Therapeutic RNA Nanotechnology

Immunomodulation and Dynamicity

edited by Kirill Afonin and Morgan Chandler

“This book comprehensively describes the pathway to progress in the field of nucleic acid nanotechnology, beginning with in silico design strategies and ending with a number of therapeutic and nanotechnological applications. The methods, big picture, and current progress presented in this book are an enormous asset to anyone endeavoring into this field.”
Prof. Yaroslava Yingling, North Carolina State University, USA

Hardcover eBook

Format: Hardcover
ISBN: 9789814877183
Subject: Drug Discovery and Development
Published: July 2021
Pages: 1228

USD $399.95

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Description
Contents
Authors
Praise

Chapter 1

Generating New Specific RNA Interaction Interfaces Using C-Loops

Kirill A. Afonin and Neocles B. Leontis

Pages: 1-20

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Chapter 2

Specific RNA Self-Assembly with Minimal Paranemic Motifs

Kirill A. Afonin, Dennis J. Cieply, and Neocles B. Leontis

Pages: 21-44

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Chapter 3

In vitro assembly of cubic RNA-Based scaffolds designed in silico

Kirill A. Afonin, Eckart Bindewald, Alan J. Yaghoubian,Neil Voss, Erica Jacovetty, Bruce A. Shapiro, and Luc Jaeger

Pages: 45-66

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Chapter 4

Self-Assembling RNA Nanorings Based on RNAI/II Inverse Kissing Complexes

Wade W. Grabow, Paul Zakrevsky, Kirill A. Afonin, Arkadiusz Chworos, Bruce A. Shapiro, and Luc Jaeger

Pages: 67-94

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Chapter 5

Multistrand RNA Secondary Structure Prediction and Nanostructure Design Including Pseudoknots

Eckart Bindewald, Kirill Afonin, Luc Jaeger, and Bruce A. Shapiro

Pages: 95-120

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Chapter 6

Computational and experimental characterization of RNA cubic nanoscaffolds

Kirill A. Afonin, Wojciech Kasprzak, Eckart Bindewald, Praneet S. Puppala, Alex R. Diehl, Kenneth T. Hall, Tae Jin Kim, Michael T. Zimmermann, Robert L. Jernigan, Luc Jaeger, and Bruce A. Shapiro

Pages: 121-150

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Chapter 7

In silico Design and Enzymatic Synthesis of Functional RNA Nanoparticles

Kirill A. Afonin, Wojciech K. Kasprzak, Eckart Bindewald, Maria Kireeva, Matthias Viard, Mikhail Kashlev, and Bruce A. Shapiro

Pages: 151-176

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Chapter 8

Ring Catalog: A Resource for Designing Self- Assembling RNA Nanostructures

Lorena Parlea, Eckart Bindewald, Rishabh Sharan, Nathan Bartlett, Daniel Moriarty, Jerome Oliver, Kirill A. Afonin, and Bruce A. Shapiro

Pages: 177-200

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Chapter 9

Programmable RNA microstructures for coordinated delivery of siRNAs

Jaimie Marie Stewart, Mathias Viard, Hari K. K. Subramanian, Brandon K. Roark, Kirill A. Afonin, and Elisa Franco

Pages: 201-222

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Chapter 10

Versatile RNA tetra-U helix linking motif as a toolkit for nucleic acid nanotechnology

My N. Bui, M. Brittany Johnson, Mathias Viard, Emily Satterwhite, Angelica N. Martins, Zhihai Li, Ian Marriott, Kirill A. Afonin, and Emil F. Khisamutdinov

Pages: 223-248

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Chapter 11

Design and self-Assembly of siRNA-Functionalized RNA nanoparticles for use in automated nanomedicine

Kirill A. Afonin, Wade W. Grabow, Faye M. Walker, Eckart Bindewald, Marina A. Dobrovolskaia, Bruce A. Shapiro, and Luc Jaeger

Pages: 249-284

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Chapter 12

Co-transcriptional Assembly of Chemically Modified RNA Nanoparticles Functionalized with siRNAs

Kirill A. Afonin, Maria Kireeva, Wade W. Grabow, Mikhail Kashlev, Luc Jaeger, and Bruce A. Shapiro

Pages: 285-294

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Chapter 13

Multifunctional RNA Nanoparticles

Kirill A. Afonin, Matthias Viard, Alexey Y. Koyfman, Angelica N. Martins, Wojciech K. Kasprzak, Martin Panigai, Ravi Desai, Arti Santhanam, Wade W. Grabow, Luc Jaeger, Eliahu Heldman, Jakob Reiser, Wah Chiu, Eric O. Freed, and Bruce A. Shapiro

Pages: 295-324

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Chapter 14

Oxime Ether Lipids Containing Hydroxylated Head Groups are More Superior siRNA Delivery Agents Than Their Nonhydroxylated Counterparts

Kshitij Gupta, Stephanie J. Mattingly, Ralph J. Knipp, Kirill A. Afonin, Mathias Viard, Joseph T. Bergman, Marissa Stepler, Michael H. Nantz, Anu Puri, and Bruce A. Shapiro

Pages: 325-354

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Chapter 15

Bolaamphiphiles as carriers for siRNA delivery: From chemical syntheses to practical applications

Kshitij Gupta, Kirill A. Afonin, Mathias Viard, Virginia Herrero, Wojciech Kasprzak, Ioannis Kagiampakis, Taejin Kim, Alexey Y. Koyfman, Anu Puri, Marissa Stepler, Alison Sappe, Vineet N. KewalRamani, Sarina Grinberg, Charles Linder, Eliahu Heldman, Robert Blumenthal, and Bruce A. Shapiro

Pages: 355-386

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Chapter 16

Magnetic nanoparticles loaded with functional RNA nanoparticles

Melissa Cruz-Acuña, Justin R. Halman, Kirill A. Afonin, Jon Dobson, and Carlos Rinaldi

Pages: 387-412

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Chapter 17

Multimodal Polysilsesquioxane Nanoparticles for Combinatorial Therapy and Gene Delivery in Triple-Negative Breast Cancer

Ridhima Juneja, Zachary Lyles, Hemapriyadarshini Vadarevu, Kirill A. Afonin, and Juan L. Vivero-Escoto

Pages: 413-450

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Chapter 18

A Cationic Amphiphilic Co-polymer as a Carrier of Nucleic Acid Nanoparticles (NANPs) for Controlled Gene Silencing, Immunostimulation, and Biodistribution

Justin R. Halman, Ki-Taek Kim, So-Jung Gwak, Richard Pace, M. Brittany Johnson, Morgan R. Chandler, Lauren Rackley, Mathias Viard, Ian Marriott, Jeoung Soo Lee, and Kirill A. Afonin

Pages: 451-476

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Chapter 19

Cellular Delivery of RNA Nanoparticles

Lorena Parlea, Anu Puri, Wojciech Kasprzak, Eckart Bindewald, Paul Zakrevsky, Emily Satterwhite, Kenya Joseph, Kirill A. Afonin, and Bruce A. Shapiro

Pages: 477-538

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Chapter 20

Exosome Mediated Delivery of Functional Nucleic Acid Nanoparticles (Nanps)

Senny Nordmeier, Weina Ke, Kirill A. Afonin, and Victoria Portnoy

Pages: 539-564

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Chapter 21

Combination of Nucleic Acid and Mesoporous Silica Nanoparticles: Optimization and Therapeutic Performance in vitro

Ridhima Juneja, Hemapriyadarshini Vadarevu, Justin Halman, Mubin Tarannum, Lauren Rackley, Jacob Dobbs, Jose Marquez, Morgan Chandler, Kirill A. Afonin, and Juan L. Vivero-Escoto

Pages: 565-604

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Chapter 22

Opportunities, Barriers, and a Strategy for Overcoming Translational Challenges to Therapeutic Nucleic Acid Nanotechnology

Kirill A. Afonin, Marina A. Dobrovolskaia, George Church, and Mark Bathe

Pages: 605-626

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Chapter 23

Activation of Different Split Functionalities on Re-association of Rna–Dna Hybrids

Kirill A. Afonin, Mathias Viard, Angelica N. Martins, Stephen J. Lockett, Anna E. Maciag, Eric O. Freed, Eliahu Heldman, Luc Jaeger, Robert Blumenthal, and Bruce A. Shapiro

Pages: 627-650

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Chapter 24

Co-transcriptional Production of Rna–Dna Hybrids for Simultaneous Release of Multiple Split Functionalities

Kirill A. Afonin, Ravi Desai, Mathias Viard, Maria L. Kireeva, Eckart Bindewald, Christopher L. Case, Anna E. Maciag, Wojciech K. Kasprzak, Taejin Kim, Alison Sappe, Marissa Stepler, Vineet N. KewalRamani, Mikhail Kashlev, Robert Blumenthal, and Bruce A. Shapiro

Pages: 651-680

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Chapter 25

Triggering of RNA Interference with RNA–RNA, RNA–DNA, and DNA–RNA Nanoparticles

Kirill A. Afonin, Mathias Viard, Ioannis Kagiampakis, Christopher L. Case, Marina A. Dobrovolskaia, Jen Hofmann, Ashlee Vrzak, Maria Kireeva, Wojciech K. Kasprzak, Vineet N. KewalRamani, and Bruce A. Shapiro

Pages: 681-706

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Chapter 26

Multistrand Structure Prediction of Nucleic Acid Assemblies and Design of RNA Switches

Eckart Bindewald, Kirill A. Afonin, Mathias Viard, Paul Zakrevsky, Taejin Kim, and Bruce A. Shapiro

Pages: 707-734

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Chapter 27

The Use of Minimal RNA Toeholds to Trigger the Activation of Multiple Functionalities

Kirill A. Afonin, Matthias Viard, Philip Tedbury, Eckart Bindewald, Lorena Parlea, Marshall Howington, Melissa Valdman, Alizah Johns-Boehme, Cara Brainerd, Eric O. Freed, and Bruce A. Shapiro

Pages: 735-754

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Chapter 28

Functionally-Interdependent Shape-Switching Nanoparticles with Controllable Properties

Justin R. Halman, Emily Satterwhite, Brandon Roark, Morgan Chandler, Mathias Viard, Anna Ivanina, Eckart Bindewald, Wojciech K. Kasprzak, Martin Panigaj, My N. Bui, Jacob S. Lu, Johann Miller, Emil F. Khisamutdinov, Bruce A. Shapiro, Marina A. Dobrovolskaia, and Kirill A. Afonin

Pages: 755-778

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Chapter 29

Dynamic Behavior of RNA Nanoparticles Analyzed by AFM on a Mica/Air Interface

Sameer Sajja, Morgan Chandler, Dmitry Fedorov, Wojciech K. Kasprzak, Alexander Lushnikov, Mathias Viard, Ankit Shah, Dylan Dang, Jared Dahl, Beamlak Worku, Marina A. Dobrovolskaia, Alexey Krasnoslobodtsev, Bruce A. Shapiro, and Kirill A. Afonin

Pages: 779-804

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Chapter 30

Broccoli Fluorets: Split Aptamers as a User-Friendly Fluorescent Toolkit for Dynamic RNA Nanotechnology

Morgan Chandler, Tatiana Lyalina, Justin Halman, Lauren Rackley, Lauren Lee, Dylan Dang, Weina Ke, Sameer Sajja, Steven Woods, Shrija Acharya, Elijah Baumgarten, Jonathan Christopher, Emman Elshalia, Gabriel Hrebien, Kinzey Kublank, Saja Saleh, Bailey Stallings, Michael Tafere, C Striplin, K Afonin

Pages: 805-824

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Chapter 31

Aptamers as Modular Components of Therapeutic Nucleic Acid Nanotechnology

Martin Panigaj, M. Brittany Johnson, Weina Ke, Jessica McMillan, Ekaterina A. Goncharova, Morgan Chandler, and Kirill A. Afonin

Pages: 825-884

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Chapter 32

Programmable Nucleic Acid Based Polygons with Controlled Neuroimmunomodulatory Properties for Predictive QSAR Modeling

Morgan Brittany Johnson, Justin R. Halman, Emily Satterwhite, Alexey V. Zakharov, My N. Bui, Kheiria Benkato, Victoria Goldsworthy, Taejin Kim, Enping Hong, Marina A. Dobrovolskaia, Emil F. Khisamutdinov, Ian Marriott, and Kirill A. Afonin

Pages: 885-910

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Chapter 33

Structure and Composition Define Immunorecognition of Nucleic Acid Nanoparticles

Enping Hong, Justing R. Halman, Ankit B. Shah, Emil F. Khisamutdinov, Marina A. Dobrovolskaia, and Kirill A. Afonin

Pages: 911-942

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Chapter 34

RNA Fibers as Optimized Nanoscaffolds for siRNA Coordination and Reduced Immunological Recognition

Lauren Rackley, Jaimie Marie Stewart, Jacqueline Salotti, Andrey Krokhotin, Ankit Shah, Justin R. Halman, Ridhima Juneja, Jaclyn Smollett, Lauren Lee, Kyle Roark, Mathias Viard, Mubin Tarannum, Juan Vivero-Escoto, Peter F. Johnson, Marina A. Dobrovolskaia, Nikolay Dokholyan, Elisa Franco, K Afonin

Pages: 943-970

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Chapter 35

RNA–DNA fibers and polygons with controlled immunorecognition activate RNAi, FRET and transcriptional regulation of NF-kB in Human Cells

Weina Ke, Enping Hong, Renata F. Saito, Maria Cristina Rangel, Jian Wang, Mathias Viard, Melina Richardson, Emil F. Khisamutdinov, Martin Panigaj, Nikolay V. Dokholyan, Roger Chammas, Marina A. Dobrovolskaia, and Kirill A. Afonin

Pages: 971-1000

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Chapter 36

Toll-Like Receptor-Mediated Recognition of Nucleic Acid Nanoparticles (NANPs) in Human Primary Blood Cells

Enping Hong, Justin R. Halman, Ankit Shah, Edward Cedrone, Nguyen Truong, Kirill A. Afonin, and Marina A. Dobrovolskaia

Pages: 1001-1022

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Chapter 37

Smart-Responsive Nucleic Acid Nanoparticles (NANPs) with the Potential to Modulate Immune Behavior

Morgan Chandler and Kirill A. Afonin

Pages: 1023-1044

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Chapter 38

Innate Immune Responses Triggered by Nucleic Acids Inspire the Design of Immunomodulatory Nucleic Acid Nanoparticles (NANPs)

Morgan Chandler, Morgan Brittany Johnson, Martin Panigaj, and Kirill A. Afonin

Pages: 1045-1060

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Chapter 39

Retinoic Acid Inducible Gene-I Mediated Detection of Bacterial Nucleic Acids in Human Microglial Cells

M. Brittany Johnson, Justin R. Halman, Amanda R. Burmeister, Saralynn Currin, Emil F. Khisamutdinov, Kirill A. Afonin, and Ian Marriott

Pages: 1061-1090

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Chapter 40

Use of Human Peripheral Blood Mononuclear Cells to Define Immunological Properties of Nucleic Acid Nanoparticles

Marina A. Dobrovolskaia and Kirill A. Afonin

Pages: 1091-1136

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Chapter 41

The Immunorecognition, Subcellular Compartmentalization, and Physicochemical Properties of Nucleic Acid Nanoparticles can be Controlled by Composition Modification

Morgan Brittany Johnson, Justin R. Halman, Daniel K. Miller, Joseph S. Cooper, Emil F. Khisamutdinov, Ian Marriott, and Kirill A. Afonin

Pages: 1137-1170

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“This book comprehensively describes the pathway to progress in the field of nucleic acid nanotechnology, beginning with in silico design strategies and ending with a number of therapeutic and nanotechnological applications. The methods, big picture, and current progress presented in this book are an enormous asset to anyone endeavoring into this field.”
~Prof. Yaroslava Yingling, North Carolina State University, USA

“Previously unknown immunostimulatory properties of nucleic acid nanomaterials have presented a translational challenge which slowed down therapeutic development of these novel materials. The timely topics covered in this book reflect the journey through these preliminary investigations and hopefully will serve as the foundation for future work in this emerging area of nanomedicine.”
~Dr. Marina Dobrovolskaia, National Cancer Institute, USA

“The programmed and rational design of nucleic acid nanoparticles have a lot to offer to the fields of modern nanomedicine and nanotechnology. Dynamic approaches to therapeutics have great potential for customizability and increased specificity, interacting with particular inputs based on nature’s data processing molecule. It is exciting to see all of the potential of this technology gathered into one book.”
~Prof. Emil Khisamutdinov, Ball State University, USA

“The book provides a very nice walkthrough for the various recent technologies, both computational and experimental, that have been developed in the past few years and are now available for end users in therapeutic nucleic acid nanotechnology.”
~Prof. Nikolay Dokholyan, Pennsylvania State University, USA

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Therapeutic RNA Nanotechnology

Immunomodulation and Dynamicity

Therapeutic RNA Nanotechnology

Immunomodulation and Dynamicity

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