Programmable Hybrid DNA-Protein Nanotechnology

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

Abstract

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

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