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

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.

Study on the Interaction of a Peptide Targeting Specific G-Quadruplex Structures Based on Chromatographic Retention Behavior

“…In order to confirm whether RHAU (N’-SMHPGHLKGREIGMWYAKKQGQKNKEAERQEAVVHMDEREE QIVQLLNSVQAK-C’, M w = 6484.3) caused similar induction, we also performed CD measurements on RHAU ( Figure 1 F) and G4–RHAU mixtures ( Figure 1 A–E in red lines). As shown in Figure 1 F, RHAU had no signals in the region of 240–330 nm, which was due to the negligible absorption of Trp and Tyr residues at the near-UV end [ 59 ]. Hence, the differences between G4s and G4–RHAU mixtures in the region of 240–330 nm were attributed to the changes in G4 structures induced by RHAU addition.…”

Why to target G‐quadruplexes using peptides: Next‐generation G4‐interacting ligands

“…It is evident that the parallel G4 topology can selectively bind with the two RHAU peptide both at the 3′ and 5′ ends via three‐anchor‐point electrostaticointeractions between G4's negatively charged phosphate groups and peptides (positively charged amino acids) Hence, Thi Truong et al [242] studied the parallel G4‐mediated dimerization of a 30‐aa RHAU peptide with a FRET pair protein (CFP/YFP) and an apoptotic casp9. They have observed an occurrence of energy transfer (from donor CFP to acceptor YFP) and enhancement of 60‐fold cleavage efficiency of casp9 in the presence of parallel‐G4, indicating that parallel G4 can induce dimerization and activation of proteins promising G4‐targeting functional dimeric proteins in cellular biology [243]. Thi Truong et al [242] studied the interaction of a 25‐aa peptide (from 52–75 aa) deriving from RHAU helicases ( Rhau25 ) with three G‐quadruplex‐forming oligonucleotide sequences, in both sodium and potassium‐containing buffers [243].…”

“…They have observed an occurrence of energy transfer (from donor CFP to acceptor YFP) and enhancement of 60‐fold cleavage efficiency of casp9 in the presence of parallel‐G4, indicating that parallel G4 can induce dimerization and activation of proteins promising G4‐targeting functional dimeric proteins in cellular biology [243]. Thi Truong et al [242] studied the interaction of a 25‐aa peptide (from 52–75 aa) deriving from RHAU helicases ( Rhau25 ) with three G‐quadruplex‐forming oligonucleotide sequences, in both sodium and potassium‐containing buffers [243]. The peptide displayed greater affinity for the patrallel‐G4 topologies; however, it showed the ability to also interact with antiparallel or hybrid G‐quadruplex structures, inducing a conformation conversion to the parallel G4‐structure.…”

Peptides and Peptide Derivatives as G‐Quadruplex Targeting Ligands: A Brief Review

“…It is very important to note that G4 of anti‐parallel or hybrid conformation undergoes a structural alteration to parallel form upon interaction with Rhau 25 peptide. K D value of T95‐2T (G4) sequence with Rhau 25 in presence of KCl and NaCl are 13.5±0.5 and 13.9±1 μM respectively [84] …”