Titlebook: RNA Nanostructures; Design, Characteriza Kirill A. Afonin Book 2023 The Editor(s) (if applicable) and The Author(s), under exclusive licens

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Bioconjugation of Functionalized Oligodeoxynucleotides with Fluorescence Reporters for Nanoparticle fic targets. Herein, we describe a generalized methodology that deploys azide-alkyne cycloaddition, a click reaction to conjugate a cyanine-3 alkyne moiety to an azide-functionalized ODN 12-mer, as well as 3-azido 7-hydroxycoumarin to an alkyne functionalized ODN 12-mer.

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Characterization of RNA Nanoparticles and Their Dynamic Properties Using Atomic Force Microscopyinguish the differences in the dynamic behavior of RNA nanoparticles not amenable to other experimental techniques. This protocol describes in detail the preparation procedures of RNA nanostructures, AFM imaging, and data analysis.

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Book 2023A 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 Molecul

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Preparation of Nucleic Acid Aptamer Functionalized Silver/Gold Nanoparticle Conjugates Using Thiol-Sify the nanoparticle-aptamer conjugates, verify aptamer attachment, and quantify aptamer-nanoparticle ratios are also discussed and compared. Additionally, a simple protocol that describes the aqueous synthesis of gold nanoparticles (~10 nm) is included.

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Structural Characterization of DNA-Templated Silver Nanoclusters by Energy Dispersive Spectroscopy the consistent number of phosphate atoms in each structure, we determine the average number of silver atoms that make up the DNA-AgNCs. Proper sample preparation and fine-tuning of the SEM/EDS system settings were combined to achieve highly repeatable data.

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Molecular Dynamics Simulations of RNA Motifs to Guide the Architectural Parameters and Design Princiulations of an RNA nanostructure is computationally expensive due to the size of nanostructure and the number of atoms. Alternatively, MD simulations of RNA motifs can be used to estimate the conformational stability of constructed RNA nanostructure due to their small sizes. In this chapter, we intr

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Combining Experimental Restraints and RNA 3D Structure Prediction in RNA Nanotechnology are limited to small RNAs with relatively simple secondary structures. Large RNA molecules usually have complex secondary structures, including multibranched loops and pseudoknots, allowing for highly flexible RNA geometries and multiple stable states. Various experiments and bioinformatics analyse

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Structural Characterization of Nucleic Acid Nanoparticles Using SAXS and SAXS-Driven MDize, shape, and flexibility of the construct. Small-angle X-ray scattering (SAXS) is a well-established method to obtain structural information of particles in solution. Here, we present a procedure for the preparation of NANPs for SAXS. This procedure outlines the steps for a successful SAXS experi

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Metalated Nucleic Acid Nanostructurestion of metal ions into these structures introduces functionality for sensor and molecular electronic applications. Here, we describe a protocol for the incorporation of silver ions into polygonal nanoshapes that self-assemble from RNA and DNA modules.

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Bioconjugation of Functionalized Oligodeoxynucleotides with Fluorescence Reporters for Nanoparticle ither chemical modification of the oligonucleotides’ structure or to covalently link them to a reporter or therapeutic moieties that possess biologically relevant properties. The chemical conjugation can thus significantly improve the intrinsic properties not only of ODNs but also reporter/therapeut