Echromatin: Developing a Cell-Free Gene Expression Platform Using Targeted Induced Steric Hinderance within DNA Arrays

Abstract

Conference InformationPoster presented at the 2025 Synthetic Biology: Engineering, Evolution & Design (SEED) conference in Houston, TX, USA. The poster abstract, presentation date, time, and list of authors can be viewed on the conference registry page here.AbstractCell-free gene expression systems can be used in the development of hybrid functional materials, to design synthetic biological and biocomputational systems, and to reduce biological complexity when investigating genetic pathways found in nature. Such systems are not without their limitations, however, such as resource depletion, limited mechanisms for real-time control of reaction timing and dynamics, and the inability to integrate spatial reaction dynamics. To address these limitations, we are building a small, automated and modifiable platform for coordinated cell-free gene expression in a biologically minimal, electronically-actuated context. We envision a design of discrete self-assembled monolayers (SAMs) of DNA on an chip array, where cell-free expression rates of surface-bound gene fragments are controlled by steric hinderance of RNA polymerase action within a desired section or sections of the array. We seek to achieve this local steric hinderance by way of electrophoretic forces, but are also exploring other means such as the predictable and reversible induction of secondary structures and the integration of reversible, light-inducible cross-linkers. Thus far, we have designed a physical system for parallel DNA monolayer generation and testing. We have also characterized the densities and compositions of these monolayers and show that we can achieve cell-free transcriptiontranslation (TXTL) activity using specifically bound DNA monolayers. Our current efforts are focused on the reduction of noise in our physical system and on achieving consistently distinguishable TXTL rates through electronically or light-induced changes in steric hinderance.