Loop-mediated fluorescent probes for selective discrimination of parallel and antiparallel G-Quadruplexes

Anup Pandith, Upendra Nagarajachari, Ravi Kumara Guralamatta Siddappa, Sungjin Lee, Chin Ju Park, Krishnaveni Sannathammegowda, Young Jun Seo

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)


Herein we report simple pyridinium (1–3) and quinolinium (4) salts for the selective recognition of G-quadruplexes (G4s). Among them, the probe 1, interestingly, selectively discriminated parallel (c-KIT-1, c-KIT-2, c-MYC) G4s from anti-parallel/hybrid (22AG, HRAS-1, BOM-17, TBA) G4s at pH 7.2, through a switch on response in the far-red window. Significant changes in the absorption (broad 575 nm → sharp 505 nm) and emission of probe 1 at 620 nm, attributed to selective interaction with parallel G4s, resulted in complete disaggregation-induced monomer emission. Symmetrical push/pull molecular confinements across the styryl units in probe 1 enhanced the intramolecular charge transfer (ICT) by restricting the free rotation of C[dbnd]C units in the presence of sterically less hindered and highly accessible G4 surface/bottom tetrads in the parallel G4s, which is relatively lower extent in antiparallel/hybrid G4s. We confirm that the disaggregation of probe 1 was very effective in the presence of parallel G4–forming ODNs, due to the presence of highly available free surface area, resulting in additional π-stacking interactions. The selective sensing capabilities of probe 1 were analyzed using UV–Vis spectroscopy, fluorescence spectroscopy, molecular dynamics (MD)–based simulation studies, and 1H NMR spectroscopy. This study should afford insights for the future design of selective compounds targeting parallel G4s.

Original languageEnglish
Article number116077
JournalBioorganic and Medicinal Chemistry
Publication statusPublished - Apr 2021
Externally publishedYes


  • Disaggregation
  • G-Quadruplexes
  • Intramolecular charge transfer
  • Molecular confinements
  • Molecular dynamics

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Pharmaceutical Science
  • Drug Discovery
  • Clinical Biochemistry
  • Organic Chemistry


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