Spherical nucleic acids: the foundation for crystal engineering with DNA and digital probe and drug design

Cover......Page 1
Half Title......Page 3
Title Page......Page 5
Copyright Page......Page 6
Table of Contents......Page 7
Part 6: Colloidal Crystallization Processes and Routes to Hierarchical Assembly......Page 17
 48: Assembly and Organization Processes in DNA-Directed Colloidal Crystallization......Page 19
  48.1 Introduction......Page 20
   48.2.1 Formation of Aggregates via Slow Cooling through the Melting Temperature......Page 21
   48.2.2 In situ Measurements of Formation......Page 27
  48.3 Conclusions......Page 34
  48.4 Materials and Methods......Page 35
 49: Critical Undercooling in DNA-Mediated Nanoparticle Crystallization......Page 39
  49.1 Introduction......Page 40
  49.2 Results and Discussion......Page 42
  49.3 Conclusion......Page 47
   49.4.2 DNA Synthesis and Characterization......Page 48
   49.4.5 Temperature-Dependent UV-Visible Spectroscopy Measurements (Freezing and Melting Experiments)......Page 49
 50: DNA-Mediated Nanoparticle Crystallization into Wulff Polyhedra......Page 55
  50.1 Introduction......Page 56
  50.2 Methods Summary......Page 64
 51: Growth Dynamics for DNA-Guided Nanoparticle Crystallization......Page 69
  51.1 Introduction......Page 70
   51.2.1 Interaction Potential......Page 72
   51.2.2 Isolated SNA Crystal Growth......Page 75
   51.2.3 Coalescence Dynamics......Page 80
  51.3 Conclusion and Outlook......Page 87
   51.4.1 Model Interaction......Page 88
   51.4.2 Grain Boundary Classification......Page 91
 52: Nonequilibrium Anisotropic Colloidal Single-Crystal Growth with DNA......Page 97
  52.1 Introduction......Page 98
   52.2.1 DNA-Programmable Assembly of Anisotropic Colloidal Crystals......Page 102
  52.3 Discussion......Page 104
 53: Density-Gradient Control over Nanoparticle Supercrystal Formation......Page 113
  53.1 Introduction......Page 114
  53.2 Materials......Page 126
  53.5 Silica Encapsulation of Microcrystals......Page 127
  53.6 Characterization Methods......Page 128
Part 7: Dynamic Nanoparticle Superlattices......Page 133
 54: Reconstitutable Nanoparticle Superlattices......Page 135
  54.1 Introduction......Page 136
 55: Contraction and Expansion of Stimuli-Responsive DNA Bonds in Flexible Colloidal Crystals......Page 149
  55.1 Introduction......Page 150
 56: Topotactic Interconversion of Nanoparticle Superlattices......Page 161
  56.1 Introduction......Page 162
 57: Dynamically Interchangeable Nanoparticle Superlattices through the Use of Nucleic Acid-Based Allosteric Effectors......Page 173
  57.1 Introduction......Page 174
 58: Transmutable Nanoparticles with Reconfigurable Surface Ligands......Page 185
  58.1 Introduction......Page 186
 59: pH-Responsive Nanoparticle Superlattices with Tunable DNA Bonds......Page 197
  59.1 Introduction......Page 198
Part 8: Surface-Based and Template-Confined Colloidal Crystallization......Page 207
 60: Stepwise Evolution of DNA-Programmable Nanoparticle Superlattices......Page 209
  60.1 Introduction......Page 210
  60.2 Methods and Results......Page 211
  60.3 Conclusion......Page 218
  60.4 Experimental Section......Page 219
 61: Epitaxial Growth of DNA-Assembled Nanoparticle Superlattices on Patterned Substrates......Page 223
  61.1 Introduction......Page 224
  61.2 Methods and Results......Page 227
  61.3 Conclusion......Page 235
 62: Epitaxy: Programmable Atom Equivalents versus Atoms......Page 239
  62.1 Introduction......Page 240
  62.2 Results and Discussion......Page 242
   62.4.1 DNA Functionalization of Gold Nanoparticles......Page 247
    62.4.2.1 Patterned template synthesis......Page 248
    62.4.2.4 Substrate DNA functionalization......Page 249
    62.4.3.2 DNA-NP superlattice thin-film assembly......Page 250
   62.4.4 Silica Embedding......Page 251
    62.4.5.2 Grazing-incidence SAXS......Page 252
    62.4.6.1 RMS roughness and mean thickness calculation......Page 253
 63: Lattice Mismatch in Crystalline Nanoparticle Thin Films......Page 257
  63.1 Introduction......Page 258
  63.2 Methods......Page 260
  63.3 Results and Discussion......Page 263
 64: Building Superlattices from Individual Nanoparticles via Template-Confined DNA-Mediated Assembly......Page 275
  64.1 Introduction......Page 276
  64.2 Methods......Page 277
  64.3 Results and Discussion......Page 282
 65: Design Rules for Template-Confined DNA-Mediated Nanoparticle Assembly......Page 289
  65.1 Introduction......Page 290
  65.2 Results and Discussion......Page 292
  65.4 Experimental Section......Page 300
 66: DNA-Mediated Size-Selective Nanoparticle Assembly for Multiplexed Surface Encoding......Page 307
  66.1 Introduction......Page 308
  66.2 Methods......Page 310
  66.3 Discussion......Page 316
  67.1 Introduction......Page 321
   67.2.3 Coupled Dipole Simulations......Page 330
Part 9: Optics and Plasmonics with Nanoparticle Superlattices......Page 335
 68. Plasmonic Photonic Crystals Realized through DNA-Programmable Assembly......Page 337
 68.1 Introduction......Page 338
  68.2.1 FDTD Calculations......Page 346
  68.2.3 Optical Experiments......Page 347
 69: Nanoscale Form Dictates Mesoscale Function in Plasmonic DNA-Nanoparticle Superlattices......Page 351
  69.1 Introduction......Page 352
  69.2 Optical Properties of Plasmonic Nanoparticle Assemblies......Page 354
  69.3 DNA-Programmable Assembly of Mesoscale Superlattices......Page 356
  69.4 Optical Characterization of Plasmonic Superlattices......Page 358
  69.5 Crystal Habit as a Design Parameter for Optical Response......Page 360
  69.6 Conclusions......Page 363
 70: Directional Emission from Dye-Functionalized Plasmonic DNA Superlattice Microcavities......Page 367
  70.1 Introduction......Page 369
   70.2.4 TCSPC Lifetime Detection Limit......Page 379
 71: Defect Tolerance and the Effect of Structural Inhomogeneity in Plasmonic DNA-Nanoparticle Superlattices......Page 383
  71.1 Introduction......Page 384
  71.2 Results......Page 386
  71.3 Discussion......Page 396
   71.4.2 Optical Measurements......Page 397
 72: Using DNA to Design Plasmonic Metamaterials with Tunable Optical Properties......Page 401
 73: Plasmonic Metallurgy Enabled by DNA......Page 419
 74: Design Principles for Photonic Crystals Based on Plasmonic Nanoparticle Superlattices......Page 431
  74.1 Introduction......Page 432
  74.2 Building PCs with Plasmonic NP Superlattices......Page 434
  74.3 PPCs Realized through DNA-Programmable Assembly......Page 441
  74.4 Building PCs with Materials Other Than Au......Page 443
  74.5 Conclusions......Page 444
   74.6.3 Superlattice Assembly......Page 445
   74.6.4 Optical Experiments......Page 446
 75: Deterministic Symmetry Breaking of Plasmonic Nanostructures Enabled by DNA-Programmable Assembly......Page 451
 76: Polarization-Dependent Optical Response in Anisotropic Nanoparticle-DNA Superlattices......Page 465
Part 10: Postsynthetic Modification and Catalysis with Nanoparticle Superlattices......Page 479
  77.1 Introduction......Page 481
   77.2.2 Silica Embedding......Page 491
   77.2.4 Transmission Electron Microscopy......Page 492
 78: Controlling Structure and Porosity in Catalytic Nanoparticle Superlattices with DNA......Page 495
  78.1 Introduction......Page 496
   78.2.2 Calcination......Page 498
   78.2.3 Catalytic Oxidation of 4-Hydroxybenzyl Alcohol......Page 500
   78.2.4 Evaluation of Structure Following Catalytic Experiments......Page 501
  78.3 Conclusions......Page 502
   78.4.1 Materials and General Procedures......Page 503
   78.4.2 Nanoparticle Assembly and Crystallization......Page 504
   78.4.4 Preparation of Supported, Nonassembled Gold Nanoparticles......Page 505
   78.4.9 Small-Angle X-ray Scattering (SAXS)......Page 506
   78.4.11 Catalysis Experiments......Page 507