Proteomic and Transcriptome Profiling of G-Quadruplex Aptamers Developed for Cell Internalization

Anal Chem. 2021 Apr 13;93(14):5744-5753. doi: 10.1021/acs.analchem.0c04862. Epub 2021 Mar 30.


Nucleic acid medicine is expected to be among the most promising next-generation therapies. Applications of nucleic acid in vivo are still challenging as a result of the difficulties in direct cell penetration without external assistance. To facilitate the cellular delivery of therapeutic nucleic acid, we developed cell-penetrating aptamers using cell-internalization Systematic Evolution of Ligands by EXponential enrichment (SELEX). Moreover, C20-4 min, a G-quadruplex-forming DNA aptamer, was discovered, showing a higher cell-penetrating capacity compared with other candidates, including AS1411. To verify the formation and understand the G-quadruplex folding topologies of enriched aptamer motifs, characteristic circular dichroism (CD) spectral features are analyzed. The CD spectra of C20-4 min strongly support the formation of parallel G-quadruplexes. Systematic analyses of the G-quadruplex regulation pathway have been performed by combining aptamer pull-down with mass spectrometry. We profiled G-quadruplex aptamers interacting with cellular proteins during internalization and identified helicases and GTPase proteins as cellular interacting partners. In addition, whole transcriptome analysis was performed to study the effects of G-quadruplex aptamers, revealing differentially expressed genes involved in the regulation of GTPase functions. Integrative analyses of transcriptome and proteomic have aided in understanding the functional hierarchy of molecular players in G-quadruplex nucleic acid mechanisms of internalization, which might facilitate developing a novel delivery system.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aptamers, Nucleotide*
  • Circular Dichroism
  • G-Quadruplexes*
  • Gene Expression Profiling
  • Proteomics


  • Aptamers, Nucleotide