Nucleic Acid‐Modified Nanostructures as Programmable Atom Equivalents: Forging a New “Table of Elements”

Macfarlane, Robert J.; O’Brien, Matthew N.; Petrosko, Sarah Hurst; Mirkin, Chad A.

doi:10.1002/anie.201209336

Cited by 150 publications

(165 citation statements)

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“…Here, we introduce a new method for effecting protein crystallization by trading protein-protein interactions for complementary oligonucleotide-oligonucleotide interactions. By using different proteins functionalized with the appropriate oligonucleotides, along with the design rules introduced for inorganic systems (7,8,28), we show that different combinations of DNAfunctionalized enzymes, and enzymes and inorganic NPs, can be assembled deliberately into preconceived lattices and, in some cases, well-defined crystal habits. Importantly, the enzymes retain their native structures and catalytic functionalities after extensive modification of their surfaces with DNA and assembly into crystalline superlattices.…”

mentioning

confidence: 99%

DNA-mediated engineering of multicomponent enzyme crystals

Brodin

Auyeung

Mirkin

2015

Proc. Natl. Acad. Sci. U.S.A.

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127

138

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The ability to predictably control the coassembly of multiple nanoscale building blocks, especially those with disparate chemical and physical properties such as biomolecules and inorganic nanoparticles, has far-reaching implications in catalysis, sensing, and photonics, but a generalizable strategy for engineering specific contacts between these particles is an outstanding challenge. This is especially true in the case of proteins, where the types of possible interparticle interactions are numerous, diverse, and complex. Herein, we explore the concept of trading protein-protein interactions for DNA-DNA interactions to direct the assembly of two nucleic-acid-functionalized proteins with distinct surface chemistries into six unique lattices composed of catalytically active proteins, or of a combination of proteins and DNA-modified gold nanoparticles. The programmable nature of DNA-DNA interactions used in this strategy allows us to control the lattice symmetries and unit cell constants, as well as the compositions and habit, of the resulting crystals. This study provides a potentially generalizable strategy for constructing a unique class of materials that take advantage of the diverse morphologies, surface chemistries, and functionalities of proteins for assembling functional crystalline materials.nanoscience | biomaterials | self-assembly | superlattice | DNA-programmable assembly D NA-mediated assembly strategies (1-3) that take advantage of rigid building blocks, functionalized with oriented oligonucleotides to create entities with well-defined "valencies," have emerged as powerful new ways for programming the formation of crystalline materials (4, 5). With such methods, one can make architectures with well-defined lattice parameters (6-12), symmetries (4,8,10,12), and compositions (10, 12, 13), but to date they have been confined primarily to the use of hard inorganic nanoparticles (NPs) or highly branched pure nucleic-acid materials (2, 14, 15). In contrast, Nature's most powerful and versatile nanostructured building blocks are proteins and are used to effect the vast majority of processes in living systems (16). Unlike most inorganic NP systems, proteins can be made in pure and perfectly monodisperse form, making them ideal synthons for supramolecular assemblies. However, the ability to engineer lattices composed of multiple proteins, or of proteins and inorganic nanomaterials, has been limited, and the choice of protein building blocks is often restricted by structural constraints, which limits the catalytic functionalities that can be incorporated into these structures. Currently, the primary methods for making protein lattices have relied on the use of natural protein-protein interactions (17), interactions between proteins and ligands on the surfaces of inorganic NPs (17, 18), metal coordination chemistry (19), small molecule ligand-protein interactions (20-23), genetically fusing protein complexes with specific symmetries (24, 25), or DNA-mediated assembly of viruses (26,27). Here, we introduce a new...

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mentioning

confidence: 99%

DNA-mediated engineering of multicomponent enzyme crystals

Brodin

Auyeung

Mirkin

2015

Proc. Natl. Acad. Sci. U.S.A.

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127

138

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“…4,41 It is also envisioned that these DNA-AuNPs can be further exploited to assemble high-ordered structures, for example, hydrogel or crystals with better control and homogeneity. [14][15][16] In addition, because we have obtained high yields of well-defined and uniform Au nanostructures, we expect that this system holds great promise for DNAregulated plasmonic applications 42,43 and biomolecular imaging. [44][45][46][47] …”

Section: Discussionmentioning

confidence: 99%

“…[9][10][11][12][13] During the past two decades, we have witnessed dramatic advances in such functional nanosystems, including the formation of molecule-like crystal structures and the assembly of dynamic nanodevices. [14][15][16][17][18] Despite the rapid progress, most of these applications used polyvalent DNA-AuNP conjugates without knowing the exact number of loaded DNA strands. Although polyvalent DNA-AuNPs possess unique merits, such as signal amplification and cellular internalization; [19][20][21] such inaccuracy may introduce potential imperfectness in the artificially constructed nanosystems.…”

Section: Introductionmentioning

confidence: 99%

“…There have been many efforts to develop DNA-AuNP conjugates of fixed valences, 16,22,23 in particular, monovalent DNA-AuNPs (mDNAAuNPs, Figure 1a). 4,9,10,[24][25][26][27][28][29][30][31][32][33] In a straightforward approach, AuNPs are titrated with DNA of different ratios, and then, the resulting conjugates are purified using gel electrophoresis to obtain mDNA-AuNPs.…”

Section: Introductionmentioning

confidence: 99%

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Clicking DNA to gold nanoparticles: poly-adenine-mediated formation of monovalent DNA-gold nanoparticle conjugates with nearly quantitative yield

et al. 2015

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Monovalent DNA-gold nanoparticle (mDNA-AuNP) conjugates hold great promise for widespread applications, especially the construction of well-defined, molecule-like nanosystems. Previously reported methods all rely on the use of thiolated DNA to functionalize AuNPs, resulting in relatively low yields. Here, we report a facile method to rapidly prepare mDNA-AuNPs using a poly-adenine (polyA)-mediated approach. As polyA can selectively bind to AuNPs with high controllability of the surface density of DNA, we can use a DNA strand with a sufficiently long polyA to wrap around the surface of an individual AuNP, preventing further the adsorption of additional strands. Based on this observation, we obtained mDNA-AuNPs with a nearly quantitative yield of~90% using 80 As, as confirmed by both gel electrophoresis and transmission electron microscope observation. The yields of mDNA-AuNPs were insensitive to the stoichiometric ratio between DNA and AuNPs, suggesting the click chemistry-like nature of this polyA-mediated reaction. mDNA-AuNPs exhibited rapid kinetics and high efficiency for sequence-specific hybridization. More importantly, we demonstrated that AuNPs of fixed valences could form well-defined heterogenous oligomeric nanostructures with precise, atom-like control.

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“…In fully addressable self-assembly, each building block is programmed 16,17 to occupy a specific site in the target structure. To achieve this level of precision, each building block must be unique and be encoded with enough information to guide it to the desired location without interference from building blocks that are not near it in the target structure.…”

Section: Introductionmentioning

confidence: 99%

Design strategies for self-assembly of discrete targets

Madge

Miller

2015

The Journal of Chemical Physics

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Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. Both biological and artificial self-assembly processes can take place by a range of different schemes, from the successive addition of identical building blocks to hierarchical sequences of intermediates, all the way to the fully addressable limit in which each component is unique. In this paper, we introduce an idealized model of cubic particles with patterned faces that allows self-assembly strategies to be compared and tested. We consider a simple octameric target, starting with the minimal requirements for successful self-assembly and comparing the benefits and limitations of more sophisticated hierarchical and addressable schemes. Simulations are performed using a hybrid dynamical Monte Carlo protocol that allows self-assembling clusters to rearrange internally while still providing Stokes-Einstein-like diffusion of aggregates of different sizes. Our simulations explicitly capture the thermodynamic, dynamic, and steric challenges typically faced by self-assembly processes, including competition between multiple partially completed structures. Self-assembly pathways are extracted from the simulation trajectories by a fully extendable scheme for identifying structural fragments, which are then assembled into history diagrams for successfully completed target structures. For the simple target, a one-component assembly scheme is most efficient and robust overall, but hierarchical and addressable strategies can have an advantage under some conditions if high yield is a priority. C 2015 AIP Publishing LLC.[http://dx

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Nucleic Acid‐Modified Nanostructures as Programmable Atom Equivalents: Forging a New “Table of Elements”

Cited by 150 publications

References 153 publications

DNA-mediated engineering of multicomponent enzyme crystals

DNA-mediated engineering of multicomponent enzyme crystals

Clicking DNA to gold nanoparticles: poly-adenine-mediated formation of monovalent DNA-gold nanoparticle conjugates with nearly quantitative yield

Design strategies for self-assembly of discrete targets

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