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Modulating Aptamer Specificity with pH-Responsive DNA Bonds.

Long Li1, Ying Jiang1,2, Cheng Cui2

  • 1Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute , University of Florida , Gainesville , Florida 32611-7200 , United States.

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|September 14, 2018
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Structure-switchable aptamers (SW-Apts) offer improved cell targeting by utilizing pH-responsive i-motifs. These aptamers bind specifically to target cells in acidic environments while avoiding non-target cells at physiological pH.

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Area of Science:

  • Biotechnology
  • Molecular Biology
  • Chemical Biology

Background:

  • Aptamers are crucial molecular tools for bioanalysis and targeted therapeutics due to their specific cell recognition.
  • Selective aptamer recognition can be hindered by shared receptors on target and non-target cells.
  • Developing aptamers with enhanced specificity in complex biological environments is essential.

Purpose of the Study:

  • To design and develop a structure-switchable aptamer (SW-Apt) with reconfigurable binding affinity based on cellular microenvironment pH.
  • To engineer aptamers that exploit pH differences for specific binding to target cells.
  • To overcome the challenge of cross-reactivity caused by shared receptors on different cell types.

Main Methods:

  • Construction of single-stranded aptamers modified with pH-responsive i-motif structures.
  • Utilizing i-motifs (cytosine-rich quadruplex structures) to modulate aptamer binding affinity.
  • Employing Förster resonance energy transfer (FRET) and circular dichroism (CD) spectroscopy to verify i-motif-induced structure-switching.
  • Assessing aptamer binding ability at different pH conditions (acidic vs. physiological).

Main Results:

  • The developed SW-Apt demonstrated high binding affinity to target cells specifically at acidic pH.
  • No significant binding of SW-Apt was observed at physiological pH, indicating pH-dependent specificity.
  • The i-motif structure was confirmed to induce the desired structure-switching behavior.
  • SW-Apt exhibited high specificity in serum and enhanced stability, attributed to the folded i-motif structure.

Conclusions:

  • This study presents a novel strategy for chemically modulating aptamer binding ability and enhancing target cell specificity.
  • The pH-responsive SW-Apt effectively distinguishes target cells from non-target cells, even with shared receptors.
  • This approach offers a promising solution for improving the efficacy of aptamer-based diagnostics and therapeutics in complex biological systems.