Designer DNA Strand Displacement Reaction toward Controlled Release of Cargos

ABSTRACT Dynamic DNA nanotechnology systems are used to design DNA logic circuits, signal amplification mechanisms for biosensing, and smart release system that could potentially be used in several biomedical applications. The toehold-mediated strand displacement reaction ( TMSDR ) is one of the main methods for designing DNA-based biomolecular logic circuits. However, the reaction behaviour such as the displacement rate and the quantity of strand released are difficult to control and often requires chemically modified strands or addition of enzymes. This makes the TMSDR versatility and specificity limited, and not always adapted for biomedical applications. Therefore, further understanding the sequence design parameters enabling fine tuning of the TMSDR behaviour without the need for complex modification, would enable its broader application. In this study, using a DNA motif developed for multiplexed release, we examine how mismatched base(s) in the trigger strand is affecting the release rate and quantity released and found that both location and type of mismatched base(s) significantly impact the displacement parameters of the TMSDR. This allows for a finer control of the cargo release for the multiplexed release system that could be used for varying biomedical applications and help developing release system mimicking the natural distribution of biomolecules.