Fast and Compact DNA Logic Circuits

DNA is a reliable biomolecule with which to build molecular computation systems. DNA logic circuits (diffusion-based) have shown good performance regarding scalability and correctness of computation. However, previous architectures of DNA logic circuits have two limitations.

1. The speed of computation is slow, often requiring hours to compute a simple function.
2. The circuits are of high complexity regarding the number of DNA strands.

Duke University researchers introduced an architecture of DNA logic circuits based on single-stranded logic gates using strand-displacing DNA polymerase. The logic gates consist of only single DNA strands, which largely reduces leakage reactions and signal restoration steps such that the circuits are improved in regard to both speed of computation and the number of DNA strands needed. Large-scale logic circuits can be constructed from the gates by simple cascading strategies. In particular, we have demonstrated a fast and compact logic circuit that computes the square-root function of four-bit input numbers.

Duke University has a range of research into DNA Computing. Here is a 76-page powerpoint deck by the lead author, John Reif
and his team Reif’s DNA Self-Assembly Group.

Duke researchers are working on
* Localized DNA Computation: Faster and Simpler Molecular-Scale Computing
* Programming DNA-based Biomolecular Reaction Networks on Cancer Cell Membranes: localized circuits, molecular reaction networks
* Compact and Fast DNA Logic Circuits Using Strand-Displacing Polymerase and Single-Stranded Logic Gates: logic circuits, enzyme-based circuits
* DNA-based Analog Computing: analog circuits

Localized DNA Computation

* Linear Cascade DNA Hybridization Chain Reactions (in solution, not localized)
* Localized DNA Hybridization Chain Reactions on DNA Tracks
* Localized DNA Hybridization Chain Reactions on DNA Origami