A New Cationic Porphyrin Derivative (TMPipEOPP) with Large Side Arm Substituents: A Highly Selective G-Quadruplex Optical Probe

Abstract

The discovery of uncommon DNA structures and speculation about their potential functions in genes has brought attention to specific DNA structure recognition. G-quadruplexes are four-stranded nucleic acid structures formed by G-rich DNA (or RNA) sequences. G-rich sequences with a high potential to form G-quadruplexes have been found in many important genomic regions. Porphyrin derivatives with cationic side arm substituents are important G-quadruplex-binding ligands. For example, 5,10,15,20-Tetrakis(N-methylpyridinium-4-yl)-21H,23H-porphyrin (TMPyP4), interacts strongly with G-quadruplexes, but has poor selectivity for G-quadruplex versus duplex DNA. To increase the G-quadruplex recognition specificity, a new cationic porphyrin derivative, 5,10,15,20-tetra-{4-[2-(1-methyl-1- piperidinyl)ethoxy]phenyl} porphyrin (TMPipEOPP), with large side arm substituents was synthesized, and the interactions between TMPipEOPP and different DNA structures were compared. The results show that G-quadruplexes cause large changes in the UV-Vis absorption and fluorescence spectra of TMPipEOPP, but duplex and single-stranded DNAs do not, indicating that TMPipEOPP can be developed as a highly specific optical probe for discriminating G-quadruplex from duplex and single-stranded DNA. Visual discrimination is also possible. Job plot and Scatchard analysis suggest that a complicated binding interaction occurs between TMPipEOPP and G-quadruplexes. At a low [G-quadruplex]/[TMPipEOPP] ratio, one G-quadruplex binds two TMPipEOPP molecules by end-stacking and outside binding modes. At a high [G-quadruplex]/[TMPipEOPP] ratio, two G-quadruplexes bind to one TMPipEOPP molecule in a sandwich-like end-stacking mode.

Two cationic porphyrin isomers showing different multimeric G-quadruplex recognition specificity against monomeric G-quadruplexes

“…A primary requirement for ideal ligands targeting a telomeric region is that they must have a high level of G-quadruplex-binding selectivity for other DNA structures, including duplex and single-stranded DNAs. Earlier, we showed p -TMPipEOPP could discriminate G-quadruplexes from duplex and single-stranded DNAs with a high level of specificity (47,48). To investigate the feasibility of using m -TMPipEOPP as a specific G-quadruplex ligand under molecular crowding conditions, binding interactions between m -TMPipEOPP and both monomeric and multimeric G-quadruplexes, duplex or single-stranded DNAs were investigated by following the effects of these DNAs on the UV-vis absorption spectrum of m -TMPipEOPP using polyethylene glycol 200 (PEG 200) as a molecular crowding agent, and the result was compared to p -TMPipEOPP (Figure 1 and Supplementary Figure S4).…”

“…Deionized and sterilized water (resistance > 18 MΩ/cm) was used throughout the experiments. p -TMPipEOPP was synthesized according to the method reported by us (48). The details of synthesis and characterization of m -TMPipEOPP are available in Supporting Information (Supplementary Figures S1–S3).…”

Specific recognition and stabilization of monomeric and multimeric G-quadruplexes by cationic porphyrin TMPipEOPP under molecular crowding conditions

“…Although the widely studied G-quadruplex ligand 5,10,15,20-tetrakis(N-methylpyridinium-4-yl)-21H,23H-porphyrin (TMPyP4, Scheme 1) shows attractive G-quadruplex-stabilizing ability, it lacks selectivity against duplex DNA (24). Recently, by changing the small side arm methylpyridine substituents of TMPyP4 to larger [2-(1-methyl-1-piperidinyl) ethoxy] phenyl substituents, our group synthesized a new cationic porphyrin derivative 5,10,15,20-tetra-{4-[2-(1-methyl-1-piperidinyl)ethoxy] phenyl} porphyrin (TMPipEOPP, Scheme 1) and found that it could be used as a highly specific optical probe for discriminating monomeric G-quadruplexes from duplex and single-stranded DNAs under dilute conditions (25). We also demonstrated that the binding stoichiometry of TMPipEOPP to monomeric G-quadruplexes changed with the G-quadruplex/TMPipEOPP concentration ratio (25).…”

“…Recently, by changing the small side arm methylpyridine substituents of TMPyP4 to larger [2-(1-methyl-1-piperidinyl) ethoxy] phenyl substituents, our group synthesized a new cationic porphyrin derivative 5,10,15,20-tetra-{4-[2-(1-methyl-1-piperidinyl)ethoxy] phenyl} porphyrin (TMPipEOPP, Scheme 1) and found that it could be used as a highly specific optical probe for discriminating monomeric G-quadruplexes from duplex and single-stranded DNAs under dilute conditions (25). We also demonstrated that the binding stoichiometry of TMPipEOPP to monomeric G-quadruplexes changed with the G-quadruplex/TMPipEOPP concentration ratio (25). At high ratios, a single TMPipEOPP molecule stacked between the ends of two monomeric G-quadruplexes like a sandwich, implying that TMPipEOPP might be developed into a ligand targeting the multimeric G-quadruplex structure (25).…”

Porphyrins in complex with DNA: Modes of interaction and oxidation reactions

“…Bulky porphyrin derivatives H 2 -TMPipEOPP, H 2 -TMPy2PP, H 2 -GP, H 2 -DIGPor and H 2 -TPyEtCAP can perfectly discriminate between quadruplex and double-stranded DNA [63,69,71,[116][117][118][119][120]. Their binding constants for quadruplex DNA is comparable to that of best G4 ligands [120].…”