Study of the interaction of the palmatine alkaloid with hybrid G-quadruplex/duplex and i-motif/duplex DNA structures

RUIZ, N., Petra JAROŠOVÁ, Petr TÁBORSKÝ and Raimundo GARGALLO. Study of the interaction of the palmatine alkaloid with hybrid G-quadruplex/duplex and i-motif/duplex DNA structures. Biophysical Chemistry. AMSTERDAM: Elsevier, 2022, vol. 281, FEB, p. 1-8. ISSN 0301-4622. Available from: https://dx.doi.org/10.1016/j.bpc.2021.106715.

Basic information

• Original name: Study of the interaction of the palmatine alkaloid with hybrid G-quadruplex/duplex and i-motif/duplex DNA structures
• Authors: RUIZ, N., Petra JAROŠOVÁ (203 Czech Republic, belonging to the institution), Petr TÁBORSKÝ (203 Czech Republic, guarantor, belonging to the institution) and Raimundo GARGALLO.
• Edition: Biophysical Chemistry, AMSTERDAM, Elsevier, 2022, 0301-4622.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10403 Physical chemistry
• Country of publisher: Netherlands
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 3.800
• RIV identification code: RIV/00216224:14310/22:00125075
• Organization unit: Faculty of Science
• Doi: http://dx.doi.org/10.1016/j.bpc.2021.106715
• UT WoS: 000722102000002
• Keywords in English: G-quadruplex; i-motif; Hybrid structures; Palmatine; Binding
• Tags: rivok
• Tags: International impact, Reviewed

Abstract

There is an increasing interest in the study of guanine or cytosine-rich sequences that may fold into G-quadruplex (G4) or i-motif (iM) structures showing a short hairpin (or stem-loop) stabilized by Watson-Crick base pairs. These hybrid spatial arrangements may be target of ligands that have been shown to interact strongly with BDNA. In this work, the interaction of the palmatine alkaloid with several sequences forming different G4s, iMs, and hybrid structures has been studied by means of spectroscopic and separation techniques, as well as multivariate data analysis methods. At the experimental conditions used in this work, the results have shown that this ligand strongly stabilizes parallel G4 structures, whereas a weaker interaction was observed with the antiparallel G4 adopted by the thrombin-binding aptamer or iMs. The presence of hairpins within the loops scarcely affects the affinity of this ligand for the hybrid G4/duplex or iM/duplex structures. Fluorescence measurements have provided evidence of a certain interaction with iMs at pH 5.1, despite the absence of thermal stabilization effects.