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Design of a DNA-based shift register

Background

DNA-based circuit design is an area of research in which traditional silicon-based technologies are replaced by naturally occurring phenomena taken from biochemistry and molecular biology. This research focuses on further developing DNA-based methodologies to mimic digital data manipulation, demonstrating how information can be parsed through a digital circuit comprised of DNA–based logic gates.

Results and conclusion

A novel logic gate design based on chemical reactions is presented in which observance of double stranded sequences indicates a truth evaluation. Circuits are obfuscated by removing of physical sequence connections, allowing client-specific representative strands for input sequences, altering the input sequence strands over time, and varying the input sequence length. Shifting along the input stream to parse individual inputs is accomplished through simulated alternative splicing of DNA sequences stored in plasmid vectors.

Acknowledgements

C. M. Gearheart would like to thank Hank and Becky Conn for their continued support. This work was supported in part by NIH-NCRR Grant P20RR16481 and NIH-NIEHS Grant P30ES014443. Its contents are solely the responsibility of the authors and do not represent the official views of NCRR, NIEHS, or NIH.

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Correspondence to Eric C Rouchka.

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Open Access This article is published under license to BioMed Central Ltd. This is an Open Access article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Gearheart, C.M., Rouchka, E.C. & Arazi, B. Design of a DNA-based shift register. BMC Bioinformatics 11, P31 (2010). https://doi.org/10.1186/1471-2105-11-S4-P31

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Keywords

  • Alternative Splice
  • Combinatorial Library
  • Input Sequence
  • Logic Gate
  • Circuit Design