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Programmable Matter: The Nanoparticle Atom and DNA Bond
Colloidal crystal engineering with DNA has led to significant advances in bottom-up materials synthesis and a new way of thinking about fundamental concepts in chemistry. Here, programmable atom equivalents (PAEs), comprised of nanoparticles (the “atoms”) functionalized with DNA (the “bonding elements”), are assembled through DNA hybridization into crystalline lattices. Unlike atomic systems, the “atom” (e.g., the nanoparticle shape, size, and composition) and the “bond” (e.g., the DNA length and sequence) can be tuned independently, yielding designer materials with unique catalytic, optical, and biological properties. Here in this review, nearly three decades of work that have contributed to the evolution of this class of programmable matter is chronicled, starting from the earliest examples based on gold-core PAEs, and then delineating how advances in synthetic capabilities, DNA design, and fundamental understanding of PAE-PAE interactions have led to new classes of functional materials that, in several cases, have no natural equivalent.
Head on Comparison of Self- and Nano-Assemblies of Gamma Peptide Nucleic Acid Amphiphiles
Peptide nucleic acids (PNAs) are nucleic acid analogs with hybridization properties and enzymatic stability superior to that of DNA. In addition to gene targeting applications, PNAs have garnered significant attention as bio-polymers due to the Watson–Crick-based molecular recognition and flexibility of synthesis. Here, in this work, PNA amphiphiles are engineered using chemically modified gamma PNA (8 mer in length) containing hydrophilic diethylene glycol units at the gamma position and covalently conjugated lauric acid (C12) as a hydrophobic moiety. Gamma PNA ($\gamma$PNA) amphiphiles self-assemble into spherical vesicles. Further, nano-assemblies (NA) are formulated using the amphiphilic $\gamma$PNA as a polymer via ethanol injection-based protocols. Comprehensive head-on comparison of the physicochemical and cellular uptake properties of PNA derived self- and NA is performed. Small-angle neutron and X-ray scattering analysis reveal ellipsoidal morphology of $\gamma$PNA NA that results in superior cellular delivery compate to the spherical self-assembly. Next, the functional activities of $\gamma$PNA self-and NA in lymphoma cells via multiple endpoints, including gene expression, cell viability, and apoptosis-based assays are compared. Overall, it is established that $\gamma$PNA amphiphile is a functionally active bio-polymer to formulate NA for a wide range of biomedical applications.
Organic Modulators Enable Morphological Diversity in Colloidal Crystals Engineered with DNA
Colloidal crystal engineering with DNA is a powerful way of generating a wide variety of crystals spanning over 90 different symmetries. However, in many cases, crystals with well-defined habits are difficult, if not impossible, to make, in part due to rapid crystal defect formation and propagation. This is especially true in the case of face-centered cubic (FCC) structures. Herein, we report a strategy that uses formamide as a chemical modulator to slow down colloidal crystal growth, which decreases defect formation and yields higher-quality crystals. Formamide forms hydrogen bonds with DNA bases and destabilizes the DNA duplex; in the context of colloidal crystallization, formamide leads to the disassembly of undercoordinated particles (defect architectures) and facilitates their reassembly into structures with the maximum number of nearest-neighbor contacts and DNA bonds. Here, when targeting an FCC lattice comprised of DNA-modified spherical 20 nm particles, formamide promotes the formation of its Wulff polyhedron (a truncated octahedron), never observed before in colloidal crystal engineering with DNA. Importantly, kinetic habits, including tetrahedra, octahedra, icosahedra, and decahedra, are also observed depending on formamide concentration.