Development of Label-free DNA Logic Gates: Interactions of Polymorphic Oligonucleotides with Metal Ions

The combination of chemical and molecular technologies to emulate silicon-based processing and computing has recently arisen as a fascinating area of research in the scientific community. Chemists have driven the forefront of this research, using molecular entities such as small molecules or DNA to devise molecular scale logic gates that mimic Boolean functions fundamental for modern digital information integration. These Boolean functions, such as the “AND”, “OR” and “NOT” logic gates, generate distinct binary (0 or 1) “outputs” depending on the combination of “inputs”.

Molecular logic gates for metal ions have received much attention due to the importance of metals in biology and in the environment. In this proposal, we aim to exploit the ability of DNA to form metal–DNA base pairs in order to generate new logic gates for metal ions, and to develop methods for the simultaneous detection and removal of metal ions using immobilized oligonucleotide-based systems. Nucleic acids are highly polymorphic, and metal ions such as mercury, silver and potassium can induce the structural conversion of DNA from one form to another. We will monitor this “structure-switching” event using transition metal complexes, producing a luminescence output in the presence or absence of metal ion inputs.

Our preliminary results have demonstrated that certain platinum(II) complexes in conjunction with a DNA oligonucleotide can function as an “OR” logic gate for mercury and silver ions. We will build on these results by synthesizing a series of new platinum(II), iridium(III) and rhodium(III) complexes as selective luminescent probes for DNA. Based on the combination of judiciously designed DNA oligonucleotide, and a DNA duplex or G-quadruplex-selective transition metal complex, we envision that a series of new logic gates such as “AND”, “OR”, “NAND” and “INHIBIT” can be developed. We anticipate that these methods could be adapted to a high-throughput, solid-supported DNA logic gate system that has the additional advantages of high sensitivity and reusability. Due to the potential practical application of DNA logic gates to construct molecular scale computers that could become the basis of modern computing, the proposed work represents an important advance in this endeavour. Our proposed approach is simple and compares favourably with previously reported DNA-based logic gates utilizing complicated and/or expensive sample preparation and procedures.