DNA computing successfully minimalized to chips.

Biocomputing is a highly sustainable burgeoning area where biological materials are used to perform computational functions. These materials are environmentally friendly, cheap, and maybe capable of providing mass storage for millions of years. A natural choice for biological computing materials, information-encoded deoxyribonucleic acid (DNA) strands provide a parallel computing process via the cascading chain reactions amongst its nitrogen base pairs.

DNA is a molecule composed of nucleotides carrying genetic instructions for the development and functioning of all known organisms. These nucleotides are attached via alternating nitrogen ‘base pairs’ that form two long strands. These, in turn, spiral to create a structure called a double helix. And as the nitrogen base pairs bond together in a set pattern – this parallel pairing property can be used to perform complex arithmetic, otherwise known as DNA computing.

However, since DNA has only two strands in its backbone, performing even a simple calculation requires multiple chemical reactions using different sets of DNA. In most existing research, the DNA for each computation is added manually, one by one, into a single reaction tube, making the process cumbersome.

Now, a study from scientists at the Incheon National University engineers a programmable DNA-based microfluidic chip – that can be controlled by a simple smartphone to perform DNA calculations. The team states their novel chip carries out complex mathematical calculations by automating reactions between DNA base pairs. The study is published in the journal ACS Nano.

Previous studies show DNA, the component which produces our genes, can generate data several times greater than the most efficient silicon-based computing devices. Due to the structure of DNA, there’s also no limitation to the amount of data storage it can achieve simply by adding more compounds. Additionally, unlike silicon transistors that conduct one rational item at a time, DNA computers can potentially run as many of the required operations concurrently to provide the desired output.

As we know, conventional computers sometimes deal with data in a binary form using Boolean logic gates – a type of logic gate that compares inputs and outputs using a value of ‘TRUE’ or ‘FALSE’ depending on the type of operation. Instead, DNA computers translate this data using selected DNA strands to represent various problems in binary form. Consequently, these binary strings are encoded as strands of DNA which are converted using a lengthy manual process.

Accordingly, using microfluidic chips for DNA-based Boolean logic gates could afford a stream-lined automated operation, programmable control, and seamless combinational logic operation, similar to electronic microprocessors. The current study presents a programmable DNA-based microfluidic processing unit (MPU) chip that can be programmed using a personal computer to perform DNA calculations.

Here, the group of engineers used 3D printing to fabricate a microfluidic chip with the ability to execute Boolean logic employing a single-stranded DNA template. This worked by using different single-stranded DNA as inputs which paired with the template DNA strand wherever the Watson-Crick sequence matched to form double-stranded DNA. Thus, the output was considered true or false based on the size of the final DNA.

The lab explains their MPU can be programmed using a personal computer or smartphone app to produce multiple logic gates. The analog machines can program the two input DNA strands and a logic template DNA strand to calculate basic AND and OR operations.

Furthermore, the MPU can also compute combinational AND and OR logic gates ramping up to a 2-to-1 multiplexer and the XOR operation. The resultant three-step cascade reaction uses the simple DNA-based MPU to perform a sequence of Boolean logic operations known as AND, OR, and NOT.

The researchers predict this programmable DNA-based MPU is expected to facilitate the development of complex functional circuits such as arithmetic logic units and neuromorphic circuits.

The team goes on to add: “We hope that DNA-based CPUs will replace electronic CPUs in the future because they consume less power, which will help with global warming. DNA-based CPUs also provide a platform for complex calculations like deep learning solutions and mathematical modeling”.

For the future, the researchers state they plan to develop a total DNA computing system incorporating complex algorithms and mass storage.

Source: Incheon National University, Korea

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