Interaction of a Short Peptide with G-Quadruplex-Forming Sequences: An SRCD and CD Study.

Claudia Honisch,Eugenio Ragazzi,John Brazier,Paolo Ruzza,Rohanah Hussain,Giuliano Siligardi

doi:10.3390/pharmaceutics13081104

Abstract

G-quadruplex (G4) forming DNA sequences were recently found to play a crucial role in the regulation of genomic processes such as replication, transcription and translation, also related to serious diseases. Therefore, systems capable of controlling DNA and RNA G-quadruplex structures would be useful for the modulation of various cellular events. In particular, peptides represent good candidates for targeting G-quadruplex structures, since they are easily tailored to enhance their functionality. In this work, we analyzed, by circular dichroism and synchrotron radiation circular dichroism spectroscopies, the interaction of a 25-residue peptide deriving from RHAU helicases (Rhau25) with three G-quadruplex-forming oligonucleotide sequences, in both sodium- and potassium-containing buffers, the most relevant monovalent cations in physiological conditions. The peptide displayed greater affinity for the G4 sequences adopting a parallel structure. However, it showed the ability to also interact with antiparallel or hybrid G-quadruplex structures, inducing a conformation conversion to the parallel structure. The stability of the oligonucleotide structure alone or in presence of the Rhau25 peptide was studied by temperature melting and UV denaturation experiments, and the data showed that the interaction with the peptide stabilized the conformation of oligonucleotide sequences when subjected to stress conditions.

Highlights

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.Licensee MDPI, Basel, Switzerland.G-quadruplex (G4) nucleic acid structures, present in guanine-rich nucleic acid sequences, result from the propensity of these sequences to form atypical and thermodynamically stable structures under physiological conditions formed by stacks of Hoogsteenbonded guanine tetrads (Figure 1) [1]
Pharmaceutics 2021, 13, 1104 benchtop CD instruments and Diamond B23 beamline for synchrotron radiation circular dichroism (SRCD). This chiroptical spectroscopy is a useful tool for the characterization of G-quadruplex structures and nucleic acids-peptides interactions
The binding of this peptide to G-quadruplex-forming sequences as well as the structure of oligonucleotide sequences and the stability of peptide/oligonucleotide complexes have been evaluated by circular dichroism (CD) spectroscopy using benchtop

Summary

Introduction

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. G-quadruplex (G4) nucleic acid structures, present in guanine-rich nucleic acid sequences, result from the propensity of these sequences to form atypical and thermodynamically stable structures under physiological conditions formed by stacks of Hoogsteenbonded guanine tetrads (Figure 1) [1]. These highly conserved structures, found in both. Pharmaceutics 2021, 13, 1104 benchtop CD instruments and Diamond B23 beamline for synchrotron radiation circular dichroism (SRCD) This chiroptical spectroscopy is a useful tool for the characterization of G-quadruplex structures and nucleic acids-peptides interactions.

Sequences

Materials and Methods

Peptide G-Quadruplex Interaction

Multivariate Statistical Analysis of G-Quadruplex Structure

Influence of Rhau25 Peptide on G4 Secondary Structure Stability