Reprogrammable self-assembling DNA computer developed.


It is known that computing with DNA relies on information being encoded very concisely into the base pair sequence on strands. That alone has made DNA a focus of attention for very high density molecular memories, however, the molecule can also be used to conduct computation.  Now, a study from researchers led by Caltech designs DNA molecules which can carry out reprogrammable computations, for the first time creating so-called algorithmic self-assembly in which the same hardware can be configured to run different software.  The team state the system can execute different algorithms ranging from copying and sorting processes, generating random walks and executing cellular automata.  The study is published in the journal Nature.

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, deploying DNA tiles which link via selective base pairing into arrays enacting a series of complex computations.

The current study develops a DNA computing system which works by self-assembly; small, specially designed DNA strands stick together to build a DNA tile logic circuit while simultaneously executing the circuit algorithm. Results show starting with the master DNA tiles which represent the six bit input, the system adds row after row of molecules, progressively running the algorithm. Data findings show that 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; the outcomes are read with an atomic force microscope, which detects a marker molecule attached to the DNA.

The group explain they can program a master set of 355 DNA tiles to compute an arbitrary six-bit circuit, and that there are 17 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 63; other circuits drew pictures, as well as exhibiting probability outcomes by obtaining a fair 50/50 random choice from a biased coin.

The team surmise they have built a self-assembling reprogrammable DNA computing system which can run six bit programs and provide outcomes.  For the future, the researchers state as well as providing a proof of principle for making the system reprogrammable and scaling-up to a new level of complexity, already the 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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