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The University of Southampton
Chemistry

The story of NMM, my favorite G-quadruplex ligand Seminar

Time:
16:00
Date:
11 March 2015
Venue:
Building 27, Room 2001 Chemistry University of Southampton Southampton SO17 1BJ

For more information regarding this seminar, please email Eugen Stulz at E.Stulz@soton.ac.uk .

Event details

Lilya Yatsunyk presents a seminar as part of the chemical Biology, Diagnostics and Therapeutics research groups seminar series.

Guanine quadruplexes (GQs) are four-stranded DNA structures formed by guanine-rich DNA sequences. They are characterized by high structural diversity forming parallel, antiparallel, mixed hybrid and other structures. Genomic distribution of sequences with quadruplex forming potential suggests their connections to cancer and aging. GQ-selective small molecule ligands are being widely developed as potential anticancer therapeutics. Through the use of circular dichroism, UV-visible and fluorescent spectroscopy, and FRET melting assay we have characterized the details of N-methyl mesoporphyrin IX (NMM) binding to biologically relevant G-rich quadruplex structures from telomeres and from oncogene promoters. The complex is formed with 1:1 stoichiometry and 1.0×105 M-1 binding constant. Remarkably, we have shown that NMM is selective for G-quadruplex (GQ) DNA vs duplex DNA and has unprecedented selectivity for parallel GQ structure as compared to an antiparallel GQ. This property, coupled with increase of NMM fluorescence in the presence of DNA, makes this ligand a possible candidate for a quadruplex probe, at least in vitro. The fluorescence of NMM increases 60-fold in the presence of parallel-stranded GQs but < 10-fold in the presence of antiparallel GQs. Single-stranded DNA, duplex, or i-motif, induce no change in NMM fluorescence. dramatically in the presence of quadruplex but not other DNA structures; this property can be exploit in fluorescent staining of quadruplexes, at least in vitro. Additionally NMM causes isomerization of human telomeric DNA into a structure with increased parallel component. We explored the kinetics of this isomerization in CD time-course experiments. Single-stranded DNA, duplex, or i-motif, induce no change in NMM fluorescence. dramatically in the presence of quadruplex but not other DNA structures; this property can be exploit in fluorescent staining of quadruplexes, at least in vitro. We determined X-ray structure of a complex between NMM and Tel22 and showed that DNA forms a 5'-5' stacked parallel-stranded quadruplexes dimers capped on both ends with NMM, supporting the spectroscopically determined 1:1 stoichiometry. The macrocycle geometry of NMM matches closely that of the terminal G-tetrad resulting in efficient π - π stacking. The out-of-plane N-methyl group of NMM fits perfectly into the center of the parallel GQ core where it aligns with potassium ions. In contrast, the interaction of the N-methyl group with duplex DNA or antiparallel GQ would lead to steric clashes that prevent NMM from binding to these structures, thus explaining its unique selectivity. Based on the biochemical data, binding of NMM to Tel22 does not rely on electrostatic interactions, which are non-specific. NMM could serve as an important prototype for the development of truly selective GQ ligands.

Speaker information

Liliya Yatsunik, Departments of Chemistry and Biochemistry. Swarthmore College, Swarthmore, 19081, USA

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