RNA Nanostructures

ISBN-13: 9781071634165 / Angielski / Twarda / 2023

Opis

This volume details protocols for computer-assisted design and experimental characterization of RNA nanostructures. Chapters guide readers through RNA nanotechnology, design and characterization of RNA nanostructures, assessment of immunology of nanomaterials, biosensing and drug delivery, various biomedical applications, and delivery approaches for therapeutic RNA nanoparticles. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.   Authoritative and cutting-edge, RNA Nanostructures: Design, Characterization, and Applications aims to address essential topics and concerns in the growing field of RNA nanotechnology. 

Spis treści

 Part I: Computational design and in silico studies of RNA nanostructures.

1. Molecular Dynamics Simulations of RNA Motifs to Guide the Architectural Parameters and Design Principles of RNA Nanostructures

Valentina Abondano Perdomo and Taejin Kim

Computer assisted design and characterization or RNA nanostructures

Christina J. Bayard and Yaroslava G. Yingling.

1. Combining Experimental Restraints and RNA 3D Structure Prediction in RNA Nanotechnology

Jian Wang, Congzhou M. Sha, Nikolay V. Dokholyan

1. Structural Characterization of Nucleic Acid Nanoparticles using SAXS and SAXS-driven MD

James Byrnes, Kriti Chopra, Lewis A. Rolband, Leyla Danai, Shirish Chodankar, Lin Yang, and Kirill A. Afonin

 

Part II: Production and storage of functional RNA Nanostructures

1. Metalated Nucleic Acid Nanostructures

Douglas Zhang and Thomas Hermann

1. Bioconjugation of Functionalized Oligodeoxynucleotides with Fluorescence Reporters for Nanoparticle Assembly

Erwin Doe, Hannah Hayth, and Emil F. Khisamutdinov

1. Light-assisted drying for the thermal stabilization of nucleic acid nanoparticles and other biologics

Susan R. Trammell

1. Preparation of Nucleic Acid Aptamer Functionalized Silver/Gold Nanoparticle Conjugates

Joshua D Quarles, Allen T Livingston, Ashley E Wood, and Timea Gerczei Fernandez

 

Part III: Characterization of RNA nanostructures

9.      Thermodynamic Characterization of Nucleic Acid Nanoparticles Hybridization by UV Melting

Megan Teter, Ross Brumett, Abigail Coffman, and Emil F. Khisamutdinov

10.  Structural Characterization of DNA Templated Silver Nanoclusters by Energy Dispersive Spectroscopy

Damian Beasock, and Kirill A. Afonin

1. Small Volume microrheology to Evaluate Viscoelastic Properties of Nucleic Acid-based Hydrogels

Akhilesh Kumar Gupta, Joel Petersen, Elizabeth Skelly, Kirill A. Afonin, and Alexey V. Krasnoslobodtsev

1. Characterization of RNA Nanoparticles and Their Dynamic Properties Using Atomic Force Microscopy

Alexander Lushnikov, Yelixza I. Avila, Kirill A. Afonin, Alexey Krasnoslobodtsev.

 

Part IV: Intracellular delivery and Immunorecognition of RNA nanostructures

13.  Synthesis of Mesoporous Silica Nanoparticles for the Delivery of Nucleic Acid Nanostructures

Tamanna Binte Huq and Juan Vivero-Escoto

1. Assessment of intracellular compartmentalization of RNA nanostructures

Yasmine Radwan, Kirill A. Afonin, M. Brittany Johnson

Discriminating immunorecognition pathways activated by RNA nanostructures

Leyla Danai, M. Brittany Johnson, Kirill A. Afonin

1. Detection of nanoparticles' ability to stimulate toll-like receptors using HEK-Blue reporter cell lines

Edward Cedrone and Marina A. Dobrovolskaia

1. Complexing PAMAM Dendrimers to Nucleic Acid Nanoparticles for their Intracellular Delivery

Yelixza I. Avila, Laura Rebolledo, Melanie Andrade-Munoz, Kirill A. Afonin

 

Part V: RNA and DNA nanostructures designed for biomedical applications

1. Reverse transfection of functional RNA rings into cancer cells followed by in vitro irradiation

Renata de Freitas Saito, Isabella Nevoni Ferreira, Maria Cristina Rangel and Roger Chammas

1. RNA/DNA nanostructures designed for efficient regulation of blood coagulation

Lewis A. Rolband, Weina Ke, Kirill A. Afonin

Detection of multiplex NASBA RNA products using colorimetric split G quadruplex probes

Maria S. Rubela, Liubov A. Shkodenko, Daria A. Gorbenko, Valeria V. Solyanikova, Yulia I. Maltzeva, Aleksandr A. Rubel, Elena I. Koshel, Dmitry M. Kolpashchikov

1. Synthesis of DNA-Templated Silver Nanoclusters and the Characterization of Their Optical Properties and Biological Activity

Elizabeth Skelly, Lewis A. Rolband, Damian Beasock, Kirill A. Afonin

1. Dynamic nanostructures for conditional activation and deactivation of biological pathways

Yasmine Radwan, Laura P. Rebolledo, Martin Panigaj, Kirill A. Afonin

Anticoagulant activity of nucleic acid nanoparticles assessed by thrombin generation dynamics on a fully-automated system

Renata de Freitas Saito, Bárbara Gomes Barion, Tania Rubia Flores da Rocha, Alex Rolband, Kirill A. Afonin, and Roger Chammas