Oligonucleotide-directed self-assembly of proteins: semisynthetic DNA—streptavidin hybrid molecules as connectors for the generation of macroscopic arrays and the construction of supramolecular bioconjugates (original) (raw)
Related papers
A polycatenated DNA scaffold for the one-step assembly of hierarchical nanostructures
Proceedings of the National Academy of Sciences, 2008
A unique DNA scaffold was prepared for the one-step self-assembly of hierarchical nanostructures onto which multiple proteins or nanoparticles are positioned on a single template with precise relative spatial orientation. The architecture is a topologically complex ladder-shaped polycatenane in which the ''rungs'' of the ladder are used to bring together the individual rings of the mechanically interlocked structure, and the ''rails'' are available for hierarchical assembly, whose effectiveness has been demonstrated with proteins, complementary DNA, and gold nanoparticles. The ability of this template to form from linear monomers and simultaneously bind two proteins was demonstrated by chemical force microscopy, transmission electron microscopy, and confocal fluorescence microscopy. Finally, fluorescence resonance energy transfer between adjacent fluorophores confirmed the programmed spatial arrangement between two different nanomaterials. DNA templates that bring together multiple nanostructures with precise spatial control have applications in catalysis, biosensing, and nanomaterials design.
Cell-targeted self-assembled DNA nanostructures
Journal of The American Chemical Society, 2009
The ability to organize materials is a core goal of bionanotechnology. Biomedically relevant examples include the organization of cells into predictable architectures on surfaces 1,2 and the delivery of diverse molecules to cells. 3 Cell surface engineering 4 seeks to localize nanoscale materials such as proteins, 5 carbon nanotubes, 6 synthetic bioactive polymers, 7 vault nanoparticles, 8 and polyelectrolyte multilayer patches 9 onto cellular membranes. Cells have been assembled into microtissues using DNA-mediated interactions. 10 DNA scaffolds, which are nanoarrays built from repeating DNA motifs, have been used for multicomponent interactions 11 to position small peptides, 12 streptavidin, 13,14 antibodies, 15,16 and inorganic materials 17,18 on the array surface into controlled networks and to detect proteins, 19,20 DNA, 21 and RNA. We demonstrate how selfassembled DNA arrays can be directed to the surface of cells, first through biotin-streptavidin interactions and second through specific antibody-cell surface interactions. The versatile cargo-carrying ability of arrays for directing cell-surface interactions, cell-cell bridging, and positioning multiple cells onto a DNA fabric is explored.
Programmable DNA Self-Assemblies for Nanoscale Organization of Ligands and Proteins
Nano Letters, 2005
We demonstrate the precise control of periodic spacing between individual protein molecules by programming the self-assembly of DNA tile templates. In particular, we report the application of two self-assembled periodic DNA structures, two-dimendional nanogrids, and one-dimensional nanotrack, as template for programmable self-assembly of streptavidin protein arrays with controlled density.
Biosensors and Bioelectronics, 2005
Highly controlled supramolecular assemblies combining a genetically engineered redox protein, cytochrome b5, and modified oligonucleotides are presented. Modified b5 and DNA are covalently assembled through a hetero bifunctional cross-linker to give a unique hybrid molecular species. Moreover, the assembly includes a histidine tag head able to bind to modified phospholipids which lead to a new generation of self-assembled dynamic DNA chips. The interaction of the construction with a complementary oligonucleotide sequence can be monitored in real time by surface plasmon resonance using Biacore technology. The biochip, presented herein, features unique properties including tunable surface density of probes, very low non-specific interactions and optimization of hybridization efficiency. In addition, we demonstrated that the phase transition of the lipidic layer can modulate the dynamic of the association of the complex to the supported membrane. Potential applications of this new device are multiple including high sensitivity and high selectivity biochips, especially for studies of the DNA-ligands interactions in a biomimetic environment.
Analytical Biochemistry, 1999
Covalent DNA-streptavidin conjugates have been utilized for the reversible and site-selective immobilization of various biotinylated enzymes and antibodies by DNAdirected immobilization (DDI). Biotinylated alkaline phosphatase, -galactosidase, and horseradish peroxidase as well as biotinylated anti-mouse and anti-rabbit immunoglobulins have been coupled to the DNAstreptavidin adapters by simple, two-component incubation and the resulting preconjugates were allowed to hybridize to complementary, surface-bound capture oligonucleotides. Quantitative measurements on microplates indicate that DDI proceeds with a higher immobilization efficiency than conventional immobilization techniques, such as the binding of the biotinylated proteins to streptavidin-coated surfaces or direct physisorption. These findings can be attributed to the reversible formation of the rigid, double-stranded DNA spacer between the surface and the proteins. Moreover, BIAcore measurements demonstrate that DDI allows a reversible functionalization of sensor surfaces with reproducible amounts of proteins. Ultimately, the simultaneous immobilization of different compounds using microstructured oligonucleotide arrays as immobilization matrices demonstrate that DDI proceeds with site selectivity due to the unique specificity of Watson-Crick base pairing.
Synthetic, biofunctional nucleic acid-based molecular devices
Current Opinion in Biotechnology, 2011
The user has requested enhancement of the downloaded file. All in-text references underlined in blue are added to the original document and are linked to publications on ResearchGate, letting you access and read them immediately. This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues.
Selective DNA-Directed Assembly on Dual-Functionalized Microparticles
2004
The bottom-up assembly of functional devices requires novel building blocks to facilitate the incorporation of functional and structural hierarchy. Anisotropic building blocks can substantially broaden the creation of self-assembled devices with unique properties because of their morphological and/or chemical asymmetry. In this regard, we have created microspheres with one hemispherical face exposing silica and the other exposing gold. These microspheres were formed by the shadow deposition of gold onto silica microspheres. The two chemical surfaces allowed use of different surface reactions-silane chemistry for the silica side and thiol chemistry for the gold side-for immobilizing different oligonucleotide sequences on each of the two faces. These dual-functionalized microspheres were used in the selective orthogonal assembly of fluorophore-tagged target oligonucleotides. The DNA-directed assembly was confirmed by confocal microscopy of the microspheres. In essence, employing DNA as the linker molecule, these "Janus" particles can be assembled into various novel 1-D, 2-D, and 3-D structures, which are difficult to realize using symmetric building blocks.
Organizing protein–DNA hybrids as nanostructures with programmed functionalities
Trends in Biotechnology, 2010
The structural and functional information encoded in the base sequence of nucleic acids provides a means to organize hybrid protein-DNA nanostructures with pre-designed, programmed functionality. This review discusses the activation of enzyme cascades in supramolecular DNA-protein hybrid structures, the bioelectrocatalytic activation of redox enzymes on DNA scaffolds, and the programmed positioning of enzymes on 1D, 2D and 3D DNA nanostructures. These systems provide starting points towards the design of interconnected enzyme networks. Substantial progress in the tailoring of functional protein-DNA nanostructures has been accomplished in recent years, and advances in this field warrant a comprehensive discussion. The application of these systems for the control of biocatalytic transformations, for amplified biosensing, and for the synthesis of metallic nanostructures are addressed, and future prospects for these systems are highlighted.
Organic & Biomolecular Chemistry, 2008
The influence of added polynucleotide on the gelation ability of nucleobase-appended organogelators was investigated. Uracil-appended cholesterol gelator formed a stable organogel in polar organic solvents such as n-butanol. It was found that the addition of the complementary polyadenylic acid (poly(A)) not only stabilizes the gel but also creates the helical structure in the original gel phase. Thymidine and thymine-appended gelators can form stable gel in apolar solvents, such as benzene, where poly(A)-lipid complex can act as a complementary template for the gelator molecules to create the fibrous composites. Based on these findings, we can conclude that self-assembling modes and gelation properties of nucleobase-appended organogelators are controllable by the addition of their complementary polynucleotide in organic solvents. We believe, therefore, that the present system can open the new paths to accelerate development of well-controlled one-dimensional molecular assembly systems, which would be indispensable for the creation of novel nanomaterials based on organic compounds.