Researchers have developed a new, fast, and rewritable method for DNA computing that promises smaller, more powerful computers.
This method mimics the sequential and simultaneous gene expression in living organisms and incorporates programmable DNA circuits with logic gates. The improved process places DNA on a solid glass surface, enhancing efficiency and reducing the need for manual transfers, culminating in a 90-minute reaction time in a single tube.
Advancements in DNA-Based Computation
DNA carries the instructions for life, guiding everything from physical traits like hair color to disease susceptibility. Its ability to store vast amounts of information and perform complex biological processes has inspired scientists to explore DNA-based computers. These futuristic devices could be faster and more compact than today’s silicon-based computers. In a new study published today (December 11) in ACS Central Science, researchers unveiled a new DNA computing method that is both fast and rewritable — much like modern digital computers.
“DNA computing as a liquid computing paradigm has unique application scenarios and offers the potential for massive data storage and processing of digital files stored in DNA,” explains Fei Wang, one of the study’s co-authors.
Developing Programmable DNA Devices
In living organisms, DNA expression follows a precise sequence: Genes are transcribed into RNA, which is then translated into proteins. This process happens simultaneously across numerous genes and is continuously repeated. If scientists can replicate this intricate biological process within DNA-based computers, they could create machines far more powerful than current silicon-based systems. While sequential DNA computing has been demonstrated for specific, narrowly focused tasks, developing flexible and programmable DNA devices that can be reused across multiple applications has remained a challenge — until now.
Innovations in DNA Circuit Design
In previous research, Chunhai Fan, Wang, and colleagues developed a programmable DNA integrated circuit with many logic gates that act as instructions for the circuit’s operations. Here’s how it worked:
- Data, 0 or 1, was represented by a short piece of single-stranded DNA, called an oligonucleotide, that contained a series of bases: adenine, thymine, guanine and cytosine. (In nature, the sequence of bases codes for a gene.)
- For example, two inputs of 1 (DNA strands 1 and 2) would interact with an OR logic gate DNA molecule.
- Then in a fluid-filled tube, the input oligonucleotide interacted with a logic gate DNA molecule and generated an output oligonucleotide.
- The output oligonucleotide bound to a different single-stranded DNA that was folded into an origami-like structure, called a register in computer lingo.
- The oligonucleotide was “read” by reviewing its base sequence, released and used in a vial containing the next gate, and so on.
Enhancing DNA Computing Efficiency
This process took hours, and someone had to manually transfer the oligonucleotide from one gate to another vial for the next computing operation. So the team, along with Hui Lv and Sisi Jia, wanted to speed things up.
To make the reaction processes more efficient and compact, the team first placed the DNA origami register onto a solid glass 2D surface. The output oligonucleotide floating in liquid from a specific logic gate then attached to the glass-mounted register. After the output oligonucleotide was read and the logic gate instructions determined, it detached, which reset the register so it could be rewritten, thereby avoiding the need to move or replace registers. The researchers also designed an amplifier that boosted the output signal so all the pieces — the gates, oligonucleotides and registers — could find one another more easily. In a proof-of-concept experiment, all the DNA computing reactions took place in a single tube within 90 minutes.
Future Perspectives
“This research paves the way for developing large-scale DNA computing circuits with high speed and lays the foundation for visual debugging and automated execution of DNA molecular algorithms,” says Wang.
Reference: “High-Speed Sequential DNA Computing Using a Solid-State DNA Origami Register” by Qian Zhang, Mingqiang Li, Yuqing Tang, Jinyan Zhang, Chenyun Sun, Yaya Hao, Jianing Cheng, Xiaodong Xie, Sisi Jia, Hui Lv, Fei Wang and Chunhai Fan, 11 December 2024, ACS Central Science.
DOI: 10.1021/acscentsci.4c01557
The authors acknowledge funding from the National Key Technologies R&D Program, the National Natural Science Foundation of China, the Science Foundation of Shanghai Municipal Commission of Science and Technology, the China Postdoctoral Science Foundation, the New Cornerstone Science Foundation, and the K.C. Wong Education Foundation.
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