Establishing the Design Rules for DNA‐Mediated Programmable Colloidal Crystallization

Abstract

The assembly of DNA-programmable colloidal crystals is presented, where the sizes of nanoparticles used vary from 5 to 80 nm and the lattice parameters of the resulting crystals vary from 25 to 225 nm. A predictable and mathematically definable relationship between particle size and DNA length is demonstrated to dictate the assembly and crystallization processes, creating a set of design rules for DNA-based nanoscale assembly. ** We acknowledge George Schatz for helpful discussions regarding the theoretical calculations of DNA flexibility and relative DNA concentrations in aggregates. C. A. M. acknowledges the NSF-NSEC and the AFOSR for grant support. He also is grateful for a NIH Director's Pioneer Award and an NSSEF Fellowship from the DoD. R. J. M. acknowledges Northwestern University for a Ryan Fellowship. M. R. J.

Importance of the DNA “bond” in programmable nanoparticle crystallization

“…This suggests that the kinetics of DNA bond formation may be of great importance to crystallization. A surprising result from prior studies is that the thermodynamic product of this reorganization can be described using the hybridization behavior and thermodynamic properties of free oligonucleotides, if one takes into account the increased oligonucleotide and salt concentration (relative to the bulk) found at the surface of a PAE (16,17). In this work, we hypothesize that the kinetics of particle reorganization in superlattices can be explained by examining the kinetics of free oligonucleotides.…”

“…Although other designs have also been used to generate colloidal crystals, the DNA design strategy used in this work enables exquisite control over crystal symmetry and lattice parameters (6,7,14,16), both of which have been difficult to realize experimentally to the same degree with systems where interparticle connections comprise long DNA linkages with large regions of single-stranded DNA (21,22). This design is also crucial for the systematic study reported herein, where DNA bond kinetics between different crystal samples can be more readily compared without concerns about variations in DNA length or solution temperature, both of which can significantly impact the mobility, structure, and orientation of DNA strands containing long singlestranded regions.…”

“…However, the fact that there is a crystalline thermodynamic product does not mean that any choice of DNA and nanoparticles will result in crystalline systems in practice (3,4). For example, crystallization has been observed for a relatively narrow class of PAEs (16) and in a manner that is primarily dependent upon the length of the DNA linker and temperature at which assembly occurs (8). Thus, absent from our understanding of these systems is a connection between the crystallization process and the properties of the DNA bonds that form the foundation of these structures.…”

DNA-mediated engineering of multicomponent enzyme crystals

“…With such methods, one can make architectures with well-defined lattice parameters (6)(7)(8)(9)(10)(11)(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).…”

“…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.…”