Incorporating a single-stranded split DNAzyme design concept for use in aptasensors

Abstract

Aptamers are single-stranded DNA or RNA molecules that have a high specificity for their target molecule. Ligands can range from small molecules to entire cells. Thus, aptamers can be used as biosensors, which is where the term aptasensor stems from. We have proposed to create a novel split-DNAzyme aptasensor for ATP, where two halves of a DNAzyme are separated by a conformation switching aptamer. In our design, when the aptamer is bound to ATP the two halves are separated. When the two halves are together, ATP is not bound and the DNAzyme is functional. DNAzymes are DNA molecules that are capable of catalysis. Our design features the peroxidase mimicking enzyme, which requires the DNAzyme to be rich in guanine residues in order to form a G-quadruplex. The G-quadruplex enables the peroxidase activity which can be detected and quantified through a color change using ABTS. To first characterize the conformational change, we have used DMS Footprinting. We have chosen to first apply our design concept to ATP, since there are readily available aptamer sequences for ATP that undergo a conformational change. However, this design concept can be applied to detect any target molecule in various fields such as microbiology, pharmacy, medicine, forensics, and agriculture.

Faculty Mentor: Dr. Nina Bernstein