molecule that binds effectively to that particular DNA sequence, a drug can be developed that shuts down protein production and stops cancer cells from proliferating.
Their next step, said Mirkin, is to challenge the research community to provide libraries of triplex binders and small molecules for his research teams to test. Any interaction with DNA, whether it be with small molecules, proteins or other DNA, can be identified by the colorimetric method. "We want to identify the real winners," said Mirkin.
In addition to Mirkin, other authors on the JACS paper are post-doctoral fellow Min Su Han (first author) and graduate student Abigail K. R. Lytton-Jean, both from Northwestern University.
Megan Fellman | EurekAlert!
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