Preferential Binding of π-Ligand Porphyrin Targeting 5'-5' Stacking Interface of Human Telomeric RNA G-Quadruplex Dimer

J Phys Chem Lett. 2019 May 2;10(9):2143-2150. doi: 10.1021/acs.jpclett.9b00637. Epub 2019 Apr 17.

Abstract

Human telomeric RNA (TERRA) containing thousands of G-rich repeats has the propensity to form parallel-stranded G-quadruplexes. The emerging crucial roles of TERRA G-quadruplexes in RNA biology fuel increasing attention for studying anticancer ligand binding with such structures, which, however, remains scarce. Here we utilized multiple steady-state and time-resolved spectroscopy analyses in conjunction with NMR methods and investigated thoroughly the binding behavior of TMPyP4 to a TERRA G-quadruplex dimer formed by the 10-nucleotide sequence r(GGGUUAGGGU). It is clearly identified that TMPyP4 intercalates into the 5'-5' stacking interface of two G-quadruplex blocks with a binding stoichiometry of 1:1 and binding constant of 1.92 × 106 M-1. This is consistent with the unique TERRA structural features of the enlarged π-π stacking plane of the A·(G·G·G·G)·A hexad at 5'-ends of each G-quadruplex block. The preferential binding of π-ligand porphyrin to the 5'-5' stacking interface of the native TERRA G-quadruplex dimer is first ascertained by the combination of dynamics and structural characterization.

MeSH terms

  • Base Sequence
  • Dimerization
  • G-Quadruplexes*
  • Humans
  • Intercalating Agents / chemistry*
  • Kinetics
  • Ligands
  • Models, Molecular
  • Molecular Structure
  • Porphyrins / chemistry*
  • RNA / chemistry*
  • Structure-Activity Relationship
  • Telomere / chemistry*

Substances

  • Intercalating Agents
  • Ligands
  • Porphyrins
  • tetra(4-N-methylpyridyl)porphine
  • RNA