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Aptamer-Based Target Detection Facilitated by a 3-Stage G-Quadruplex Isothermal Exponential Amplification Reaction
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Aptamer-Based K(+) Sensor: Process of Aptamer Transforming into G-Quadruplex.

Dongju Zhang1, Juan Han1, Yunchao Li1

  • 1Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University , Beijing 100875, China.

The Journal of Physical Chemistry. B
|June 21, 2016
PubMed
Summary

G-rich aptamers form G-quadruplex structures in response to potassium ions (K+). This study clarifies the K+-dependent transformation process of the PW17 aptamer, revealing distinct stages crucial for biosensor design.

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Area of Science:

  • Biochemistry and Molecular Biology
  • Analytical Chemistry
  • Materials Science

Background:

  • G-rich aptamers are widely used in biosensors, relying on target-induced conformational changes to G-quadruplex structures.
  • The precise mechanism and stages of G-quadruplex formation induced by specific ions remain unclear.
  • Understanding this transformation is key to optimizing aptamer-based sensor performance and reliability.

Purpose of the Study:

  • To investigate and elucidate the step-by-step process of G-quadruplex formation in the PW17 aptamer induced by potassium ions (K+).
  • To characterize the conformational changes from an unstable single strand to a stable G-quadruplex structure.
  • To correlate these structural changes with K+ concentration and explore their implications for biosensing applications.

Main Methods:

  • Circular dichroism (CD) spectroscopy to monitor structural changes.
  • Electrospray ionization mass spectrometry (ESI-MS) for molecular characterization.
  • Native gel electrophoresis to assess complex formation and stability.

Main Results:

  • PW17 undergoes a K+-dependent conformational transition from a loose, unstable structure to a compact, stable G-quadruplex.
  • Three distinct stages of G-quadruplex formation were identified based on K+ concentration: <0.5 mM (loose), 0.5-7 mM (transition), and >7 mM (compact).
  • Dimeric G-quadruplex formation via 5'-5' stacking occurs during the process, stabilizing at 40 mM K+; the overall process is thermodynamically controlled.

Conclusions:

  • The study clarifies the multi-stage, K+-dependent formation of G-quadruplex structures in aptamers.
  • The findings provide a detailed understanding of aptamer conformational dynamics, essential for designing robust biosensors and logic devices.
  • The observed linear fluorescent responses corresponding to G-quadruplex formation stages demonstrate potential for K+ detection.