Issue 3, 2023

A direct approach toward investigating DNA–ligand interactions via surface-enhanced Raman spectroscopy combined with molecular dynamics simulations

Abstract

Small molecules that interfere with DNA replication can trigger genomic instability, which makes these molecules valuable in the search for anticancer drugs. Thus, interactions between DNA and its ligands at the molecular level are of great significance. In the present study, a new method based on surface-enhanced Raman spectroscopy (SERS) combined with molecular dynamics simulations has been proposed for analyzing the interactions between DNA and its ligands. The SERS signals of DNA hairpins (ST: d(CGACCAACGTGTCGCCTGGTCG), AP1: d(CGCACAACGTGTCGCCTGTGCG)), pure argininamide, and their complexes, were obtained, and the characteristic peak sites of the DNA secondary structure and argininamide ligand-binding region were analyzed. Molecular dynamics calculations predicted that argininamide binds to the 8C and 9G bases of AP1 via hydrogen bonding. Our method successfully detected the changes of SERS fingerprint peaks of hydrogen bonds and bases between argininamide and DNA hairpin bases, and their binding sites and action modes were consistent with the predicted results of the molecular dynamics simulations. This SERS technology combined with the molecular dynamics simulation detection platform provides a general analysis tool, with the advantage of effective, rapid, and sensitive detection. This platform can obtain sufficient molecular level conformational information to provide avenues for rapid drug screening and promote progress in several fields, including targeted drug design.

Graphical abstract: A direct approach toward investigating DNA–ligand interactions via surface-enhanced Raman spectroscopy combined with molecular dynamics simulations

Supplementary files

Article information

Article type
Paper
Submitted
30 সেপ্টে. 2022
Accepted
04 ডিসে. 2022
First published
23 ডিসে. 2022

Phys. Chem. Chem. Phys., 2023,25, 2153-2160

A direct approach toward investigating DNA–ligand interactions via surface-enhanced Raman spectroscopy combined with molecular dynamics simulations

Y. Wang, N. Shi, Y. He, Y. Li and Q. Zheng, Phys. Chem. Chem. Phys., 2023, 25, 2153 DOI: 10.1039/D2CP04566D

To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements