Engineers control cellular proteins with biological computing
DNA has an important job—it tells your cells which proteins to make. Now, a research team at the University of Delaware has developed technology to program strands of DNA into switches that turn proteins on and off.
UD’s Wilfred Chen Group describes their results in a paper published Monday, March 12 in the journal Nature Chemistry. This technology could lead to the development of new cancer therapies and other drugs.
Computing with DNA
This project taps into an emerging field known as DNA computing. Data we commonly send and receive in everyday life, such as text messages and photos, utilize binary code, which has two components—ones and zeroes. DNA is essentially a code with four components, the nucleotides guanine, adenine, cytosine, and thymine. In cells, the arrangement of these four nucleotides determines the output—the proteins made by the DNA. Here, scientists have repurposed the DNA code to design logic-gated DNA circuits.
“Once we had designed the system, we had to first go into the lab and attach these DNA strands to various proteins we wanted to be able to control,” said study author Rebecca P. Chen, a doctoral student in chemical and biomolecular engineering (no relation to Wilfred Chen). The custom sequence designed DNA strands were ordered from a manufacturer while the proteins were made and purified in the lab. Next, the protein was attached to the DNA to make protein-DNA conjugates.
The group then tested the DNA circuits on E. coli bacteria and human cells. The target proteins organized, assembled, and disassembled in accordance with their design.
“Previous work has shown how powerful DNA nanotechnology might possibly be, and we know how powerful proteins are within cells,” said Rebecca P. Chen. “We managed to link those two together.”
Applications to drug delivery
The team also demonstrated that their DNA-logic devices could activate a non-toxic cancer prodrug, 5-fluorocytosine, into its toxic chemotherapeutic form, 5-fluorouracil. Cancer prodrugs are inactive until they are metabolized into their therapeutic form. In this case, the scientists designed DNA circuits that controlled the activity of a protein that was responsible for conversion of the prodrug into its active form. The DNA circuit and protein activity was turned “on” by specific RNA/DNA sequence inputs, while in the absence of said inputs the system stayed “off.
To do this, the scientists based their sequence inputs on microRNA, small RNA molecules that regulate cellular gene expression. MicroRNA in cancer cells contains anomalies that would not be found in healthy cells. For example, certain microRNA are present in cancer cells but absent in healthy cells. The group calculated how nucleotides should be arranged to activate the cancer prodrug in the presence of cancer microRNA, but stay inactive and non-toxic in a non-cancerous environment where the microRNA are missing. When the cancer microRNAs were present and able to turn the DNA circuit on, cells were unable to grow. When the circuit was turned off, cells grew normally.
This technology could have wide applications not only to other diseases besides cancer, but also beyond the biomedical field. For example, the research team demonstrated that their technology could be applied to the production of biofuels, by utilizing their technology to guide an enzymatic cascade, a series of chemical reactions, to break down a plant fiber.
Using the newly developed technology, researchers could target any DNA sequence of their choosing and attach and control any protein they want. Someday, researchers could “plug and play” programmed DNA into a variety of cells to address a variety of diseases, said study author Wilfred Chen, Gore Professor of Chemical Engineering.
“This is based on a very simple concept, a logical combination, but we are the first to make it work,” he said. “It can address a wide scope of problems, and that makes it very intriguing.”
Learn more: PROGRAMMING DNA TO DELIVER CANCER DRUGS
The Latest on: DNA computing
via Google News
The Latest on: DNA computing
- DNA Testing Kits & The Security Risks in Digitized DNA on December 7, 2018 at 6:43 am
they could construct a sample of DNA to match that profile without obtaining any tissue from that person.” Giovanni Vigna, professor of computer science at University of California Santa Barbara and c... […]
- Innovations in AI and deep learning can help scientists predict the impact of changes in DNA structures on November 28, 2018 at 3:36 am
Researchers need to understand the effects of changing a piece of DNA, especially when multiple changes are done In the current study, conducted with Stanford University School of Medicine, Chan-Zucke... […]
- How DNA Technology Became Cheap, Fast and Easily Accessible on November 26, 2018 at 6:43 am
Eighteen years ago, scientists decoded the human genome. But what was supposed to create an era of new cures didn't work out that way, at least not at first. In episode four of Prognosis, some of the ... […]
- A DNA computer has a trillion siblings and replicates itself to make a decision on November 18, 2018 at 4:00 pm
You’re probably imagining a smartphone or laptop, or even one of Google or Amazon’s huge server buildings if you’re in the know about the physical internet. Only one in five people take up this incred... […]
- DNA Leads To Accused Panty-Raider's Arrest: OCDA on October 16, 2018 at 12:01 pm
Semen left on at least one female victim's laptop computer was submitted for forensic analysis in the Rapid DNA program, according to OCDA spokesperson, Michelle Van Der Linden. Jonathon Jose Ruiz, 19 ... […]
- DNA Leads to Arrest in Alleged Sexually Motivated Break-In in Orange on October 15, 2018 at 1:19 pm
DNA technology helped investigators identify a man they say broke into a home where four female college students live, scattering their underwear around and leaving behind bodily fluid on a laptop com... […]
- Nanopore technology with DNA computing easily detects microRNA patterns of lung cancer on October 8, 2018 at 5:03 am
DNAs autonomously recognized two microRNAs, miR-20a and miR-17-5p, and formed a four-way junction structure that was captured in the nanopore, showing long blocking currents. Credit: Figure adapted wi... […]
- New DNA tool predicts height, shows promise for serious illness assessment on October 4, 2018 at 9:30 am
Using data from the UK Biobank, an international resource for health information, Hsu and his team put the algorithm to work, evaluating each participant's DNA and teaching the computer to pull out th... […]
- DNA Computing Gets a Boost With This Machine Learning Hack on July 24, 2018 at 8:03 am
In a brilliant study published in Nature, a team from Caltech cleverly hacked the properties of DNA, essentially turning it into a molecular artificial neural network. When challenged with a classic m... […]
via Bing News