Discrete-time signal processing with DNA

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

Research output: Contribution to journalArticle

16 Citations (Scopus)

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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Signal processing
DNA
Drug delivery
Fast Fourier transforms
Reaction rates
Clocks
Rate constants
Synchronization
Fourier Analysis
Specifications
Molecules
Kinetics
Pharmaceutical Preparations

Keywords

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

Cite this

Discrete-time signal processing with DNA. / Jiang, Hua; Salehi, Sayed Ahmad; Riedel, Marc; Parhi, Keshab K.

In: ACS Synthetic Biology, Vol. 2, No. 5, 17.05.2013, p. 245-254.

Research output: Contribution to journalArticle

Jiang, Hua ; Salehi, Sayed Ahmad ; Riedel, Marc ; Parhi, Keshab K. / Discrete-time signal processing with DNA. In: ACS Synthetic Biology. 2013 ; Vol. 2, No. 5. pp. 245-254.
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