Three-dimensional cages are one of the most important molecular nanotechnology targets both for their simplicity and their application as drug carriers for medicine. DNA nanotechnology uses DNA molecules as programmable “Legos” to assemble structures with a control not possible with other molecules.
The structure of DNA is very simple and lacks the diversity of proteins that make up most natural cages, like viruses. Unfortunately, it is very difficult to control the assembly of proteins with the precision of DNA. That is, until recently. Nicholas Stephanopoulos — an assistant professor in Arizona State University’s Biodesign Center for Molecular Design and Biomimetics, and the School of Molecular Sciences — and his team built a cage constructed from both protein and DNA building blocks through the use of covalent protein-DNA conjugates.
Stephanopoulos modified a homotrimeric protein (a natural enzyme called KDPG aldolase) with three identical single strand DNA handles by functionalizing a reactive cysteine residue they introduced onto the protein surface. This protein-DNA “Lego” was co-assembled with a triangular DNA structure bearing three complementary arms to the handles, resulting in tetrahedral cages comprised of six DNA sides capped by the protein trimer. The dimensions of the cage could be tuned through the number of turns per DNA arm and the hybrid structures were purified and characterized to confirm the three-dimensional structure.
Cages were also modified with DNA using click chemistry, which is a customized type of chemistry, to create elements rapidly with great reliability joining microscopic units together demonstrating the generality of the method.
“My lab’s approach will allow for the construction of nanomaterials that possess the advantages of both protein and DNA nanotechnology, and find applications in fields such as targeted delivery, structural biology, biomedicine, and catalytic materials,” Stephanopoulos said.
Stephanopoulos and his team see an opportunity with hybrid cages — merging self-assembling protein building blocks with a synthetic DNA scaffold — that could combine the bioactivity and chemical diversity of the former with the programmability of the latter. And that is what they set out to create — a hybrid structure constructed through chemical conjugation of oligonucleotide (a synthetic DNA strand) handles on a protein building block. The triangular base bearing three complementary single-stranded DNA handles is self-assembled and purified separately by heating it to alter its properties.
DNA enables the tuning of the cage size without having to redesign all the components.
These cages are the first one constructed through chemical conjugation of oligonucleotide handles on a protein building block. This strategy can in principle be expanded to a wide range of proteins and some of those could have cancer targeting abilities.
This can create a whole new hybrid field of protein-DNA nanotechnology with capabilities beyond DNA and Protein nanotechnology alone.
ACS Nano – Tunable Nanoscale Cages from Self-Assembling DNA and Protein Building Blocks
Three-dimensional (3D) cages are one of the most important targets for nanotechnology. Both proteins and DNA have been used as building blocks to create tunable nanoscale cages for a wide range of applications, but each molecular type has its own limitations. Here, we report a cage constructed from both protein and DNA building blocks through the use of covalent protein–DNA conjugates. We modified a homotrimeric protein (KDPG aldolase) with three identical single-stranded DNA handles by functionalizing a reactive cysteine residue introduced via site-directed mutagenesis. This protein–DNA building block was coassembled with a triangular DNA structure bearing three complementary arms to the handles, resulting in tetrahedral cages comprising six DNA sides capped by the protein trimer. The dimensions of the cage could be tuned through the number of turns per DNA arm (3 turns ∼ 10 nm, 4 turns ∼ 14 nm), and the hybrid structures were purified and characterized to confirm the three-dimensional structure. Cages were also modified with DNA using click chemistry and using aldolase trimers bearing the noncanonical amino acid 4-azidophenylalanine, demonstrating the generality of the method. Our approach will allow for the construction of nanomaterials that possess the advantages of both protein and DNA nanotechnology and find applications in fields such as targeted delivery, structural biology, biomedicine, and catalytic materials.
SOURCES – Arizona State University, ACS Nano
Written By Brian Wang, Nextbigfuture.com
Brian Wang is a Futurist Thought Leader and a popular Science blogger with 1 million readers per month. His blog Nextbigfuture.com is ranked #1 Science News Blog. It covers many disruptive technology and trends including Space, Robotics, Artificial Intelligence, Medicine, Anti-aging Biotechnology, and Nanotechnology.
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4 thoughts on “Programmable Hybrid DNA-Protein Nanotechnology”
The common example is drug delivery. You make a cage to hold the drug, and the protein bits can selectively bind to the target. Antibodies are also proteins.
You could potentially design it to release only on certain conditions. The specific target is one such condition. Another is concentration of some molecule. Blood sugar level, for example. So you could make a diabetes drug that stays in your system for several hours, and only releases insulin when it’s needed. You can actually do some basic computation with DNA, so the conditions can be rather sophisticated.
If you think about it, viruses and CRISPR are both simple combinations of proteins and DNA (or RNA, but it’s similar). So you could use this to make both the delivery vector and the payload for gene therapy.
DNA origami has been used to construct simple mechanical devices, and proteins can do all sorts of things, so one could envision lots of different nano-devices given enough creativity.
So can you give any insight into real world applications? Just….what can we do with this.
DNA is made of 4 nucleobases (Adenine, Guanine, Cytosine, Thymine), arranged in different sequences. DNA can be easily folded and assembled into specific geometries by controlling the sequences of multiple DNA strands. However, with only 4 bases, DNA has limited function.
On the other hand, protein is made of 20 amino acids in various sequences, so has much more functionality. Nearly all of our body’s functions are performed by different proteins. It’s very difficult to design proteins for a particular function, but we can select natural proteins that already have the function we want. We can also evolve artificial proteins starting from natural ones, to tune their function towards what we want. But even then, it’s very difficult to get them to fold or assemble into a desired geometry.
So: DNA: easy to control geometry, limited functionality; Proteins: diverse functionality, very difficult to control geometry.
But by combining them, we can get the best of both: diverse functionality from the protein parts, and controlled geometry from the DNA parts. That’s what they did here. They attached some DNA to an existing protein, and then used more DNA to incorporate that protein into a specific geometrical structure.
Can’t wait for the English version.
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