Binding of topotecan to a nicked DNA oligomer in solution

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Topotecan (TPT) is an established antitumor agent.
• TPT functions by inhibiting topoisomerase I and DNA religation.
• Previous crystal structure analysis provided insights into TPT-DNA binding.

Purpose of the Study:

• To elucidate the solution structure of the Topotecan-nicked DNA complex.
• To compare the solution structure with the previously determined crystal structure.
• To investigate the binding affinity of different Topotecan forms.

Main Methods:

• Nuclear Magnetic Resonance (NMR) spectroscopy.
• Molecular modeling.
• Analysis of DNA-topoisomerase I-drug ternary complex.

Main Results:

• The solution structure of the Topotecan-nicked DNA complex is similar but not identical to the crystal conformation.
• Alternative geometries of the complex exist but are in very low population.
• The lactone form of Topotecan exhibits approximately 40-fold greater binding affinity compared to the ring-opened carboxylate form.

Conclusions:

• NMR and molecular modeling reveal subtle differences between crystal and solution structures of the Topotecan-DNA complex.
• The lactone form of Topotecan is the predominant and more potent binding species.
• These findings enhance understanding of Topotecan's mechanism of action at a molecular level.