Capturing and Stabilizing Folded Proteins in Lattices Formed with Branched Oligonucleotide Hybrids

Abstract

The encapsulation of folded proteins in stabilizing matrices is one of the challenges of soft-matter materials science. Capturing such fragile bio-macromolecules from aqueous solution, and embedding them in a lattice that stabilizes them against denaturation and decomposition is difficult. Here, we report that tetrahedral oligonucleotide hybrids as branching elements, and connecting DNA duplexes with sticky ends can assemble into materials. The material-forming property was used to capture DNA-binding proteins selectively from aqueous protein mixtures. The three-dimensional networks also encapsulate guest molecules in a size-selective manner, accommodating proteins up to a molecular weight of approximately 159 kDa for the connecting duplex lengths tested. Exploratory experiments with green fluorescent protein showed that, when embedded in the DNA-based matrix, the protein is more stable toward denaturation than in the free form, and retains its luminescent properties for at least 90 days in dry form. The noncrystalline biohybrid matrices presented herein may be used for capturing other proteins or for producing functional materials.

Hybridization Networks of mRNA and Branched RNA Hybrids

“…Material formation through multivalent hybridization of the arms of branched DNA hybrids alone, or in combination with connector duplexes featuring sticky ends, has been reported before. [5][6][7][8][9][10][11][12] The underlying multivalent hybridization events usually require shorter duplex lengths than those of linear strands, so that dinucleotides can suffice to induce assembly into a material. [5] Even in light of these earlier findings, the current results are surprising.…”

“…The hybridization networks formed by such species can capture a range of different active pharmaceutical ingredients and release them into serum from the resulting solid [11] . Further, it was recently shown that hybridization networks made up of hybrids and linear duplexes as spacers or binding sites can encapsulate proteins, either by non‐specific capture upon precipitation or based on sequence‐specific binding events [12] . The resulting hybrid materials can stabilize proteins against denaturation.…”

“…[11] Further, it was recently shown that hybridization networks made up of hybrids and linear duplexes as spacers or binding sites can encapsulate proteins, either by non-specific capture upon precipitation or based on sequence-specific binding events. [12] The resulting hybrid materials can stabilize proteins against denaturation. Encapsulation and protection of sensitive biomolecules is an important issue for medical applications.…”

DNA Functional Materials Assembled from Branched DNA: Design, Synthesis, and Applications

“…For example, the hybridization of aptamer and complementary sequences induced the disintegration of DNA hydrogel with aptamer functionalized. , A photoresponsive base had the capability of controlled disassembly of hydrogel under UV irradiation . The characteristic of this dynamic controlled disassembly, coupled with excellent biocompatibility, made DNA hydrogel suitable for in situ encapsulation and controlled release of proteins, while maintaining their activities. , On the other hand, the enzyme-free process was advantageous to the adjustment of size of hydrogel, from macroscale to nanoscale, in a more controlled fashion, such as adding blocking chains. Regulating the concentration ration of branched DNA tiles, DNA linkers, and blocking chains effectively controlled the size of nanohydrogel.…”