New DNA Computer Opens Door to Future Medical Breakthroughs

Method uses linear-DNA -- compatible with standard cell enzymes -- to process signals and produce outputs

A team of researchers from the Univ. of Washington (UW), theCalifornia Institute of Technology (CalTech), the Univ. of California (UC) and Microsoft Corp. (MSFT) have come up with a "toolbox" which they say represents the most promising DNA based computer network yet.

The basic idea of a DNA (deoxyribonucleic acid) toolbox is to take inputs -- small strands of DNA or microRNA (micro-ribonucleic acid) -- perform a series of displacement reactions on "Gate" strands, and selectively put out a set of desired outputs that can be used to activate man-made molecules to deliver drugs, turn on sensors, or feed into other DNA networks.

The attractiveness of making DNA computers is that the tools to preserve and replicate your network are already on hand -- in the various cellularnucleases, ligases, topoisomerases, helicases, and polymerases that the cell uses to processes DNA. Thus future DNA computers composed of inputs (sensors, delivered drug molecules) and outputs (releasable drug packages, selective protein transcription) can be made to be self-repairing and programmable.

The latest work builds on an earlier 2007 paper published inScience by the authors. It uses a DNA displacement approach (like most DNA computer efforts), which implements a basic set of logic "gates" for the DNA computer as a series of DNA reactions.

Among the many proposed architectures for strand displacement computation, ours is unique in that it relies exclusively on linear, double-stranded DNA complexes (processed by nicking one of the strands). Because this structure is compatible with natural DNA, we are able to produce our computational elements in a highly pure form by bacterial cloning. Thus, we bypass the practical limitations in the length and purity of synthetic strands.

I think this is appealing because it allows you to solve more than one problem. If you want a computer to do something else, you just reprogram it. This project is very similar in that we can tell chemistry what to do.

Of course there's also a downside (or upside, depending on your perspective) which the authors don't mention. The ability to build DNA computers which generate responses that can interact with the cell's natural DNA and biomolecules is highly weaponizable. For example future researchers could make a DNA computer that lay dormant for some given amount of time, then triggered cells to become aggressive cancer tumors, and then release yet more factors that encouraged those deadly tumor cells to metastasize.

The current work was published in the journal Nature, one of academia's most prestigious peer-reviewed journals. It was funded in part by a $2M USD grant from the National Science Foundation (NSF) to UW electrical engineering professorEric Klavins, a co-author on the work.

Sources: Univ. of Wash., Nature [abstract]

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New DNA Computer Opens Door to Future Medical Breakthroughs