Computing using DNA relies on information being encoded very concisely onto the base pair sequence joining strands, making DNA a focus of attention for very high-density molecular memories, however, the molecule can also be used to perform computations. 

Now, a study from researchers led by Caltech designs a DNA molecule capable of carrying out reprogrammable computations. Indeed, creating so-called algorithmic self-assembly where the same hardware can be reconfigured to run different software.  The team states the system can execute different algorithms ranging from copying and sorting processes, generating random walks, as well as executing cellular automata.  The study is published in the journal Nature.

Origami DNA computers

Previous studies have used long single-stranded DNA folded into complex 3D structures through base pairing, known as DNA origami.  This is where numerous DNA strands act like staples to fold a long single DNA strand called a scaffold. By programming the sequence of the staples to bind at specific locations, a scaffold can be folded into virtually any shape. 

These, in turn, can be compressed down into multiple surface areas or processors, to build a rectangular tile, known as a DNA tile, consisting of hundreds of short strands carrying a single-stranded DNA probe, each of which contains a unique sequence. 

However, these molecules were specially designed to execute only a single computation.  The current study uses DNA self-assembly to embody an algorithmic process. This works by deploying DNA tiles linking via selective base pairing into arrays enacting a series of complex computations.

The current study develops a DNA computing system consisting of small, artificial DNA strands that self-assemble to build a DNA tile logic circuit while simultaneously executing the circuit algorithm. Starting with master DNA tiles representing the six-bit input, the system adds row after row of molecules, progressively running the algorithm.

Results show the completion of the program is something like a knitted scarf of DNA, made of tiles stuck together in a pattern set by the original program. Data findings show the outcomes are read with an atomic force microscope to detect a marker molecule attached to the DNA.

The group explains they can program a master set of 355 DNA tiles to compute an arbitrary six-bit circuit, with seventeen trillion such circuits possible.  They go on to add their circuits tested inputs to assess if they were multiples of three, performed equality checks, and counted to sixty-three. 

A reprogrammable DNA computer

They also observed other circuits capable of drawing pictures, as well as exhibiting probability outcomes by obtaining a fair 50/50 random choice from a biased coin.

The team surmises they have built a self-assembling reprogrammable DNA computing system able to run six-bit programs and provide outcomes.  For the future, the researchers state their results suggest how this kind of molecular computation might offer new possibilities for making materials, smart drugs, and nanostructures.

Source: Caltech

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