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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 work focuses on moving nucleic acid strand displacement circuits developed for DNA computing from the test tube to living cells. Current DNA-based circuits cannot be easily genetically encoded, suffer from degradation in cells and dilution from cell division, and are difficult to operate multiple times without external intervention, limiting their practical applications. Sam’s research focuses on developing transcriptionally encoding RNA-based strand exchange 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
- ~$100,000 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)
- Jurado, Z., Taghon, G., Schaffter, S.W., Towards interoperable modeling of toehold-mediated strand exchange circuits across DNA nanotechnology and engineering biology. bioRxiv. 2026. DOI: https://www.biorxiv.org/content/10.64898/2026.07.22.739222v1.full
- Schaffter, S.W., Vasilyeva, O.B., Wintenberg, M.E., Hurley, J.M., Alperovich, N.Y. Genetically encoded RNA strand exchange circuits for programmable protein expression and computation in cells. bioRxiv. 2025. DOI: https://doi.org/10.1101/2025.09.24.678369
- Piorino, F., Romantseva, E., Schaffter, S.W., Cell-free systems enable mechanistic characterization of genetically encoded RNA strand exchange circuits for programmable protein expression. bioRxiv. 2025. DOI: https://doi.org/10.1101/2025.09.25.678518
- Wintenberg, M.E., Vasilyeva, O.B., Schaffter, S.W., Comparative transcriptomic analysis of perfluoroalkyl substances-induced responses of exponential and stationary phase Escherichia coli. BMC Genomics. 2025. DOI: https://link.springer.com/article/10.1186/s12864-025-12109-4
- 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. RNA. 2025. DOI: https://rnajournal.cshlp.org/content/31/5/633.short
- 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., 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.; Murphy, T. M. ctRSD_simulator_2.0. https://ctrsd-simulator.readthedocs.io/en/latest/
Selected podcasts
Sam Schaffter Interviewed on EBRC's In Translation Podcast: https://ebrcintranslation.buzzsprout.com/1581817/episodes/19300201-36-rna-powered-cellular-computing-w-sam-schaffter
Sam Schaffter Presents at Build-A-Cell Seminar: https://www.youtube.com/watch?v=vSkwl4x6JP0
Sam Schaffter Interviewed on Meet the Molecular Programmer Podcast: https://podcast.molpi.gs/media/schaffter-s-1c8799780ad4af6f/
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
