Analytical and Bioanalytical Chemistry

, Volume 410, Issue 7, pp 1991–2000 | Cite as

G-quadruplex aptamer selection using capillary electrophoresis-LED-induced fluorescence and Illumina sequencing

  • Audrey Ric
  • Vincent Ecochard
  • Jason S. Iacovoni
  • Audrey Boutonnet
  • Frédéric Ginot
  • Varravaddheay Ong-Meang
  • Véréna Poinsot
  • Laurent Paquereau
  • François CoudercEmail author
Research Paper


One of the major difficulties that arises when selecting aptamers containing a G-quadruplex is the correct amplification of the ssDNA sequence. Can aptamers containing a G-quadruplex be selected from a degenerate library using non-equilibrium capillary electrophoresis (CE) of equilibrium mixtures (NECEEM) along with high-throughput Illumina sequencing? In this article, we present some mismatches of the G-quadruplex T29 aptamer specific to thrombin, which was PCR amplified and sequenced by Illumina sequencing. Then, we show the proportionality between the number of sequenced molecules of T29 added to the library and the number of sequences obtained in Illumina sequencing, and we find that T29 sequences from this aptamer can be detected in a random library of ssDNA after the sample is fractionated by NECEEM, amplified by PCR, and sequenced. Treatment of the data by the counting of double-stranded DNA T29 sequences containing a maximum of two mismatches reveals a good correlation with the enrichment factor (fE). This factor is the ratio of the number of aptamer sequences found in the collected complex sample divided by the total number of sequencing reads (aptamer and non-aptamer) plus the quantity of T29 molecules (spiked into a DNA library) injected into CE.


Aptamer Capillary electrophoresis Biomolecule Thrombin 



We thank La Région Occitanie (grant no. 13053107) and ANRT for their financial support.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Audrey Ric
    • 1
    • 2
    • 3
  • Vincent Ecochard
    • 2
  • Jason S. Iacovoni
    • 4
  • Audrey Boutonnet
    • 3
  • Frédéric Ginot
    • 3
  • Varravaddheay Ong-Meang
    • 1
  • Véréna Poinsot
    • 1
  • Laurent Paquereau
    • 2
  • François Couderc
    • 1
    Email author
  1. 1.Laboratoire des IMRCP, UMR 5623Université de Toulouse, Université Paul SabatierToulouseFrance
  2. 2.Institut de Pharmacologie et de Biologie Structurale, IPBSUniversité de Toulouse, CNRS, UPSToulouseFrance
  3. 3.Picometrics TechnologiesLabègeFrance
  4. 4.I2MC, UMR1048Toulouse Cedex 4France

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