Spherical nucleic acids. Volume 1 9781003056676, 9789814800358, 9780429200151, 9789814877213, 1031071121, 9781000092356, 1000092356, 9781000092394, 1000092399, 9781000092431, 1000092437, 1003056679

Spherical Nucleic Acids (SNAs) are typically comprised of a nanoparticle core and a densely packed and highly oriented n

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English Pages xiv, 494 [510] Year 2020

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Spherical nucleic acids. Volume 1
 9781003056676, 9789814800358, 9780429200151, 9789814877213, 1031071121, 9781000092356, 1000092356, 9781000092394, 1000092399, 9781000092431, 1000092437, 1003056679

Table of contents :
Cover......Page 1
Half Title......Page 3
Title Page......Page 5
Copyright Page......Page 6
Table of Contents......Page 7
Part 1: Overview......Page 17
1: A DNA-Based Method for Rationally Assembling Nanoparticles into Macroscopic Materials......Page 19
2.1 Introduction......Page 29
2.1.1 Background and Perspectives......Page 30
2.1.2 Why Nanomaterials?......Page 31
2.2.1.1 Nucleic acids......Page 33
2.2.1.2 Proteins and biologically relevant small molecules......Page 44
2.2.1.3 Metal ions......Page 47
2.2.2.1 Nucleic acids......Page 48
2.2.3.1 Nucleic acids......Page 50
2.2.3.2 Proteins and viruses......Page 51
2.3.1.1 Nucleic acids......Page 52
2.3.1.2 Proteins, viruses, and biologically relevant small molecules......Page 53
2.4.1 Nanopatterning......Page 54
2.4.2 Nanoelectromechanical Devices......Page 56
2.5 Conclusions and Outlook......Page 57
3: Gold Nanoparticles for Biology and Medicine......Page 71
3.1 Introduction......Page 72
3.2 Citrate and Transferrin......Page 74
3.3 Amines......Page 75
3.3.1 Gene Transfection......Page 76
3.3.2 Drug Delivery......Page 77
3.4 Oligonucleotides......Page 79
3.4.1 Synthesis......Page 80
3.4.2 Properties......Page 81
3.4.3 Cellular Uptake......Page 82
3.4.4 Applications in Cells......Page 84
3.4.4.1 Antisense gene control......Page 85
3.4.4.2 Intracellular detection and imaging......Page 87
3.4.4.3 RNA interference......Page 88
3.5 Peptides......Page 89
3.5.1 Peptide Nanoconjugates......Page 90
3.5.3 Multifunctional and Multicomponent DNA Nanoconjugates......Page 91
3.6.1 Imaging......Page 92
3.7.1 Therapeutics......Page 93
3.7.2 Imaging......Page 94
3.8.2 Targeting......Page 95
3.8.3 Toxicity......Page 96
3.8.4 Conclusion......Page 98
4: Spherical Nucleic Acids......Page 107
4.1 Introduction......Page 108
4.2 The Emergence of DNA as a Surface Ligand for Nanoparticles......Page 110
4.3 Structural Considerations for SNA and SNA-NP Conjugates......Page 111
4.4 Controlling the Density of SNA Conjugates......Page 116
4.5 Cooperative Binding with High-Density SNA Conjugates......Page 119
4.6 Nanoparticle Assembly and Crystallization Programmed with Spherical and Other 3D Nucleic Acid Nanostructures......Page 123
4.7 Moving beyond Spherical Conjugates to Other Forms of 3D Nucleic Acids......Page 128
4.8 Diagnostics......Page 130
4.9 Spherical Nucleic Acids as Single-Entity Gene Regulation Constructs......Page 134
4.10 Combined Intracellular Diagnostics and Imaging......Page 140
4.11 Conclusions and Outlook......Page 142
5.1 Introduction......Page 153
5.2 Discussion......Page 159
5.3 Outlook......Page 170
6: Programmable Materials and the Nature of the DNA Bond......Page 183
6.1 Introduction......Page 184
6.3 Advances......Page 189
6.5 Hybridization-Based DNA Bonds: Tiles......Page 190
6.6 Hybridization-Based DNA Bonds: Origami......Page 195
6.7 Nanoparticle-Templated DNA Bonds......Page 199
6.8 Conclusions......Page 206
7: The Nature and Implications of Uniformity in the Hierarchical Organization of Nanomaterials......Page 215
7.1 Hierarchical Organization......Page 216
7.2.1 What Does It Mean to Be Uniform at This Length Scale?......Page 218
7.2.2 Successful Approaches to Control Uniformity at This Scale......Page 221
7.3 Ligands Arranged on Nanoparticle Surfaces......Page 223
7.3.1 What Does It Mean to Be Uniform at This Length Scale?......Page 224
7.3.2 Successful Approaches to Control Uniformity at This Scale......Page 227
7.4 From Nanoparticles to Colloidal Crystals......Page 229
7.4.1 What Does It Mean to Be Uniform at This Length Scale?......Page 230
7.4.2 Successful Approaches to Control Uniformity at This Scale......Page 233
7.5 Beyond Colloidal Crystals......Page 237
8: Crystal Engineering with DNA......Page 243
8.1 Introduction......Page 244
8.2.1 The Anatomy of a Building Block......Page 246
8.2.2 Primarily Double-Stranded with Linkers (DNA Design 1)......Page 249
8.2.3 Single-Stranded with No Linkers (DNA Design 2)......Page 253
8.2.4 Single-Stranded with Linkers (DNA Design 3)......Page 255
8.2.5 DNA Surface Density......Page 256
8.2.6 Temperature Control......Page 258
8.3 Crystal Symmetry and Habit Engineering......Page 259
8.3.1 Isotropic Building Blocks......Page 261
8.3.2 Building Blocks with Anisotropic Particle Cores......Page 268
8.3.3 Chemically Anisotropic Building Blocks......Page 275
8.3.4 Template-Directed Crystallization......Page 278
8.4.1 Functional Behavior Driven by DNA......Page 283
8.4.2 Functional Behavior Driven by Particle Core......Page 286
8.5 Outlook......Page 291
9: What Controls the Optical Properties of DNA-Linked Gold Nanoparticle Assemblies?......Page 309
9.1 Introduction......Page 310
9.2.2 Instrumentation......Page 312
9.2.4 Preparation and Characterization of Linker DNA......Page 313
9.2.5 Preparation and Characterization of DNA-Linked Au Nanoparticle Aggregates......Page 315
9.2.8 Small-Angle X-ray Scattering......Page 316
9.4.1 DNA-Linked Au Nanoparticle Assemblies from 24-, 48-, and 72-Base-Pair Linkers......Page 317
9.4.2 Melting Analyses......Page 321
9.4.3 Annealing Studies of the 24-, 48-, and 72-Base Linked Aggregates......Page 323
9.4.4 Theoretical Studies of the Dependence of the UV-Visible Spectra upon Aggregate Size and Volume Fraction......Page 326
9.4.5 Small-Angle X-ray Scattering......Page 328
9.4.6 Dynamic Light Scattering of DNA-Linked Aggregates......Page 329
9.4.7 Sedimentation Rates of the DNA-Linked Aggregates before and after Annealing......Page 331
9.4.8 TEM of the DNA-Linked Aggregates before and after Annealing......Page 332
9.4.9 Ostwald Ripening of DNA-Linked Aggregates......Page 335
9.5 Conclusions......Page 337
10: What Controls the Melting Properties of DNA-Linked Gold Nanoparticle Assemblies?......Page 341
10.1 Introduction......Page 342
10.2.1 Assay Formats......Page 344
10.2.2 Effect of Probe Oligonucleotide Density on the Au Nanoparticle Surface......Page 346
10.2.3 Effect of Au Nanoparticle Size......Page 348
10.2.4 Effect of Salt Concentration......Page 349
10.2.5 Effect of Interparticle Distance......Page 352
10.2.6 Mechanistic Studies of DNA Melting in the Presence of Nanoparticles......Page 355
10.3.1 The Model......Page 357
10.4.1 Fitting the Experimental Data......Page 361
10.4.2 Effect of Nanoparticle Size......Page 363
10.4.3 Salt-Induced Melting......Page 364
10.4.4 Effect of Probe DNA Density......Page 365
10.5 Conclusions......Page 366
10.6.1 Synthesis of DNA......Page 368
10.6.2 Functionalization of Au Nanoparticles 353......Page 369
10.6.3 Functionalization of Glass Substrates......Page 370
10.6.4 Hybridization of Nanoparticles with Targets in the Solution System......Page 371
10.6.6 Melting Analyses......Page 372
10.6.8 Circular Dichroism......Page 373
11.1 Introduction......Page 379
11.2 Results and Discussion......Page 380
11.3 Conclusion......Page 385
12: What Controls the Hybridization Thermodynamics of Spherical Nucleic Acids?......Page 387
12.1 Introduction......Page 388
12.2 Methods......Page 391
12.3 Results and Discussion......Page 392
12.4 Conclusion......Page 396
13: The Role of Structural Enthalpy in Spherical Nucleic Acid Hybridization......Page 401
13.1 Introduction......Page 402
13.2 Results and Discussion......Page 403
13.3 Conclusion......Page 410
14: Nanoparticle Shape Anisotropy Dictates the Collective Behavior of Surface-Bound Ligands......Page 415
14.1 Introduction......Page 416
14.2 Results and Discussion......Page 418
14.3 Conclusions......Page 425
15: Oligonucleotide Loading Determines Cellular Uptake of DNA-Modified Gold Nanoparticles......Page 429
15.1 Introduction......Page 430
15.2 Results and Discussion......Page 431
16: Polyvalent DNA-Nanoparticle Conjugates Stabilize Nucleic Acids......Page 441
16.2 Results and Discussion......Page 442
17: Cellular Response of Polyvalent Oligonucleotide- Gold Nanoparticle Conjugates......Page 453
17.1 Introduction......Page 454
17.2 Results and Discussion......Page 455
17.3 Conclusions......Page 461
17.4.2 Nanoparticle Synthesis and Functionalization......Page 462
17.4.5 Cellular Assays......Page 463
17.4.6 Nanoparticle Uptake......Page 464
18: Strategy for Increasing Drug Solubility and Efficacy through Covalent Attachment to Polyvalent DNA-Nanoparticle Conjugates......Page 467
18.1 Introduction......Page 468
18.2 Results and Discussion......Page 471
18.3 Conclusion......Page 480
18.4.1 Synthesis of Paclitaxel- Oligonucleotide Conjugate 2......Page 481
18.4.3 Quantification of Alkanethiol Oligonucleotides Loaded on Gold Nanoparticles......Page 482
18.4.4 Dynamic Light Scattering (DLS) and Transmission Electron Microscopy (TEM)......Page 483
18.4.7 TUNEL Assay......Page 484
18.4.8 MTT Assay......Page 485
19: Mechanism for the Endocytosis of Spherical Nucleic Acid Nanoparticle Conjugates......Page 491
19.1 Introduction......Page 492
19.2.1 Cellular Uptake Kinetics and Intracellular Transport......Page 494
19.2.2 Caveolae/Lipid-Raft as the Major Pathway of Endocytosis......Page 496
19.2.3 Endocytosis via Class A Scavenger Receptors......Page 499
19.2.4 Collective Involvement of SR-A and Lipid-Raft Proteins......Page 501
19.2.5 Effect of CAV-1 and SR-A on Endocytosis of SNAs in Multiple Cell Types......Page 503
19.3 Conclusions......Page 504
19.4.3 Generation of Stably Transfected Deficient Cells......Page 505
19.4.6 TEM......Page 506
19.4.8 Chemical Blocking Studies......Page 507
19.4.10 Protein Precipitation Assay......Page 508

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