Spherical nucleic acids. Volume 1

510 Pages·2020·36.764 MB·English

by  Mirkin, Chad A

Spherical Nucleic Acids

Spherical Nucleic Acids
Volume 1
edited by
Chad A. Mirkin
Published by
Jenny Stanford Publishing Pte. Ltd.
Level 34, Centennial Tower
3 Temasek Avenue
Singapore 039190
Email: [email protected]
Web: www.jennystanford.com
British Library Cataloguing-in-Publication Data
A catalogue record for this book is available from the British Library.
Spherical Nucleic Acids, Volume 1
AClol priygrhitgsh rte s©er v2e0d2. T0h bisy b Joeonkn, oyr S ptaarntfso thrder Peoufb, mlisahyi nnogt Pbete r.e Lptrdod.uced in any form
or by any means, electronic or mechanical, including photocopying, recording
or any information storage and retrieval system now known or to be invented,
without written permission from the publisher.
For photocopying of material in this volume, please pay a copying fee through
the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923,
USA. In this case permission to photocopy is not required from the publisher.
ISBN 978-981-4800-35-8 (Set) (Hardcover)
ISBN 978-0-429-20015-1 (Set) (eBook)
ISBN 978-981-4877-21-3 (Volume 1) (Hardcover)
ISBN 978-1-003-05667-6 (Volume 1) (eBook)
Contents
Part 1 Overview
1. A DNA-Based Method for Rationally Assembling
Nanoparticles into Macroscopic Materials 3
Chad A. Mirkin, Robert L. Letsinger, Robert C. Mucic,
and James J. Storhoff
2. Nanostructures in Biodiagnostics 13
Nathaniel L. Rosi and Chad A. Mirkin
2.1 Introduction 13
2.1.1 Background and Perspectives 14
2.1.2 Why Nanomaterials? 15
2.2 Nanoparticle-Based Detection Methods 17
2.2.1 Optical Detection 17
2.2.1.1 Nucleic acids 17
2.2.1.2 Proteins and biologically
relevant small molecules 28
2.2.1.3 Metal ions 31
2.2.2 Electrical and Electrochemical
Detection 32
2.2.2.1 Nucleic acids 32
2.2.3 Magnetic Relaxation Detection 34
2.2.3.1 Nucleic acids 34
2.2.3.2 Proteins and viruses 35
2.3 Nanowire- and Nanotube-Based Detection
Methods 36
2.3.1 Electrical Detection 36
2.3.1.1 Nucleic acids 36
2.3.1.2 Proteins, viruses, and
biologically relevant
small molecules 37
2.4 Nanofabrication 38
2.4.1 Nanopatterning 38
vi Contents
2.4.2 Nanoelectromechanical Devices 40
3. 2G.o5l d NaCnoonpcalrutsiciolenss f oanr dB iOoluotgloy o k 41
and Medicine 55
David A. Giljohann, Dwight S. Seferos, Weston L. Daniel,
Matthew D. Massich, Pinal C. Patel, and Chad A. Mirkin

3.1 Introduction 56
3.2 Citrate and Transferrin 58
3.3 Amines 59
3.3.1 Gene Transfection 60
3.3.2 Drug Delivery 61
3.3.3 Stability 63
3.4 Oligonucleotides 63
3.4.1 Synthesis 64
3.4.2 Properties 65
3.4.3 Cellular Uptake 66
3.4.4 Applications in Cells 68
3.4.4.1 Antisense gene control 69
3.4.4.2 Intracellular detection and
imaging 71
3.4.4.3 RNA interference 72
3.4.4.4 Cellular detection 73
3.5 Peptides 73
3.5.1 Peptide Nanoconjugates 74
3.5.2 Peptide/DNA-Gold Nanoparticle
Conjugates 75
3.5.3 Multifunctional and Multicomponent
DNA Nanoconjugates 75
3.6 Antibodies 76
3.6.1 Imaging 76
3.6.2 Photothermal Therapy 77
3.7 Lipids 77
3.7.1 Therapeutics 77
3.7.2 Imaging 78
3.8 Summary and Outlook 79
3.8.1 Mechanism of Uptake in Cells 79
3.8.2 Targeting 79
3.8.3 Toxicity 80
3.8.4 Conclusion 82
Contents vii
4. Spherical Nucleic Acids 91
Joshua I. Cutler, Evelyn Auyeung, and Chad A. Mirkin
4.1 Introduction 92
4.2 The Emergence of DNA as a Surface Ligand
for Nanoparticles 94
4.3 Structural Considerations for SNA and
SNA−NP Conjugates 95
4.4 Controlling the Density of SNA Conjugates 100
4.5 Cooperative Binding with High-Density SNA
Conjugates 103
4.6 Nanoparticle Assembly and Crystallization
Programmed with Spherical and Other 3D
Nucleic Acid Nanostructures 107
4.7 Moving beyond Spherical Conjugates to Other
Forms of 3D Nucleic Acids 112
4.8 Diagnostics 114
4.9 Spherical Nucleic Acids as Single-Entity Gene
Regulation Constructs 118
4.10 Combined Intracellular Diagnostics and
Imaging 124
5. 4N.u1c1le ic CAocindc-lMusoidoinfise adn Nda Onuotsltoroukct ures as 126
Programmable Atom Equivalents: Forging a New
“Table of Elements” 137
Robert J. Macfarlane, Matthew N. O’Brien,
Sarah Hurst Petrosko, and Chad A. Mirkin
5.1 Introduction 137
5.2 Discussion 143
6. 5Pr.3o gramOmuatlboloek M aterials and the Nature of the 154
DNA Bond 167
Matthew R. Jones, Nadrian C. Seeman, and
Chad A. Mirkin

6.1 Introduction 168
6.2 Background 173
6.3 Advances 173
6.4 Outlook 174
viii Contents
6.5 Hybridization-Based DNA Bonds: Tiles 174
6.6 Hybridization-Based DNA Bonds: Origami 179
6.7 Nanoparticle-Templated DNA Bonds 183
7. 6Th.8e NatCuoren calnuds iIomnpsl ications of Uniformity in the 190
Hierarchical Organization of Nanomaterials 199
Matthew N. O’Brien, Matthew R. Jones, and
Chad A. Mirkin

7.1 Hierarchical Organization 200
7.2 From Atoms to Crystalline Nanoparticles 202
7.2.1 What Does It Mean to Be Uniform at
This Length Scale? 202
7.2.2 Successful Approaches to Control
Uniformity at This Scale 205
7.3 Ligands Arranged on Nanoparticle Surfaces 207
7.3.1 What Does It Mean to Be Uniform at
This Length Scale? 208
7.3.2 Successful Approaches to Control
Uniformity at This Scale 211
7.4 From Nanoparticles to Colloidal Crystals 213
7.4.1 What Does It Mean to Be Uniform at
This Length Scale? 214
7.4.2 Successful Approaches to Control
Uniformity at This Scale 217
8. 7Cr.5y stal EBnegyionneedr Cinogl lwoiidtha lD CNryAs tals 222217
Christine R. Laramy, Matthew N. O’Brien, and
Chad A. Mirkin

8.1 Introduction 228
8.2 DNA Design Elements 230
8.2.1 The Anatomy of a Building Block 230
8.2.2 Primarily Double-Stranded with
Linkers (DNA Design 1) 233
8.2.3 Single-Stranded with No Linkers
(DNA Design 2) 237
8.2.4 Single-Stranded with Linkers
(DNA Design 3) 239