Chad A Mirkin

Northwest University, Evanston, Illinois, United States

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Publications (633)5435.41 Total impact

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    ABSTRACT: Using on-wire lithography to synthesize well-defined nanorod dimers and trimers, we report a systematic study of the plasmon coupling properties of such materials. By comparing the dimer/trimer structures to discrete nanorods of the same overall length, we demonstrate many similarities between antibonding coupled modes in the dimers/trimers and higher-order resonances in the discrete nanorods. These conclusions are validated with a combination of discrete dipole approximation and finite-difference time-domain calculations and lead to the observation of antibonding modes in symmetric structures by measuring their solution-dispersed extinction spectra. Finally, we probe the effects of asymmetry and gap size on the occurrence of these modes and demonstrate that the delocalized nature of the antibonding modes lead to longer-range coupling compared to the stronger bonding modes.
    Nano letters. 11/2014;
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    ABSTRACT: Herein, we report the synthesis of DNA-functionalized infinite-coordination-polymer (ICP) nanoparticles as biocompatible gene-regulation agents. ICP nanoparticles were synthesized from ferric nitrate and a ditopic 3-hydroxy-4-pyridinone (HOPO) ligand bearing a pendant azide. Addition of Fe(III) to a solution of the ligand produced nanoparticles, which were colloidally unstable in the presence of salts. Conjugation of DNA to the Fe(III) -HOPO ICP particles by copper-free click chemistry afforded colloidally stable nucleic-acid nanoconstructs. The DNA-ICP particles, when cross-linked through sequence-specific hybridization, exhibited narrow, highly cooperative melting transitions consistent with dense DNA surface loading. The ability of the DNA-ICP particles to enter cells and alter protein expression was also evaluated. Our results indicate that these novel particles carry nucleic acids into mammalian cells without the need for transfection agents and are capable of efficient gene knockdown.
    Angewandte Chemie International Edition in English 11/2014; · 13.45 Impact Factor
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    ABSTRACT: Herein, we demonstrate that the activity of a hydrogen-bond-donating (HBD) catalyst embedded within a coordination framework can be allosterically regulated in situ by controlling oligomerization via simple changes in coordination chemistry at distal Pt(II) nodes. Using the halide-induced ligand rearrangement reaction (HILR), a heteroligated Pt(II) triple-decker complex, which contains a catalytically active diphenylene squaramide moiety and two hydrogen-bond-accepting (HBA) ester moieties, was synthesized. The HBD and HBA moieties were functionalized with hemilabile ligands of differing chelating strengths, allowing one to assemble them around Pt(II) nodes in a heteroligated fashion. Due to the hemilabile nature of the ligands, the resulting complex can be interconverted between a flexible, semiopen state and a rigid, fully closed state in situ and reversibly. FT-IR spectroscopy, (1)H DOSY, and (1)H NMR spectroscopy titration studies were used to demonstrate that, in the semiopen state, intermolecular hydrogen-bonding between the HBD and HBA moieties drives oligomerization of the complex and prevents substrate recognition by the catalyst. In the rigid, fully closed state, these interactions are prevented by steric and geometric constraints. Thus, the diphenylene squaramide moiety is able to catalyze a Friedel-Crafts reaction in the fully closed state, while the semiopen state shows no reactivity. This work demonstrates that controlling catalytic activity by regulating aggregation through supramolecular conformational changes, a common approach in Nature, can be applied to man-made catalytic frameworks that are relevant to materials synthesis, as well as the detection and amplification of small molecules.
    Journal of the American Chemical Society 11/2014; · 10.68 Impact Factor
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    ABSTRACT: Precise control of molecular assembly is a challenging goal facing supramolecular chemists. Herein, we report the highly specific assembly of a range of supramolecular nanotubes from the enantiomeric triangular naphthalenediimide-based macrocycles (RRRRRR)- and (SSSSSS)-NDI-Δ and a class of similar solvents—namely, the 1,2-dihalo-ethanes and -ethenes (DXEs). Three kinds of supramolecular nanotubes are formed from the columnar stacking of NDI-Δ units with a 60° mutual rotation angle as a result of cooperative [C–H•••O] interactions, directing interactions of the [X•••X]-bonded DXE chains inside the nanotubes, and lateral [X•••π] or [π•••π] interactions. They include (i) semiflexible infinite supramolecular nanotubes formed in the gel state from NDI-Δ and (E)-1,2-dichloroethene (DCE), (ii) rigid infinite non-helical supramolecular nanotubes produced in the solid state from NDI-Δ and BrCH2CH2Br, ClCH2CH2Br, and ClCH2CH2I, and (iii) a pair of rigid tetrameric, enantiomeric single-handed (P)- and (M)-helical supramolecular nanotubes formed in the solid state during crystallization from the corresponding (RRRRRR)- and (SSSSSS)-NDI-Δ with ClCH2CH2Cl. In case (i), only the electron-rich C=C double bond of (E)-DCE facilitates the gelation of NDI-Δ. In cases (ii) and (iii), the lengths of anti-DXEs determine the translation of the chirality of NDI-Δ into the helicity of nanotubes. Only ClCH2CH2Cl induces single-handed helicity into these nanotubes. The subtle interplay of noncovalent bonding interactions, resulting from the tiny variations involving the DXE guests, is responsible for the diverse and highly specific assembly of NDI-Δ. This research highlights the critical role that guests play in constructing assembled superstructures of hosts and offers a novel approach to creating supramolecular nanotubes.
    Journal of the American Chemical Society 10/2014; 136(47):16651–16660. · 10.68 Impact Factor
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    ABSTRACT: If a solution of DNA-coated nanoparticles is allowed to crystallize, the thermodynamic structure can be predicted by a set of structural design rules analogous to Pauling's rules for ionic crystallization. The details of the crystallization process, however, have proved more difficult to characterize as they depend on a complex interplay of many factors. Here, we report that this crystallization process is dictated by the individual DNA bonds and that the effect of changing structural or environmental conditions can be understood by considering the effect of these parameters on free oligonucleotides. Specifically, we observed the reorganization of nanoparticle superlattices using time-resolved synchrotron small-angle X-ray scattering in systems with different DNA sequences, salt concentrations, and densities of DNA linkers on the surface of the nanoparticles. The agreement between bulk crystallization and the behavior of free oligonucleotides may bear important consequences for constructing novel classes of crystals and incorporating new interparticle bonds in a rational manner.
    Proceedings of the National Academy of Sciences of the United States of America. 10/2014;
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    ABSTRACT: A novel, apertureless, cantilever-free pen array can be used for dual scanning photochemical and molecular printing. Serial writing with light is enabled by combining self-focusing pyramidal pens with an opaque backing between pens. The elastomeric pens also afford force-tuned illumination and simultaneous delivery of materials and optical energy. These attributes make the technique a promising candidate for maskless high-resolution photopatterning and combinatorial chemistry.
    Small 10/2014; · 7.82 Impact Factor
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    ABSTRACT: The evolution of crystallite size and microstrain in DNA-mediated nanoparticle superlattices is dictated by annealing temperature and the flexibility of interparticle bonds. This work addresses a major challenge in synthesizing optical metamaterials based upon noble metal nanoparticles by enabling the crystallization of large nanoparticles (100 nm diameter) at high volume fractions (34% metal).
    Advanced Materials 09/2014; · 14.83 Impact Factor
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    ABSTRACT: Herein, we describe a rapid, divergent method for using spherical nucleic acids (SNAs) as a universal platform for attaching RNA to DNA-modified nanoparticles using enzyme-mediated techniques. This approach provides a sequence-specific method for the covalent attachment of one or more in vitro transcribed RNAs to a universal SNA scaffold, regardless of RNA sequence. The RNA-nanoparticle constructs are shown to effectively knock down two different gene targets using a single, dual-ligated nanoparticle construct.
    ACS Nano 08/2014; · 12.03 Impact Factor
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    ABSTRACT: Many nanoparticle adsorption processes are dictated by the collective interactions of surface-bound ligands. These adsorption processes define how nanoparticles interact with biological systems and enable the assembly of nanoparticle-based materials and devices. Herein, we present an approach for quantifying nanoparticle adsorption thermodynamics in a manner that satisfies the assumptions of the Langmuir model. Using this approach, we study the DNA-mediated adsorption of polyvalent anisotropic nanoparticles on surfaces and explore how deviations from model assumptions influence adsorption thermodynamics. Importantly, when combined with a solution-based van’t Hoff analysis, we find that polyvalency plays a more important role as the individual interactions become weaker. Furthermore, we find that the free energy of anisotropic nanoparticle adsorption is consistent across multiple shapes and sizes of nanoparticles based on the surface area of the interacting facet.
    Angewandte Chemie International Edition 07/2014; · 11.34 Impact Factor
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    ABSTRACT: A biomimetic, ion-regulated molecular receptor was synthesized via the Weak-Link Approach (WLA). This structure features both a calix[4]arene moiety which serves as a molecular recognition unit and an activity regulator composed of hemilabile phosphine alkyl thioether ligands (P,S) chelated to a Pt(II) center. The host-guest properties of the ion-regulated receptor were found to be highly dependent upon the coordination of the Pt(II) center, which is controlled through the reversible coordination of small molecule effectors. The environment at the regulatory site dictates the charge and the structural conformation of the entire assembly resulting in three accessible binding configurations: one closed, inactive state and two open, active states. One of the active states, the semiopen state, recognizes a neutral guest molecule, while the other, the fully open state, recognizes a cationic guest molecule. Job plots and (1)H NMR spectroscopy titrations were used to study the formation of these inclusion complexes, the receptor binding modes, and the receptor binding affinities (Ka) in solution. Single crystal X-ray diffraction studies provided insight into the solid-state structures of the receptor when complexed with each guest molecule. The dipole moments and electrostatic potential maps of the structures were generated via DFT calculations at the B97D/LANL2DZ level of theory. Finally, we describe the reversible capture and release of guests by switching the receptor between the closed and semiopen configurations via elemental anion and small molecule effectors.
    Journal of the American Chemical Society 07/2014; · 10.68 Impact Factor
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    ABSTRACT: A novel class of metal-free spherical nucleic acid nanostructures was synthesized from readily available starting components. These particles consist of 30 nm liposomal cores, composed of an FDA-approved 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid monomer. The surface of the liposomes was functionalized with DNA strands modified with a tocopherol tail that intercalates into the phospholipid layer of the liposomal core via hydrophobic interactions. The spherical nucleic acid architecture not only stabilizes these constructs but also facilitates cellular internalization and gene regulation in SKOV-3 cells.
    Journal of the American Chemical Society 07/2014; · 10.68 Impact Factor
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    ABSTRACT: Here, we explore fluid transfer from a nanoscale tip to a surface and elucidate the role of fluid flows in dip-pen nanolithography (DPN) of liquid inks. We find that while fluid transfer in this context is affected by dwell time and tip retraction speed from the substrate, their specific roles are dictated by the contact angle of the ink on the surface. This is shown by two observations: (1) the power law scaling of transferred fluid with dwell time depends on contact angle, and (2) slower retraction speeds result in more transfer on hydrophilic surfaces, but less transfer on hydrophobic surfaces. These trends, coupled with the observation of a transition from quasi-static to dynamic capillary rupture at a capillary number of 6 × 10(-6), show that the transfer process is a competition between surface energy and viscosity. Based on this, we introduce retraction speed as an important parameter in DPN and show that it is possible to print polymer features as small as 14 nm. Further explorations of this kind may provide a useful platform for studying capillary phenomena at the nanoscale.
    Soft Matter 06/2014; · 4.15 Impact Factor
  • Stacey N Barnaby, Andrew Lee, Chad A Mirkin
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    ABSTRACT: Small interfering RNA (siRNA) is a powerful and highly effective method to regulate gene expression in vitro and in vivo. However, the susceptibility to serum nuclease-catalyzed degradation is a major challenge and it remains unclear whether the strategies developed to improve the stability of siRNA free in serum solution are ideal for siRNA conjugated to nanoparticle surfaces. Herein, we use spherical nucleic acid nanoparticle conjugates, consisting of gold nanoparticles (AuNPs) with siRNA chemisorbed to the surface, as a platform to study how a model siRNA targeting androgen receptor degrades in serum (SNA-siRNAAR). In solutions of 10% (vol/vol) FBS, we find rapid endonuclease hydrolysis at specific sites near the AuNP-facing terminus of siRNAAR, which were different from those of siRNAAR free in solution. These data indicate that the chemical environment of siRNA on a nanoparticle surface can alter the recognition of siRNA by serum nucleases and change the inherent stability of the nucleic acid. Finally, we demonstrate that incorporation of 2'-O-methyl RNA nucleotides at sites of nuclease hydrolysis on SNA-siRNAAR results in a 10-fold increase in siRNA lifetime. These data suggest that strategies for enhancing the serum stability of siRNA immobilized to nanoparticles must be developed from a dedicated analysis of the siRNA-nanoparticle conjugate, rather than a reliance on strategies developed for siRNA free in solution. We believe these findings are important for fundamentally understanding interactions between biological media and oligonucleotides conjugated to nanoparticles for the development of gene regulatory and therapeutic agents in a variety of disease models.
    Proceedings of the National Academy of Sciences of the United States of America. 06/2014;
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    ABSTRACT: Herein we utilize on-wire lithography (OWL) to synthesize a composite plasmonic–semiconductor material composed of Au nanorod dimers embedded within anatase TiO2 sheets. We demonstrate that, despite the harsh conditions necessary to synthesize crystalline TiO2, the gapped nanostructures remain intact. Additionally, we show that the optical properties of these structures can be tailored via the geometric control afforded by the OWL process to produce structures with various gap sizes exhibiting different electric field intensities near the surface of the metal particles and that those fields penetrate into the semiconductor material. Finally, we show that this composite amplifies the electric field of incident light on it by a factor of 103, which is more that 750 times greater than the isotropic materials typically used for these systems.
    Chemistry of Materials 06/2014; 26(12):3818–3824. · 8.24 Impact Factor
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    ABSTRACT: The ability of Rh(i) centers to undergo photoinduced electron transfer from discrete metal orbitals to Bodipy fluorophores is mediated through reversible coordination chemistry.
    Chemical communications (Cambridge, England). 05/2014;
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    ABSTRACT: Spherical nucleic acid (SNA) nanoparticle conjugates are a class of bionanomaterials that are extremely potent in many biomedical applications. Their unique ability to enter multiple mammalian cell types as single-entity agents arises from their novel three-dimensional architecture, which consists of a dense shell of highly oriented oligonucleotides chemically attached typically to a gold nanoparticle core. This architecture allows SNAs to engage certain cell surface receptors to facilitate entry. Here, we report studies aimed at determining the intracellular fate of SNAs and the trafficking events that occur inside C166 mouse endothelial cells after cellular entry. We show that SNAs traffic through the endocytic pathway into late endosomes and reside there for up to 24 h after incubation. Disassembly of oligonucleotides from the nanoparticle core is observed 16 h after cellular entry, most likely due to degradation by enzymes such as DNase II localized in late endosomes. Our observations point to these events being likely independent of core composition and treatment conditions, and they do not seem to be particularly dependent upon oligonucleotide sequence. Significantly and surprisingly, the SNAs do not enter the lysosomes under the conditions studied. To independently track the fate of the particle core and the fluorophore-labeled oligonucleotides that comprise its shell, we synthesized a novel class of quantum dot SNAs to determine that as the SNA structures are broken down over the 24 h time course of the experiment, the oligonucleotide fragments are recycled out of the cell while the nanoparticle core is not. This mechanistic insight points to the importance of designing and synthesizing next-generation SNAs that can bypass the degradation bottleneck imposed by their residency in late endosomes, and it also suggests that such structures might be extremely useful for endosomal signaling pathways by engaging receptors that are localized within the endosome.
    Journal of the American Chemical Society 05/2014; · 10.68 Impact Factor
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    ABSTRACT: Control over nanoparticle shape and size is commonly achieved via a seed-mediated approach, where nanoparticle precursors, or seeds, are hypothesized to act as templates for the heterogeneous nucleation of anisotropic products. Despite the wide variety of shapes that have been produced via this approach, high yield and uniformity have been more difficult to achieve. These shortcomings are attributed to limited structural control and characterization of the initial distribution of seeds. Herein, we report how iterative reductive growth and oxidative dissolution reactions can be used to systematically control seed structural uniformity. Using these reactions, we verify that seed structure dictates anisotropic nanoparticle uniformity and show that iterative seed refinement leads to unprecedented noble metal nanoparticle uniformities and purities for eight different shapes produced from a single seed source. Because of this uniformity, the first nanoparticle optical extinction coefficients for these eight shapes were analytically determined.
    Journal of the American Chemical Society 05/2014; · 10.68 Impact Factor
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    ABSTRACT: Nanoparticles of a metal-organic framework (MOF), UiO-66-N3 (Zr6O4OH4(C8H3O4-N3)6), were synthesized. The surface of the MOF was covalently functionalized with oligonucleotides, utilizing a strain promoted click reaction between DNA appended with dibenzylcyclooctyne and azide-functionalized UiO-66-N3 to create the first MOF nanoparticle-nucleic acid conjugates. The structure of the framework was preserved throughout the chemical transformation, and the surface coverage of DNA was quantified. Due to the small pore sizes, the particles are only modified on their surfaces. When dispersed in aqueous NaCl, they exhibit increased stability and enhanced cellular uptake when compared with unfunctionalized MOF particles of comparable size.
    Journal of the American Chemical Society 05/2014; · 10.68 Impact Factor
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    ABSTRACT: Microfluidic sensing platforms facilitate parallel, low sample volume detection using various optical signal transduction mechanisms. Herein, we introduce a simple mixing microfluidic device, enabling serial dilution of introduced analyte solution that terminates in five discrete sensing elements. We demonstrate the utility of this device with on-chip fluorescence and surface-enhanced Raman scattering (SERS) detection of analytes, and we demonstrate device use both when combined with a traditional inflexible SERS substrate and with SERS-active nanoparticles that are directly incorporated into microfluidic channels to create a flexible SERS platform. The results indicate, with varying sensitivities, that either flexible or inflexible devices can be easily used to create a calibration curve and perform a limit of detection study with a single experiment.
    The Analyst 04/2014; · 4.23 Impact Factor
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    ABSTRACT: We report the large-area assembly of anisotropic gold nanoparticles into lithographically defined templates with control over their angular position using a capillary force-based approach. We elucidate the role of the geometry of the templates in the assembly of anisotropic nanoparticles consisting of different shapes and sizes. These insights allow us to design templates that immobilize individual triangular nanoprisms and concave nanocubes in a shape-selective manner and filter undesired impurity particles from a mixture of triangular prisms and other polyhedra. Furthermore, by studying the assembly of two particles in the same template, we elucidate the importance of interparticle forces in this method. These advances allow for the construction of face-to-face and edge-to-edge nanocube dimers as well as triangular nanoprism bowtie antennas. As an example of the fundamental studies enabled by this assembly method, we investigate the surface-enhanced Raman scattering (SERS) of face-to-face concave cube dimers both experimentally and computationally and reveal a strong polarization dependence of the local field enhancement.
    Nano Letters 03/2014; · 13.03 Impact Factor

Publication Stats

28k Citations
5,435.41 Total Impact Points

Institutions

  • 2004–2014
    • Northwest University
      Evanston, Illinois, United States
  • 1995–2014
    • Northwestern University
      • • Department of Materials Science and Engineering
      • • Department of Chemistry
      Evanston, Illinois, United States
  • 2011
    • University of Washington Seattle
      • Department of Chemistry
      Seattle, WA, United States
    • University of Virginia
      Charlottesville, Virginia, United States
    • University of New Mexico
      • Department of Chemical and Nuclear Engineering
      Albuquerque, NM, United States
  • 2010
    • University of Toronto
      Toronto, Ontario, Canada
  • 2009
    • Nanyang Technological University
      • School of Chemical and Biomedical Engineering
      Singapore, Singapore
  • 1997–2009
    • University of Illinois, Urbana-Champaign
      • • Department of Bioengineering
      • • Department of Electrical and Computer Engineering
      • • Department of Physics
      Urbana, IL, United States
  • 2008
    • Massachusetts Institute of Technology
      Cambridge, Massachusetts, United States
  • 2007
    • Johns Hopkins University
      Baltimore, Maryland, United States
  • 2006
    • Yonsei University
      • Department of Chemistry
      Seoul, Seoul, South Korea
    • International Council on Nanotechnology
      Evanston, Illinois, United States
    • Sogang University
      Sŏul, Seoul, South Korea
  • 2005
    • Linköping University
      • Department of Physics, Chemistry and Biology (IFM)
      Linköping, OEstergoetland, Sweden
  • 2003
    • The Scripps Research Institute
      La Jolla, California, United States
  • 1970–2001
    • Rice University
      • • Department of Chemistry
      • • Department of Civil and Environmental Engineering
      Houston, TX, United States
    • Arizona State University
      • College of Liberal Arts and Sciences
      Tempe, AZ, United States
    • University of California, Los Angeles
      • California NanoSystems Institute
      Los Angeles, CA, United States
  • 1987–1999
    • University of Delaware
      • Department of Chemistry and Biochemistry
      Newark, DE, United States