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

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

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

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
Volume122
Issue number43
DOIs
StatePublished - Nov 1 2018
Externally publishedYes

Fingerprint

Quinine
Raman Spectrum Analysis
Molecular Dynamics Simulation
Raman spectroscopy
Molecular dynamics
DNA
deoxyribonucleic acid
quinoline
molecular dynamics
Computer simulation
Base Pairing
simulation
rings
Antimalarials
interactions
Vibration
Quinuclidines
spectral correlation
Stark effect
parasites

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

Cite this

Punihaole, D., Workman, R., Upadhyay, S., Van Bruggen, C., Schmitz, A. J., Reineke, T. M., & Frontiera, R. R. (2018). New Insights into Quinine-DNA Binding Using Raman Spectroscopy and Molecular Dynamics Simulations. Journal of Physical Chemistry B, 122(43), 9840-9851. https://doi.org/10.1021/acs.jpcb.8b05795

New Insights into Quinine-DNA Binding Using Raman Spectroscopy and Molecular Dynamics Simulations. / Punihaole, David; Workman, Riley; Upadhyay, Shiv; Van Bruggen, Craig; Schmitz, Andrew J.; Reineke, Theresa M.; Frontiera, Renee R.

In: Journal of Physical Chemistry B, Vol. 122, No. 43, 01.11.2018, p. 9840-9851.

Research output: Contribution to journalArticle

Punihaole, D, Workman, R, Upadhyay, S, Van Bruggen, C, Schmitz, AJ, Reineke, TM & Frontiera, RR 2018, 'New Insights into Quinine-DNA Binding Using Raman Spectroscopy and Molecular Dynamics Simulations', Journal of Physical Chemistry B, vol. 122, no. 43, pp. 9840-9851. https://doi.org/10.1021/acs.jpcb.8b05795
Punihaole, David ; Workman, Riley ; Upadhyay, Shiv ; Van Bruggen, Craig ; Schmitz, Andrew J. ; Reineke, Theresa M. ; Frontiera, Renee R. / New Insights into Quinine-DNA Binding Using Raman Spectroscopy and Molecular Dynamics Simulations. In: Journal of Physical Chemistry B. 2018 ; Vol. 122, No. 43. pp. 9840-9851.
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