Stimulation of DNA strand slippage synthesis by a bulge binding synthetic agent

It has been postulated that bulged structures may be intermediates in the DNA strand slippage synthesis associated with the expansion of nucleotide repeats in various neurodegenerative diseases and cancer. To probe the possible role of bulged structures in this process, we have synthesized a wedge-shaped spirocyclic molecule, DDI (double-decker intercalator), on the basis of our earlier work with the bulge-specific derivative prepared from the enediyne antitumor antibiotic neocarzinostatin chromophore. Using a series of primers/templates containing nucleotide repeats [(AAT)(3)/(ATT)(5), (ATT)(3)/(AAT)(5), (CAG)(3)/(CTG)(5), (CA)(4)C/(GT)(7)G, (GT)(4)G/(CA)(7)C, T(9)/A(30), T(20)/A(30)] with the Klenow fragment of Escherichia coli DNA polymerase I, we find that DDI markedly enhances the formation of long DNA products, whose synthesis would require strand slippage to occur. DDI-induced slippage synthesis is more pronounced as the incubation proceeds and at limiting enzyme levels. The gel band pattern of the synthesized DNA products reflects the particular nucleotide repeat unit and is not altered by DDI. The lack of any drug effect on primer extension on M13 DNA and heteropolymeric 62-mer templates, where strand slippage is much less likely to occur, suggests that stimulation of slippage synthesis by DDI is not due to a direct effect on the enzyme. By contrast, other DNA-binding agents, such as ethidium bromide, distamycin, and doxorubicin, inhibit the formation of slippage-induced DNA products, but this block can be overcome by DDI, presumably by its destabilizing duplex DNA-binding sites for these other agents. We propose that DDI binds to or induces the formation of a bulge or related structure, which promotes DNA strand slippage and its consequent expansion of nucleotide repeats during replication by DNA polymerase I and that this action provides insight into the development of agents that interfere with nucleotide expansions found in various disease states.