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Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
Published on: January 7, 2017
Preliminary nanopore cheminformatics analysis of aptamer-target binding strength
Karen Thomson1, Iftekhar Amin, Eric Morales
1Department of Computer Science, University of New Orleans, New Orleans, LA 70148, USA. kthomson@uno.edu
BMC Bioinformatics
|December 6, 2007
Summary
Bifunctional aptamers detected conformational changes using nanopore analysis. This DNA aptamer research advances potential new medicines with adjustable binding strengths.
Area of Science:
- Biotechnology
- Molecular Biology
- Nanotechnology
Background:
- Aptamers are nucleic acid-based molecules with therapeutic potential.
- Bifunctional aptamers combine DNA binding with specific molecular recognition.
- Adjustable binding strength can be achieved using DNA overhangs.
Purpose of the Study:
- To investigate the binding characteristics of bifunctional aptamers using a nanopore detector.
- To analyze the signal modulation and conformational changes associated with aptamer-target binding.
Main Methods:
- Utilized a nanopore detector to analyze two distinct bifunctional aptamers.
- Designed aptamers with duplex DNA for capture and single-stranded DNA for target binding.
- Studied binding interactions with short complementary single-stranded DNA (5- and 6-base overhangs).
Main Results:
- Observed sensitive and modulated blockade signals from aptamer-target interactions.
- Preliminary statistical analysis using hidden Markov models (HMMs) indicated distinct blockade pattern changes.
- Binding events correlated with significant conformational alterations in the aptamer structure.
Conclusions:
- Nanopore detection effectively reveals conformational changes in aptamers upon target binding.
- The study provides a foundation for developing more complex aptamer-based systems.
- Future work aims to integrate longer, well-characterized aptamer sequences onto the bifunctional platform.
