Effects of the central potassium ions on the G-quadruplex and stabilizer binding

Zhiguo Wang, Jun Ping Liu

Research output: Contribution to journalArticleResearchpeer-review

28 Citations (Scopus)


Human telomeres undertake the structure of intra-molecular parallel G-quadruplex in the presence of K+ in eukaryotic cell. Stabilization of the telomere G-quadruplex represents a potential strategy to prevent telomere lengthening by telomerase in cancer therapy. Current work demonstrates that the binding of central K+ with the parallel G-quadruplex is a coordinated water directed step-wise process. The K+ above the top G-tetrad is prone to leak into environment and the 5′-adenine quickly flips over the top G-tetrad, leading to the bottom gate of G-tetrads as the only viable pathway of K+ binding. Present molecular dynamics studies on the two most potent stabilizers RHPS4 and BRACO-19 reveal that the central K+ has little influence on the binding conformations of the bound stabilizers. But without the central K+, either RHPS4 or BRACO-19 cannot stabilize the structure of G-quadruplex. The binding strength of stabilizers evaluated by the MM-PBSA method follows the order of BRACO-19> RHPS4, which agrees with the experimental results. The difference in binding affinities between RHPS4 and BRACO-19 is probably related to the ability to form intramolecular hydrogen bonds and favorable van del Waals interactions with G-quadruplex. In the models that have one central K+ located at the upper/lower binding site, the corresponding top/bottom stacked stabilizers show more favorable binding affinities, indicating the apparent promoting effect of central K+ on the stabilizer binding. Our findings provide further insights into the regulatory effect of K+ on the G-quadruplex targeted binding, which is meaningful to the development of G-quadruplex stabilizers.

Original languageEnglish
Pages (from-to)168-177
Number of pages10
JournalJournal of Molecular Graphics and Modelling
Publication statusPublished - 1 Mar 2017


  • Binding free energy
  • Binding process
  • G-Quadruplex
  • Potassium ion

Cite this