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Samuel Schaffter (Fed)
Chemical Engineer
Sam Schaffter is the lead scientist for RNA Synthetic Biology in the Cellular Engineering Group at NIST. His recent work focuses on moving nucleic acid strand displacement circuits developed for DNA computing from the test tube to living cells. Current DNA-based circuits are single use, suffer from degradation in cells, and cannot be easily genetically encoded, limiting their practical applications. Sam’s research focuses on developing transcriptionally encoding RNA-based strand displacement circuits, equivalent to those developed in DNA computing, that can be genetically encoded and operated continuously in cells. These circuits could be programmed to recognize complex differential gene expression patterns in real-time inside cells, potentially enabling a new class of living measurement systems. To support the development of this, and other RNA biotechnologies, the RNA Synthetic Biology team also develops measurements for characterizing RNA across different environments, from in vitro transcription to cell-free expression systems to living cells.
POSTDOCTORAL RESEARCH OPPORTUNITIES
National Research Council Research Associateship Program at NIST:
- Rolling application deadlines Feb. 1 and Aug. 1
- US citizens only
- ~$80,000 annual salary plus benefits
- Please contact Dr. Schaffter directly and see the following link for further details:
Positions for non-US citizens:
- Please contact Dr. Schaffter directly
Dr. Schaffter is currently an advisor on the following projects:
- RNA computation and metrology for engineering biology: We are developing predictable and versatile RNA circuits to meet emerging molecular computation and measurement needs in biological systems. We are also developing measurement techniques to characterize these RNA circuits in diverse environments.
Selected publications (Google scholar)
- Alperovich, N.Y., Vasilyeva, O.B., Schaffter, S.W., Prevention of ribozyme catalysis through cDNA synthesis enables accurate RT-qPCR measurements of context-dependent ribozyme activity. bioRxiv. 2024. DOI: https://doi.org/10.1101/2024.07.19.604288
- Lee, H., Xie, T., Kang, B., Yu, X., Schaffter, S.W., Schulman, R. Plug-and-play protein biosensors using aptamer-regulated in vitro transcription. Nature Communications. 2024. DOI: https://doi.org/10.1038/s41467-024-51907-4
- Schaffter, S.W., Kengmana, E., Fern, J., Byrne, S.R., Schulman, R. Strategies to Reduce Promoter-Independent Transcription of DNA Nanostructures and Strand Displacement Complexes. ACS Synthetic Biology. 2024. DOI: https://pubs.acs.org/doi/10.1021/acssynbio.3c00726
- Schaffter, S.W., Wintenberg, M.E., Murphy, T.M., Strychalski, E.A. Design approaches to expand the toolkit for building cotranscriptionally encoded RNA strand displacement circuits. ACS Synthetic Biology. 2023. DOI: https://pubs.acs.org/doi/abs/10.1021/acssynbio.3c00079
- Schaffter, S. W.; Murphy, T. M. ctRSD_simulator_2.0. https://ctrsd-simulator.readthedocs.io/en/latest/
- Schaffter, S.W., Strychalski, E.A. Cotranscriptionally encoded RNA strand displacement circuits. Science Advances. 2022;8(12). DOI: https://www.science.org/doi/10.1126/sciadv.abl4354
- Schaffter, S.W., Chen, K.L., O’Brien, J., Noble, M., Murugan, A., Schulman, R. Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks. Nature Chemistry. 2022;1-9. DOI: https://doi.org/10.1038/s41557-022-01001-3
- Schaffter, S.W., Scalise, D., Patel, A.*, Murphy, T.M., Schulman, R. Feedback regulation of crystal growth by buffering monomer concentrations. Nature Communications. 2020;11(1)6057. DOI: https://doi.org/10.1038/s41467-020-19882-8
- Schaffter, S.W., Green, L.N., Schneider, J.*, Subramanian, H.K.K., Schulman, R., Franco, E. T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures. Nucleic Acids Research. 2018;46(10):5332-5343. DOI: https://doi.org/10.1093/nar/gky283
Awards
2016 NSF Graduate Research Fellowship
2020 NRC Postdoctoral Research Fellowship
2021 Robert Dirks Molecular Programming Prize: https://isnsce.org/awards/dirksprize/
2024 NIST Postdoctoral and Early-career Association of Researchers Technical Accolade