We have developed and applied enzyme-free, DNA-based reaction motifs that allow for copying of sequence information in DNA templates. Theoretical work from my group [J. Juritz et al., J. Chem. Phys. 2022] showed that a deceptively simple mechanism allows, in principle, for the reliable production of polymer copies from molecular templates. At the heart of that mechanism is a motif in which the copy polymer rips itself off from the template as it forms. We demonstrated that such a motif can be engineered using synthetic DNA alone [J. Cabello Garcia et al., ACS Nano 2021], and then that two variants can be used to produce copies of dimer templates with high accuracy [J. Cabello Garcia et al., Nature Chemistry 2025, Mitra et al., submitted to J. Am. Chem. Soc]. By the end of the project, we had successfully shown that this basic idea can be applied to the copying of trimeric, tetrameric and pentameric templates [Mukherjee et al., manuscript in preparation - results presented at Foundations of Nanoscience 2025 and Functional DNA Nanotechnology 2025]. We have also shown that this mechanism can be used in conjunction with the biologically prevalent scheme of kinetic proofreading [Mukherjee et al., J. Am. Chem. Soc. 2024], wherein a molecular fuel is used to enhance the specificity of a biological process. Although kinetic proofreading is extremely common in nature, our work is the first demonstration of the celebrated motif in a synthetic context.
Alongside this experimental work, we pursued theory and simulation to guide the experiments and explore the principles of molecular templating more generally. We have simulated key DNA reaction mechanisms, identifying important differences in the underlying process relative to similar approaches in DNA nanotechnology [Bakhtawar et al, Nano Lett. 2026, Stannard et al. and Sengar et al., latter two manuscripts in preparation and presented at oxDNA users and developers workshop 2026]. We have developed two frameworks that allow for improved theoretical analysis of models of copying processes in different contexts [Qureshi et al., J. Chem. Phys. 2023 and Guntoro et al., J. Chem. Phys. 2025], and applied them to exemplar models. We have also resolved a long-standing paradox by explaining how accurate information propagation in arbitrarily complex molecular templating networks is constrained by the thermodynamic properties of those networks [Qureshi et al., Newton 2026].
As part of this process, and to help disseminate our results, we produced extensive reviews on how the coarse-grained model oxDNA can be used as a simulation tool [A. Sengar et al., Front. Mol. Biosci. 2021] and on the design of systems based on DNA strand displacement [Jurinovic et al., Curr. Op. Biotech. 2026]. As a result of our paper on kinetic proofreading, we were invited to write a "News and Views" for Nature Nanotechnology on enhancing recognition beyond equilibrium in synthetic systems [Ouldridge et al., Nat. Nano., 2025]. In addition, my team has given talks at 36 different scientific events, and poster presentations at a number of others, reaching an estimate 4500 people. We have also sought to reach out beyond academia, communicating directly with an estimated 500 members of the general public through outreach activities and also recording a number of publicly available videos.
The work performed here has led to additional funding from the EIC, the Royal Society and the Defence Science and Technology Laboratory to explore variant molecular templating systems. We have also submitted a patent based on an auto-catalytic extension to the templating mechanism.
