Reversible Conductance Modulation in Metalated DNA Using pH-Dependent Transmetalation

The rational design of molecular electronics remains a grand challenge of materials science. Strides toward molecular devices composed of organic polymers have yielded some success, but the composability and synthetic challenge of such structures have limited the scalability of such platforms. In parallel, DNA nanotechnology has offered unmatched control over the local geometry of oligomers, but direct electronic functionalization has been a challenge. We present here a generalized method for tuning the local band structure, enhancement of electronic conductivity, and pH-based reconfigurability using metal-mediated DNA base pairs.
We develop a method using self-assembling DNA crystals to carry out time-resolved transmetalation between Ag⁺- and Hg²⁺-mediated thymine-thymine base pairs, and we extensively characterize the reaction mechanisms that drive Ag⁺/Hg²⁺ competition. We observe that O4-metal bonds have higher crystallographic B-factors, yielding a wider binding site. Indeed, the structure of single-metal T: Hg²⁺:T relying on N3-metal bonds showed measurably better conductance than the O4-Ag⁺ analog. We conclude that molecular electronics based on metal-mediated DNA (mmDNA) will likely require an N3 metal in pyrimidine-pyrimidine base pairs to ensure the planarity of the base pair and good orbital alignment.
Our computational findings reveal that even a single metal atom can induce a LUMO energy level while also modifying the conduction pathway at the HOMO level. From our results, it can be extrapolated that the effect of metal ions will be more pronounced with more metalated bases. For dinuclear coordinated motifs, we observed that the zero bias conductance contrast (defined as the ratio of DNA conductance with/without metal) at the HOMO is approximately 1 to 4, whereas at the LUMO, it ranges from 8 to 16, indicating that metal ion doping predominantly influences the LUMO energy levels. This influence is further evidenced by the broadening of LUMO orbitals on metal and metalated base pairs. The interplay between the nature of the coordinated metal and the coordination site plays a crucial role in governing the extent of LUMO orbital broadening. From our single metal intercalation results, we determined that the nature of coordination significantly affects charge transport, with N3-N3 coordination having a greater impact than O4-O4. Furthermore, our results highlight the pronounced effect of protonation states on charge transport. During the neutral to-alkaline pH transition, at intermediate pHs (9, 10), deprotonation leads to reduced bandgap in comparison to protonated states.
The proposed method leverages the pH-dependent activity of modified DNA base pairs to reconfigure Ag⁺ and Hg²⁺ ions, leading to measurable changes in the DNA energy levels and resulting in conductance switching and amplification. This switching can be achieved with (electrically) or without (chemically) external bias, underscoring the flexibility of the proposed metal-DNA system. Reconfigurable mmDNA offers the potential for multiple conductance states depending on the pH. This capability forms the foundation for bioelectronic rewritable memory devices.
We anticipate that these experiments can serve as a template for time-resolved crystallography in self-assembled DNA crystals to elucidate the kinetics of drug release, molecular switching, and other metal-mediated phenomena. Indeed, the observation that Hg²⁺ causes orbital broadening to neighboring metals may inform the design of synthetic DNA nanowires, where the placement of Hg²⁺ at strategic positions along an axial chain of extended metal arrays may enable electron delocalization and highly efficient electrical conductivity for bioelectronic applications.