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Analyzing and Building Nucleic Acid Structures with 3DNA

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Structure of the first parallel DNA quadruplex-drug complex.

George R Clark¹, Patrycja D Pytel, Christopher J Squire

¹Department of Chemistry, University of Auckland, Auckland, New Zealand. g.clark@auckland.ac.nz

Journal of the American Chemical Society

|April 3, 2003

Summary

The first high-resolution crystal structure reveals how daunomycin binds to a parallel DNA quadruplex. This finding offers insights for developing new telomerase inhibitors.

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Area of Science:

Structural Biology
Medicinal Chemistry
Biochemistry

Background:

Telomeric G4 quadruplexes are crucial in telomere maintenance and cancer.
Small molecules targeting G4 structures are potential anticancer agents.
Understanding drug-G4 interactions is key for drug design.

Purpose of the Study:

To determine the high-resolution crystal structure of daunomycin bound to a parallel-stranded intermolecular telomeric G4 quadruplex (d(TGGGGT)4).
To elucidate the binding mode and interactions between daunomycin and the G4 structure.
To provide a structural basis for the design of novel telomerase inhibitors.

Main Methods:

High-resolution X-ray crystallography.
Structural analysis and molecular modeling.

Main Results:

The first crystal structure of daunomycin complexed with a parallel-stranded intermolecular telomeric G4 quadruplex (d(TGGGGT)4) was determined.
Three daunomycin molecules were observed to stack planarly at the 5' end of the G4 structure.
Daunomycin's daunosamine substituents occupied three of the four grooves of the quadruplex.

Conclusions:

The terminal G-quartet surface is large enough to accommodate additional telomerase inhibitors.
The determined structure provides a template for designing more effective G4-targeting anticancer drugs.
This work facilitates the development of new therapeutic strategies against cancer by targeting telomerase.