Discrete-time signal processing with DNA

Hua Jiang, Sayed Ahmad Salehi, Marc D. Riedel, Keshab K. Parhi

Research output: Contribution to journalArticle

16 Scopus citations

Abstract

We present a methodology for implementing discrete-time signal processing operations, such as filtering, with molecular reactions. The reactions produce time-varying output quantities of molecules as a function of time-varying input quantities according to a functional specification. This computation is robust and independent of the reaction rates, provided that the rate constants fall within coarse categories. We describe two approaches: one entails synchronization with a clock signal, implemented through sustained chemical oscillations; the other is "self-timed" or asynchronous. We illustrate the methodology by synthesizing a simple moving-average filter, a biquad filter, and a Fast Fourier Transform (FFT). Abstract molecular reactions for these filters and transforms are translated into DNA strand displacement reactions. The computation is validated through mass-action simulations of the DNA kinetics. Although a proof of concept for the time being, molecular filters and transforms have potential applications in fields such as biochemical sensing and drug delivery.

Original languageEnglish (US)
Pages (from-to)245-254
Number of pages10
JournalACS Synthetic Biology
Volume2
Issue number5
DOIs
StatePublished - May 17 2013

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Keywords

  • DNA computing
  • DNA strand displacement
  • molecular computing
  • recurrent circuits
  • sequential circuits
  • signal processing

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