New Insights into Quinine-DNA Binding Using Raman Spectroscopy and Molecular Dynamics Simulations

David Punihaole, Riley J. Workman, Shiv Upadhyay, Craig Van Bruggen, Andrew J. Schmitz, Theresa M Reineke, Renee R Frontiera

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Quinine's ability to bind DNA and potentially inhibit transcription and translation has been examined as a mode of action for its antimalarial activity. UV absorption and fluorescence-based studies have lacked the chemical specificity to develop an unambiguous molecular-level picture of the binding interaction. To address this, we use Raman spectroscopy and molecular dynamics (MD) to investigate quinine-DNA interactions. We demonstrate that quinine's strongest Raman band in the fingerprint region, which derives from a symmetric stretching mode of the quinoline ring, is highly sensitive to the local chemical environment and pH. The frequency shifts observed for this mode in solvents of varying polarity can be explained in terms of the Stark effect using a simple Onsager solvation model, indicating that the vibration reports on the local electrostatic environment. However, specific chemical interactions between the quinoline ring and its environment, such as hydrogen bonding and π-stacking, perturb the frequency of this mode in a more complicated but predictable manner. We use this vibration as a spectroscopic probe to investigate the binding interaction between quinine and DNA. We find that, when the quinoline ring is protonated, quinine weakly intercalates into DNA by forming π-stacking interactions with the base pairs. The Raman spectra indicate that quinine can intercalate into DNA with a ratio reaching up to roughly one molecule per 25 base pairs. Our results are confirmed by MD simulations, which also show that the quinoline ring adopts a t-shaped π-stacking geometry with the DNA base pairs, whereas the quinuclidine head group weakly interacts with the phosphate backbone in the minor groove. We expect that the spectral correlations determined here will enable future studies to probe quinine's antimalarial activities, such as disrupting hemozoin biocrystallization, which is hypothesized to be, among other things, one of its primary modes of action against Plasmodium parasites.

Original languageEnglish (US)
Pages (from-to)9840-9851
Number of pages12
JournalJournal of Physical Chemistry B
Issue number43
StatePublished - Nov 1 2018

Bibliographical note

Funding Information:
We thank Professor Nicholas Levinson (University of Minnesota) for useful discussions. Funding for this work was provided by the National Institutes of Health, 5R35-GM119441 (DP, RRF), and the University of Minnesota (CVB, TMR). D.P. gratefully acknowledges postdoctoral funding from the Ford Foundation. C.V.B. acknowledges graduate student funding under the Frieda Martha Kunze and College of Science and Engineering Graduate Fellowships (University of Minnesota). MD simulation and DFT calculation computer time was supported by XSEDE MCB060069, and the computer equipment was purchased from funds provided by the National Science Foundation, CHE-1126465 and P116Z080180 (RJW and SU). Part of this work was carried out in the College of Science and Engineering Polymer Characterization Facility, University of Minnesota, which has received capital equipment funding from the NSF through the UMN MRSEC program under Award Number DMR-1420013.

Publisher Copyright:
Copyright © 2018 American Chemical Society.

How much support was provided by MRSEC?

  • Shared

Reporting period for MRSEC

  • Period 5

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.


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