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General approach for engineering small-molecule-binding DNA split aptamers.

Alexandra D Kent¹, Nicholas G Spiropulos, Jennifer M Heemstra

¹Department of Chemistry and the Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112, United States.

Analytical Chemistry

|September 17, 2013

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Researchers developed a new method to engineer DNA aptamers into split aptamers for biosensing. This breakthrough provides a reliable way to create more split aptamers for detecting small molecules.

Area of Science:

Biochemistry
Molecular Biology
Biosensor Technology

Background:

Split aptamers are promising recognition elements for biosensing applications.
Current methods for generating split aptamers lack reliability.
DNA aptamers engineered from three-way junctions offer potential for split aptamer development.

Purpose of the Study:

To develop a general and reliable method for engineering three-way junction DNA aptamers into split aptamers.
To demonstrate the efficacy of this method for creating novel split aptamers for small molecule detection.
To advance the potential substrate scope of DNA assembly-based biosensors.

Main Methods:

Engineering three-way junction DNA aptamers into split aptamers by removing loop regions and modifying stem regions.

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Systematic modification of stem regions to achieve target-specific assembly.

Screening and validation using split aptamer proximity ligation (StAPL) technology and noncovalent assembly systems.

Main Results:

A general method for split aptamer engineering was successfully developed.
Four new small-molecule-binding DNA split aptamer sequences were introduced.
The number of reported small-molecule-binding DNA split aptamers was tripled.
The developed method demonstrated reliable translation to noncovalent assembly systems.

Conclusions:

The three-way junction serves as a privileged architecture for split aptamer engineering.
The proposed method provides a reliable route for generating diverse split aptamers.
This work significantly expands the capabilities of DNA assembly-based biosensors for small molecule detection.