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Here, we investigate and repurpose a ubiquitous, indirect gene regulation mechanism from nature, which uses decoy protein-binding DNA sites, named DNA sponge, to modulate target gene expression in <jats:italic>Escherichia coli<\/jats:italic>. We show that synthetic DNA sponges can be designed to reshape the response profiles of gene circuits, lending multifaceted tuning capacities including reducing basal leakage by &gt;20-fold, increasing system output amplitude by &gt;130-fold and dynamic range by &gt;70-fold, and mitigating host growth inhibition by &gt;20%. Further, multi-layer DNA sponges for decoying multiple regulatory proteins provide an\u00a0additive tuning effect on the responses of layered circuits compared to single-layer sponges. Our work shows synthetic DNA sponges offer a simple yet generalizable route to systematically engineer the performance of synthetic gene circuits, expanding the current toolkit for gene regulation with broad potential applications.<\/jats:p>","DOI":"10.1038\/s41467-020-19552-9","type":"journal-article","created":{"date-parts":[[2020,11,24]],"date-time":"2020-11-24T11:16:29Z","timestamp":1606216589000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":37,"title":["Synthetic protein-binding DNA sponge as a tool to tune gene expression and mitigate protein toxicity"],"prefix":"10.1038","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5250-9277","authenticated-orcid":false,"given":"Xinyi","family":"Wan","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8554-6648","authenticated-orcid":false,"given":"Filipe","family":"Pinto","sequence":"additional","affiliation":[]},{"given":"Luyang","family":"Yu","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4858-8937","authenticated-orcid":false,"given":"Baojun","family":"Wang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,11,24]]},"reference":[{"key":"19552_CR1","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1146\/annurev-biochem-060815-014607","volume":"85","author":"H Wang","year":"2016","unstructured":"Wang, H., La Russa, M. & Qi, L. 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