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A sequence-specific threading tetra-intercalator with an extremely slow dissociation rate constant

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Abstract

A long-lived and sequence-specific ligand–DNA complex would make possible the modulation of biological processes for extended periods. For this purpose, we are investigating a polyintercalation approach to DNA recognition in which flexible chains of aromatic units thread back and forth repeatedly through the double helix. Here we describe the DNA-binding behaviour of a threading tetra-intercalator. Specific binding was observed on a relatively long DNA strand that strongly favoured a predicted 14 base-pair sequence. Kinetic studies revealed a multistep association process, with sequence specificity that primarily derives from large differences in dissociation rates. The rate-limiting dissociation rate constant of the tetra-intercalator complex dissociating from its preferred binding site was extremely slow, corresponding to a half-life of 16 days. This is one of the longest non-covalent complex half-lives yet reported and, to the best of our knowledge, the longest for a DNA-binding molecule.

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Figure 1: Chemical structures of the intercalator ligands and models of the resulting ligand–DNA complexes.
Figure 2: DNase I footprinting of 3 bound to a 467 bp DNA segment.
Figure 3: Oligonucleotide duplex sequences, dissociation gel mobility shifts from oligo A and absorbance trace of the stopped-flow dissociation from oligo B.
Figure 4: 1H NMR kinetic titrations of 3 binding to oligo C.
Figure 5: Stopped-flow association absorbance traces of 3 binding to oligo B with proposed models for association of 3 to both oligo A and oligo B.

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Acknowledgements

This work was supported by the Robert A. Welch Foundation (grant F1188 to B.L.I., F1604 to K.A.J. and departmental grant AF-0005 to M.Z.F.) and the National Institutes of Health (grant GM-069647 to B.L.I.). Acknowledgement is made to the Donors of the American Chemical Society Petroleum Research Fund for partial support of this research (M.Z.F.). M.Z.F. was also supported by the Southwestern University faculty sabbatical program. We thank Steven Sorey for his help with the 1H NMR spectra.

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G.G.H., M.Z.F. and A.R.S. performed the experiments. G.G.H., M.Z.F., A.R.S., K.A.J. and B.L.I. designed the experiments and analysed the data. G.G.H., M.Z.F. and B.L.I. co-wrote the paper.

Corresponding author

Correspondence to Brent L. Iverson.

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The authors declare no competing financial interests.

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Holman, G., Zewail-Foote, M., Smith, A. et al. A sequence-specific threading tetra-intercalator with an extremely slow dissociation rate constant. Nature Chem 3, 875–881 (2011). https://doi.org/10.1038/nchem.1151

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