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Molecular Dynamics Insights into Polyamine-DNA Binding Modes: Implications for Cross-Link Selectivity.

Emmanuelle Bignon^1,2, Chen-Hui Chan², Christophe Morell¹

¹Institut des Sciences Analytiques, UMR 5280, Université de Lyon 1 (UCBL) CNRS, ENS Lyon, Lyon, France.

Chemistry (Weinheim an Der Bergstrasse, Germany)

|August 18, 2017

Summary

Biogenic polyamines interact with DNA, with longer chains favoring major groove binding. This interaction facilitates the formation of harmful DNA-polyamine cross-links after guanine oxidation.

Keywords:

DNA cross-coupling molecular dynamics noncovalent interactions polyamines

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Area of Science:

Biochemistry
Molecular Biology
Computational Chemistry

Background:

Biogenic polyamines are crucial for DNA condensation and stabilization in eukaryotic cells.
Polyamines like putrescine, spermine, and spermidine are found at high concentrations in the cell nucleus.

Purpose of the Study:

To investigate the interaction modes of putrescine, spermine, and spermidine with a DNA duplex.
To elucidate the noncovalent interactions governing polyamine-DNA complex stability and reactivity.
To understand the mechanism of deleterious DNA-polyamine cross-link formation.

Main Methods:

All-atom explicit-solvent molecular dynamics simulations.
Molecular mechanics generalized Born surface area (MM-GBSA) for binding free energy calculations.
Analysis of binding modes, distances, and interactions.

Main Results:

Polyamines exhibit distinct interaction modes with DNA, shifting from minor to major groove binding with increasing aliphatic chain length.
Noncovalent interactions stabilizing the polyamine-DNA complex were identified.
A mechanism for low-barrier DNA-polyamine cross-link formation post-guanine oxidation was revealed.
Binding affinity order was determined as Put

Conclusions:

Polyamines' interaction mode with DNA is dependent on their aliphatic chain length.
The study provides insights into the molecular basis of DNA-polyamine cross-link formation.
Positively charged polyamines are essential for cross-link formation via guanine radical cation attack.