Modular system of DNA origami voxels with programmable 3D connections

Amazing stuff!

"Researchers in the field of molecular robotics have created programmable, 3-dimensional nanoscale objects – such as a nano-dinosaur, dancing robot, and a mini-Australia – using “DNA origami”. ..."

"... This innovative approach has potential across a range of applications, from targeted drug delivery systems to responsive materials and energy-efficient optical signal processing. The method uses ‘DNA origami’, so-called as it uses the natural folding power of DNA, the building blocks of human life, to create new and useful biological structures.

As a proof-of-concept, the researchers made more than 50 nanoscale objects, including a ‘nano-dinosaur’, a ‘dancing robot’ and a mini-Australia that is 150 nanometres wide, a thousand times narrower than a human hair. ...

One of the most exciting applications of this technology is its potential to create nanoscale robotic boxes capable of delivering drugs directly to targeted areas within the body. By using DNA origami, researchers can design these nanobots to respond to specific biological signals, ensuring medications are released only when and where they are needed. This targeted approach could enhance the effectiveness of cancer treatments while minimising side effects. ...

the development of new materials that can change properties in response to environmental stimuli. For instance, these materials could be engineered to be responsive to higher loads or alter their structural characteristics based on changes in temperature or acidic (pH) levels. Such responsive materials have the potential to transform medical, computing and electronics industries. ..."

From the editor's summary and abstract:

"Editor’s summary

The development of synthetic molecular structures that can self-assemble into unique complex machines is a challenge. Inspired by protein folding, Luu et al. have developed a modular system of origami voxels made from DNA nanostructures. These voxels contain internal and external connections that can be switched between various states. They can be combined to form two-dimensional and three-dimensional hierarchical assemblies and be reconfigured into new shapes. The modular system could potentially be adapted for environment-adaptive switching and reconfiguration in response to temperature and pH. ...

Abstract

In cells, proteins rapidly self-assemble into sophisticated nanomachines. Bioinspired self-assembly approaches, such as DNA origami, have been used to achieve complex three-dimensional (3D) nanostructures and devices. However, current synthetic systems are limited by low yields in hierarchical assembly and challenges in rapid and efficient reconfiguration between diverse structures. Here, we developed a modular system of DNA origami “voxels” with programmable 3D connections. We demonstrate multifunctional pools of up to 12 unique voxels that can assemble into many shapes, prototyping 50 structures. Programmable switching of local connections between flexible and rigid states achieved rapid and reversible reconfiguration of global structures in three dimensions. Multistep assembly pathways were then explored to increase the yield. Voxels were assembled via flexible chain intermediates into rigid structures, increasing yield up to 100-fold. We envision that foldable chains of DNA origami voxels can achieve increased complexity in reconfigurable nanomaterials, providing modular components for the assembly of nanorobotic systems with future applications in synthetic biology, assembly of inorganic materials, and nanomedicine."

DNA origami could create cancer-destroying nanorobots

'Velcro' DNA origami helps build nanorobotic Meccano "Innovative structures pave the way for advanced robotics – and mini dinosaurs"

Reconfigurable nanomaterials folded from multicomponent chains of DNA origami voxels

Researchers have built tiny dinosaurs and even a ‘mini Australia’ just 150 nanometres wide as a proof of concept.

Nanorobot hand made of DNA grabs viruses for diagnostics and blocks cell entry

Amazing stuff!

"... researchers report. Dubbed the NanoGripper, the nanorobotic hand also could be programmed to interact with other viruses or to recognize cell surface markers for targeted drug delivery, such as for cancer treatment. ...

Inspired by the gripping power of the human hand and bird claws, the researchers designed the NanoGripper with four bendable fingers and a palm, all in one nanostructure folded from a single piece of DNA. Each finger has three joints, like a human finger, and the angle and degree of bending are determined by the design on the DNA scaffold. ...

The fingers contain regions called DNA aptamers that are specially programmed to bind to molecular targets—the spike protein of the virus that causes COVID-19, for this first application—and trigger the fingers to bend to wrap around the target. On the opposite side, where the wrist would be, the NanoGripper can attach to a surface or other larger complex for biomedical applications such as sensing or drug delivery. ..."

From the editor's summary and abstract:

"Editor’s summary

Recent DNA nanostructures have been functionalized to detect or block viruses but have lacked the dexterity to grasp individual virus particles. Here, Zhou et al. designed and synthesized a DNA NanoGripper from a single DNA origami piece that resembles a hand with a palm and four bendable finger-like structures. The NanoGripper’s fingers can be functionalized with ssDNA or aptamers to recognize and bind to different targets such as gold nanoparticles and SARS-CoV-2. Experiments showed that the NanoGripper can successfully detect SARS-CoV-2 virions in a human saliva sample with comparable sensitivity to a PCR test and has the potential to inhibit virus infections. ...

Abstract

DNA has shown great biocompatibility, programmable mechanical properties, and precise structural addressability at the nanometer scale, rendering it a material for constructing versatile nanorobots for biomedical applications. Here, we present the design principle, synthesis, and characterization of a DNA nanorobotic hand, called DNA NanoGripper, that contains a palm and four bendable fingers as inspired by naturally evolved human hands, bird claws, and bacteriophages. Each NanoGripper finger consists of three phalanges connected by three rotatable joints that are bendable in response to the binding of other entities. NanoGripper functions are enabled and driven by the interactions between moieties attached to the fingers and their binding partners. We demonstrate that the NanoGripper can be engineered to effectively interact with and capture nanometer-scale objects, including gold nanoparticles, gold NanoUrchins, and SARS-CoV-2 virions. With multiple DNA aptamer nanoswitches programmed to generate a fluorescent signal that is enhanced on a photonic crystal platform, the NanoGripper functions as a highly sensitive biosensor that selectively detects intact SARS-CoV-2 virions in human saliva with a limit of detection of ~100 copies per milliliter, providing a sensitivity equal to that of reverse transcription quantitative polymerase chain reaction (RT-qPCR). Quantified by flow cytometry assays, we demonstrated that the NanoGripper-aptamer complex can effectively block viral entry into the host cells, suggesting its potential for inhibiting virus infections. The design, synthesis, and characterization of a sophisticated nanomachine that can be tailored for specific applications highlight a promising pathway toward feasible and efficient solutions to the detection and potential inhibition of virus infections."

Nanorobot hand made of DNA grabs viruses for diagnostics and blocks cell entry

Nanorobot hand made of DNA grabs viruses for diagnostics and blocks cell entry (original news release)

Bioinspired designer DNA NanoGripper for virus sensing and potential inhibition (no public access)

Illinois researchers developed a nanorobotic hand made of DNA that can grab viruses for detection or inhibition. In this artist’s rendering, three “NanoGripper” hands wrap around a COVID-19 virus.

Inspired by the human hand or bird claws, the NanoGripper has four fingers and a palm, all folded from one piece of DNA.

Toward nanoscale DNA writers: Unlocking scalable DNA data writing technology

Food for thought! Towards synthetic DNA storage technology!

"... Available methods of storage are having difficulty keeping up with the increasing demand in the long term. Synthetic DNA, at its root a tiny storer of information, offers a potential pathway toward significantly reducing the amount of space and material needed for future archival storage needs. Revisiting the projection of growth above, it would take millions of tape cartridges—the current densest commercial storage media—to store 9 zettabytes of information, whereas it would take the footprint of one small refrigerator if stored in DNA.

DNA not only offers a clear advantage over existing storage media with density at over 1 exabyte per cubic inch, but also is a potential solution to present-day challenges in data archival storage systems. DNA can be incredibly durable and can last thousands of years ...

Additionally, evidence points to potential for DNA storage to have lower greenhouse gas emissions, water consumption, and energy consumption. Despite these advantages, one key impediment to large-scale deployment of DNA data storage has been its low DNA synthesis throughput, resulting in low throughput of writing and relatively high cost. ..."

Toward nanoscale DNA writers: Unlocking scalable DNA data writing technology - Microsoft Research

Scaling DNA data storage with nanoscale electrode wells (open access)

Memory-making involves extensive DNA breaking

Recommendable!

"The urgency to remember a dangerous experience requires the brain to make a series of potentially dangerous moves: Neurons and other brain cells snap open their DNA in numerous locations — more than previously realized, according to a new study — to provide quick access to genetic instructions for the mechanisms of memory storage. ...

The extent of these DNA double-strand breaks (DSBs) in multiple key brain regions is surprising and concerning ..., because while the breaks are routinely repaired, that process may become more flawed and fragile with age. Tsai’s lab has shown that lingering DSBs are associated with neurodegeneration and cognitive decline and that repair mechanisms can falter. ...
The creation of a fear memory doubled the number of DSBs among neurons in the hippocampus and the prefrontal cortex, affecting more than 300 genes in each region. Among 206 affected genes common to both regions ..."

Memory-making involves extensive DNA breaking | MIT News | Massachusetts Institute of Technology To quickly express learning and memory genes, brain cells snap both strands of DNA in many more places and cell types than previously realized, a new study shows.

Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes (open access)

Could all your digital photos be stored as DNA?

Recommendable! Sounds almost to good to be true!

An unsustainable situation:

"On Earth right now, there are about 10 trillion gigabytes of digital data, and every day, humans produce emails, photos, tweets, and other digital files that add up to another 2.5 million gigabytes of data. Much of this data is stored in enormous facilities known as exabyte data centers (an exabyte is 1 billion gigabytes), which can be the size of several football fields and cost around $1 billion to build and maintain."

"... DNA, which evolved to store massive quantities of information at very high density. A coffee mug full of DNA could theoretically store all of the world’s data ...
Scientists have already demonstrated that they can encode images and pages of text as DNA. ...

MIT biological engineers have demonstrated a way to easily retrieve data files stored as DNA. This could be a step toward using DNA archives to store enormous quantities of photos, images, and other digital content. ..."

Could all your digital photos be stored as DNA? | MIT News | Massachusetts Institute of Technology A technique for labeling and retrieving DNA data files from a large pool could help make DNA data storage feasible.

Left-Handed DNA Has a Biological Role Within a Dynamic Genetic Code

Very recommendable! Nice overview article! Left-handed DNA was only discovered in 1970 and appears for a long time was treated more like a curiosity.

"... Whether this bizarre form of DNA existed in cells and had any function, and what that might be, was hotly debated for nearly half a century. But research has recently confirmed its biological relevance. ...
So-called Z-DNA is now thought to play roles in cancer and autoimmune diseases, and last year scientists confirmed its link to three inherited neurological disorders. ..."

Left-Handed DNA Has a Biological Role Within a Dynamic Genetic Code | The Scientist Magazine®

Enzymatic DNA synthesis to store digital data in DNA

Good news! Given the exponential explosion of digital data new storage technologies need to be developed fast.

"... DNA is an ideal storage medium because it is stable over hundreds or thousands of years, has an extraordinary information density, and its information can be efficiently read (decoded) again with advanced sequencing techniques that are continuously getting less expensive. ..."

"... Now, the researchers have applied [maskless] photolithographic techniques from the computer chip industry to enzymatic DNA synthesis, and thus developed a new method to multiplex TdT’s [Terminal deoxynucleotidyl Transferase ] superior DNA writing ability. In their study published in Nature Communications, they demonstrated the parallel synthesis of 12 DNA strands with varying sequences on a 1.2 square millimeter array surface. ..."

Enzymatic DNA synthesis sees the light Controlling a DNA-synthesizing enzyme with photolithographic methods from the computer chip industry facilitates multiplexed writing and storage of digital data in DNA

Here is the link to the underlying research paper:

Photon-directed multiplexed enzymatic DNA synthesis for molecular digital data storage | Nature Communications