Multistate Stochastic Models for Data Analysis

Section I Introduction: Principles and Fundamentals of RNA Nanotechnology


The Emerging Field of RNA Nanotechnology


Peixuan Guo


Uniqueness, Advantages, Challenges, Solutions, and Perspectives in Therapeutics Applying RNA Nanotechnology


Peixuan Guo, Farzin Haque, Brent Hallahan, Randall Reif, Hui Li, and Shaoying Wang





Section II RNA Folding, Structure, and Motifs in RNA Nanoparticle Assembly





Kink Turn Structural Motif in RNA


Peter Daldrop, Lin Huang, Kersten T. Schroeder, Jia Wang, and David M. J. Lilley


RNA Nanotechnology: Learning from Biologically Active RNA Nanomachines


Neocles B. Leontis and Emil F. Khisamutdinov


Natural Selection and Structural Polymorphism of RNA 3D Structures Involving GNRA Loops and Their Receptor Motifs


Takahiro Tanaka, Hiroyuki Furuta, and Yoshiya Ikawa


RNA Junction Motifs as Scaffolds for Construction of Multifunctional RNA Nanoparticles


Farzin Haque and Peixuan Guo





Section III RNA Computation and Structure Prediction for RNA Nanoparticle Construction





Role of Dynamics in RNA Nanostructure Design


Wojciech Kasprzak and Bruce A. Shapiro


RNA Three-Dimensional Structure Determination Using Experimental Constraints


Feng Ding and Nikolay V. Dokholyan





Section IV RNA Chemistry for Nanoparticle Synthesis, Conjugation, and Labeling





Nucleotide Chemistry for RNA Nanoparticle Labeling, Conjugation, and Synthesis


Brian M. Laing and Donald E. Bergstrom


RNA Conjugations and Ligations for RNA Nanotechnology


Eduardo Paredes and Subha R. Das


Atom-Specific Mutagenesis of RNAs for Structure, Function, and Therapeutics Studies


Huiyan Sun and Zhen Huang





Section V Single-Molecule and Biophysical Techniques in RNA Nanostructure Analysis





Atomic Force Microscopy of RNA: Imaging and Beyond


Peter M. Schoen, Luda S. Shlyakhtenko, and Yuri L. Lyubchenko


Single-Molecule Approach to Study RNA Nanoparticles


Hui Zhang, Chris Richards, Zhengyi Zhao, and Peixuan Guo





Section VI Methods for the Assembly of RNA Nanoparticles





Fabrication Methods for RNA Nanoparticle Assembly Based on Bacteriophage phi29 Packaging RNA Structural Features


Yi Shu, Bahar Seremi, and Peixuan Guo


Synthetic RNA-Protein Nanostructures and Their Potential Applications


Hirohisa Ohno, Eriko Osada, Tan Inoue, and Hirohide Saito


DNA Nanotechnology as Reference for RNA Nanotechnology


Zhen-Gang Wang and Baoquan Ding





Section VII RNA Nanoparticles for Therapy of Cancer, Viral Infections, and Genetic Diseases





Thermodynamically Stable RNA Three-Way Junction for Constructing Multifunctional Nanoparticles for Delivery of Therapeutics


Dan Shu, Yi Shu, Farzin Haque, Sherine Abdelmawla, and Peixuan Guo


Design and Construction of RNA Nanoparticles Targeting Prostate Cancer


Randall Reif and Peixuan Guo


Conjugation of RNA Aptamer to RNA Nanoparticles for Targeted Drug Delivery


Katherine Germer, Fengmei Pi, Peixuan Guo, and Xiaoting Zhang


Extracellular Membrane Vesicles and Extracellular Membrane Vesicle-Based Therapeutics for Brain Diseases


Jayden A. Smith, Clara Alfaro-Cervello, Chiara Cossetti, Nunzio Iraci, Matilde Stefanini, and Stefano Pluchino


Pharmacokinetics and Pharmacodynamics of RNA Nanoparticles


Markos Leggas





Section VIII RNA Nanotechnology for Diagnostic Applications





RNA Nanotechnology in Sensing, Detection, and Disease Diagnosis


Ping Lei and Guanxin Shen


Potentials of RNA Aptamers for Viral Detection and Treatment


Longxin Chen, Runting Li, and Runlin Z. Ma





Section IX Application of RNA Aptamers in RNA Nanotechnology and Therapeutics





Application of RNA Aptamers in Nanotechnology and Therapeutics


Hua Shi


Aptamers Targeting a Subunit or a Conformation of Glutamate Ion Channel Receptors


Zhen Huang, William Jaremko, Chi-yen Lin, and Li Niu





Section X Application of miRNAs in RNA Nanotechnology and Therapeutics





Application of MicroRNAs in RNA Nanotechnology and Antiviral Therapeutics


Ye Qiu, Xin Ye, Maged Hemida, Mary Zhang, Paul Hanson, and Decheng Yang


MicroRNAs: Biology and Role in RNA Nanotechnology


Bin Guo and Daniel W. Binzel





Section XI Application of siRNAs in RNA Nanotechnology and Therapeutics





Current Advances in Self-Assembly RNAi Nanoparticles


Ka-To Shum, Jiehua Zhou, and John J. Rossi


Self-Assembly of siRNA Containing Nanoparticles


Mengyao Zheng, Thomas Kissel, and Olivia M. Merkel


Index