Duplexed aptamers: history, design, theory, and application to biosensing

Area of Science:

• Biotechnology
• Analytical Chemistry
• Molecular Biology

Background:

• Nucleic acid aptamers are DNA/RNA sequences that bind specific ligands.
• Aptasensors are biosensors engineered from aptamers for ligand detection.
• Duplexed aptamers (DAs) are a common aptasensor format using two hybridized nucleic acid strands.

Purpose of the Study:

• To define and provide a framework for duplexed aptamers (DAs) based on aptamer-complementary elements (ACEs).
• To distinguish DAs from other aptasensor formats and categorize cis- and trans-DA designs.
• To explore the ligand binding dynamics, chemical properties, and applications of DAs.

Main Methods:

• Reviewing literature on aptamer and aptasensor design.
• Introducing a framework based on ACEs for DA classification.
• Analyzing ligand binding models (conformational selection, induced fit) and chemical properties.
• Surveying in vitro and in vivo applications of DAs.

Main Results:

• DAs are defined by the interaction between an aptamer and an ACE, with ligand binding causing dehybridization and signal generation.
• A framework is proposed to distinguish DAs from other aptasensor formats.
• DA systems exhibit ligand binding dynamics mirroring classical nucleophilic substitution models.
• DAs have diverse applications in chemical and biological sciences, including riboswitches and riboregulators.

Conclusions:

• Duplexed aptamers offer a tunable, versatile, and broadly applicable platform for biosensing.
• Clarifying DA definitions and frameworks enhances their understanding and development.
• DAs hold significant potential for advancing fields like analytical chemistry, medicine, and synthetic biology.