Keywords

DNA, half-adder, gates, molecular beacon

Abstract

DNA nanostructures have computing functions due to the predictable base pairing of nucleic acids (Watson–Crick). This property allows the programming of DNA circuits that integrate DNA logic gates capable of recognizing oligonucleotides. This molecular device offers the advantages of biocompatibility and potential applications in personalized medicine for diagnosis and therapies.

Our lab has developed DNA logic gates formed by the connection of YES strands via DNA four-way junctions (4J), which can function as molecular switches to develop a DNA-based calculator. Our DNA half-adder calculator nanostructure is designed to recognize up to three combinations of DNA inputs using three DNA strands that can fold into a DNA 4J upon recognition of the inputs, create a DNA gate and produce two new DNA sequences as outputs.

The molecular switching between DNA strands is achieved by hierarchical binding driven by thermodynamic disparities between gate and input binding. The new output sequence is detected by a molecular beacon (MB) probe that is complementary to each output sequence and differentiates the outputs as SUM or CARRY in the fluorescence readout.

We represent our expected results using a truth table, where high fluorescence is represented by digital 1 and low fluorescence is represented by digital 0. We have designed two different inputs, A4 and B4. When inputs are tested in individual samples, we expect the formation of the SUM gate, resulting in high fluorescence for SUM output. When both inputs are present in the same sample, we expect the formation of the CARRY gate, resulting in high fluorescence for the CARRY output.

Our research focus has been to optimize the DNA calculator half-adder structure so that the inputs bind with the expected affinity to the gates and the fluorescence readout corresponds accurately to the SUM and CARRY outputs. Additionally, we aim to develop a full-adder nanostructure in future work.

Thesis Completion Year

2026

Thesis Completion Semester

Summer

Thesis Chair

Kolpashchikov, Dmitry

College

College of Medicine

Department

Chemistry

Thesis Discipline

DNA Nanotechnology

Language

English

Access Status

Open Access

Length of Campus Access

None

Campus Location

Orlando (Main) Campus

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