G-quadruplex DNA is a family of diverse DNA structures that are formed from the hydrogen bonding association of four guanine bases. Compounds that bind selectively to G-quadruplex DNA structures and not to double-stranded DNA may be useful tools for studying the potential roles of these unusual DNA structures in cellular processes such as transcription, recombination, and senescence.

TEL-01 is a member of al class of G-quadruplex DNA ligands known as perylene diimides (core structure highlighted in red). We first predicted the ability of this class of compounds to interact with G-quadruplex DNA by searching a virtual library of potential ligands using the program DOCK, developed by Irwin Kuntz and co-workers at the University of California, San Francisco. We synthesized a number of these perylene diimides, and found that many bind to G-quadruplex DNA. What was striking was the difference in the binding selectivity for G-quadruplex DNA versus double-stranded DNA exhibited by different perylene diiimides. While TEL-01 displayed a high level of G-quadruplex DNA binding selectivity in our spectroscopic assays, the structurally similar analog PIPER did not.

We eventually found that the DNA binding assay pH affected the observed G-quadruplex DNA binding selectivity; under slightly more acidic conditions, the selectivity of TEL-01 was diminished so that it resembled that exhibited by PIPER. This led to the discovery that the G-quadruplex DNA binding selectivity of these compounds is mediated by their aggregation state. Under acidic conditions, the amino groups on the perylene diimide side chains (blue in the structures of Tel-01 and PIPER) are protonated, and this prevents aggregation. At higher pH, the side chains are not protonated and aggregation is favored. The pH at which aggregation is observed is dependent upon the nature of the side chain; TEL-01, with the less basic morpholino side chain groups, undergoes aggregation at a lower pH than does PIPER, which contains more basic piperidino side chain groups.

We are currently exploring the precise means by which perylene diimide aggregation mediates G-quadruplex DNA binding selectivity. Our studies also focus on other classes of G-quadruplex DNA ligands. We continue to use DOCK and other computational tools to design highly selective G-quadruplex DNA ligands as potential inhibitors of telomerase, G-quadruplex DNA helicases, and as tools for studying the roles of G-quadruplex DNA in cells.

For more information on perylene diimides and other G-quadruplex DNA ligands, see the following papers:

1. Fedoroff, O. Y.; Salazar, M.; Han, H.; Chemeris, V. V.; Kerwin, S. M.; Hurley, L. H. "NMR-Based Model of a Telomerase-Inhibiting Compound Bound to G-Quadruplex DNA" Biochemistry 1998, 36, 12367-12374.


2. Kerwin, S. M. "G-Quadruplex DNA as a Target for Drug Design" Curr. Pharm. Design 2000, 6, 441-471.


3. Kerwin, S. M.; Sun, D.; Kern, J. T.; Rangan, A.; Thomas, P. W. "G-Quadruplex DNA Binding by a Series of Carbocyanine Dyes" Bioorg. Med. Chem. Lett. 2001, 11, 2411-2414.


4. David, W. M.; Brodbelt, J.; Kerwin, S. M.; Thomas, P. W. "Investigation of Quadruplex Oligonucleotide-Drug Interactions by Electrospray Ionization-Mass Spectrometry" Anal. Chem. 2002, 74, 2029-2033.


5. Kern, J. T.; Thomas, P. W.; Kerwin, S. M. "The Relationship between Ligand Aggregation and G-quadruplex DNA Selectivity in a Series of 3,4,9,10-Perylenetetracarboxylic Acid Diimides" Biochemistry, 2002, 41, 11379-11389.


6. Kern, J. T.; Kerwin, S. M. "The Aggregation and G-Quadruplex DNA Selectivity of Charged 3,4,9,10-perylenetetracarboxylic Acid Diimides" Bioorg. Med. Chem. Lett., 2002, 12, 3395-3398.


7. Pothukuchy, A.; Mazzitelli, C.; Rodriguez, M. L.; Tuesuwan, B.; Salazar, M.; Brodbelt, J. S.; Kerwin, S. M. "Duplex and Quadruplex DNA binding and Photocleavage by Trioxatriangulenium Ion" Biochemistry 2005, 44, 2163 - 2172.

College of Pharmacy at UT Austin