Quadruplex Structure In Cell-Like Solution

In work with potential implications for the development of anticancer therapeutics, the folding pattern of DNA quadruplexes formed by human telomeres in a solution of potassium ions, a medium closely resembling the cellular environment, has been found by three groups. Two of the groups have also succeeded in obtaining the first 3-D nuclear magnetic resonance spectrometry K⁺-solution structures of a human telomeric quadruplex.

Telomeres are guanine-rich protein-DNA assemblies that protect chromosome ends. The single-stranded telomere terminus can adopt the shape of a quadruplex, a folded conformation formed by some guanine-rich DNA repeat sequences. The 3-D structure adopted by human telomeric quadruplexes is of particular interest for anticancer drug discovery efforts, as drugs are being designed to interact with such structures to inhibit telomere extension, a process that occurs selectively in cancer cells.

Various groups have obtained 3-D human telomeric quadruplex structures. For example, structural biologist Dinshaw J. Patel of Memorial Sloan-Kettering Cancer Center and coworkers obtained the NMR structure of human telomeric quadruplexes in Na⁺ solution in 1993. And a group led by professor Stephen Neidle of the School of Pharmacy at the University of London, obtained X-ray structures of human quadruplexes in a K⁺-containing crystal in 2002.

K⁺ solution is considered much more biologically relevant than Na⁺ solution because K⁺ predominates in cells. And a solution structure in K⁺ solution has been especially sought, because a crystal structure may not always accurately reflect the conformations molecules adopt in living cells. But the structure of the human quadruplex in K⁺ solution has resisted analysis.

Now three groups have determined the folding pattern, or topology, of the human telomeric quadruplex. Chemistry professor Hiroshi Sugiyama and coworkers at Kyoto University, in Japan, obtained topological models by circular dichroism spectroscopy (Bioorg. Med. Chem., 2006, 14, 5584). And in independent studies, assistant professor of pharmacology and toxicology Danzhou Yang of the University of Arizona and coworkers (Nucleic Acids Res. 2006, 34, 2723) and Patel, senior research scientist Anh Tuan Phan, and coworkers (J. Am. Chem. Soc., DOI:10.1021/ja062791w) used NMR to obtain similar topological models.

Patel's group also obtained a more detailed 3-D K⁺-solution structure of the quadruplex by making minor substitutions in the human telomeric DNA sequence, rendering the structure NMR-interpretable for the first time. In a yet unpublished study, Yang and coworkers have also determined a 3-D NMR structure of another slightly modified telomere sequence in K⁺ solution. Although structures of native sequences would have been more desirable, these provide probably about as close an approximation to the fully human structure as can currently be achieved. Different quadruplex structures are believed to be in equilibrium at telomere ends, so these structures are probably not the end of the story in any case.

Nevertheless, the work represents a key step toward the goal of understanding the structure of human telomeres. "These papers concur in finding an important new category of fold for this structure, with two lateral loops and one propeller loop, although it is not clear to what extent it is the dominant species in solution," Neidle comments. "There is still much to learn about these complex molecules, and we all agree that more high-resolution structure analyses will continue to be important as the best way of obtaining topological information."