DNA-based molecular architecture with spatially localized components

Abstract

Performing computation inside living cells offers life-changing applications, from improved medical diagnostics to better cancer therapy to intelligent drugs. Due to its bio-compatibility and ease of engineering, one promising approach for performing in-vivo computation is DNA strand displacement. This paper introduces computer architects to DNA strand displacement "circuits", discusses associated architectural challenges, and proposes a new organization that provides practical composability. In particular, prior approaches rely mostly on stochastic interaction of freely diffusing components. This paper proposes practical spatial isolation of components, leading to more easily designed DNA-based circuits. DNA nanotechnology is currently at a turning point, with many proposed applications being realized [20,9]. We believe that it is time for the computer architecture community to take notice and contribute.

A DNA-Based Archival Storage System

“…Researchers have proposed the use of DNA for Boolean circuits [26], neural networks [21], and chemical reaction networks [5]. DNA computing has also begun making inroads in the architecture community: Muscat et al explore the architectural challenges of DNA stranddisplacement circuits [19], and Talawar examines the design of a DNA-based crossbar interconnection network [27].…”

Logic circuits based on molecular spider systems

“…Molecular circuits with spatial locality overcome the challenges of computation speed-up and sequence reuse in molecular computing in a well-mixed environment, but there are still other issues. Previous work on tethered circuits [11,12] In diagram (5), the spider cannot move to sites s t and s I r since no complementary domains exist between the leg and these sites. Therefore, the backward route of the spider is cut off when the spider moves through the exit mechanism.…”

“…isolates different gates on a surface, e.g., a DNA origami tile [27], such that only gates in close proximity can interact with each other, and two computation units that are not adjacent to each other can use the same sequence. However, the tethered circuits [11,12] lack a direct implementation of the NOT gate, and circuit verification needs to verify many complicated reactions involved in the computation. Previous work [28] has used a walker system to construct logic circuits with spatial locality, but it lacks modularity and is limited to sequential evaluation due to its design where the circuit constructed is in the form of a Binary Decision Diagram (BDD).…”

“…Previous studies [1][2][3][4][5][6][7][8][9][10] have shown that walkers can move directionally and autonomously on a pre-programmed track via localized reactions. Spatial locality can meet the challenges of computation speed-up and sequence reuse that are faced in molecular computing when all the reactants diffuse freely in a well-mixed solution [11,12]. Hence, a walker system with inherent spatial locality has potential to perform more complex computational tasks.…”

“…We can encode signals into functional sites. Signal transmission [11,18] is triggered locally when a spider interacts with a signal-carrying site, which dynamically changes the state of the spider or of the environment. We call this extended system an active molecular spider system.…”