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Samuel Schaffter (Fed)

Chemical Engineer

Sam Schaffter is leading research in RNA computation and metrology for engineering biology in the Cellular Engineering Group at NIST. His recent work focuses on moving 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.

In graduate school, Sam conducted research in DNA nanotechnology and DNA computing. He developed synthetic transcription-based networks with dynamics programmed via nucleic acid base pairing rules. These in vitro networks emulated key functionalities of cellular genetic regulatory networks and thus could serve as a programmable ‘synthetic genome’ for controlling nucleic acid materials, such as DNA nanostructures and DNA-responsive hydrogels. This research could enable materials capable of sophisticated behaviors seen in biology including hierarchical differentiation or self-healing.


National Research Council Research Associateship Program at NIST:

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)

  • 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:
  • Schaffter, S.W., Strychalski, E.A. Cotranscriptionally encoded RNA strand displacement circuits. Science Advances. 2022;8(12). DOI:
  • 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:
  • 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:
  • 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:



2021 Robert Dirks Molecular Programming Prize:


Patents (2018-Present)

CTRSD Gate And Performing Co-Transcriptional Encoding

NIST Inventors
Samuel Schaffter
A method for the production and use of scalable co-transcriptional RNA strand displacement (ctRSD) circuits using RNA toehold exchange gates is described. The ctRSD circuits described address the limitations of existing DNA-based strand displacement circuits by isothermally producing circuit
Created September 1, 2020, Updated December 13, 2023