RNA origami: design, simulation and application

3D RNA-scaffolded wireframe origami

(2023) Molly F. Parsons et al.   Nature Communications

DNA synthesis technologies to close the gene writing gap

(2023) Alex Hoose et al.   Nature Reviews Chemistry

Active Nuclear Import of Mammalian Cell-Expressible DNA Origami

(2023) Anna Liedl et al.   Journal of the American Chemical Society

RNA origami scaffolds facilitate cryo-EM characterization of a Broccoli–Pepper aptamer FRET pair

(2023) Néstor Sampedro Vallina et al.   NUCLEIC ACIDS RESEARCH

Gene-encoding DNA origami for mammalian cell expression

(2023) Jessica A. Kretzmann et al.   Nature Communications

Utilizing RNA origami scaffolds in Saccharomyces cerevisiae for dCas9-mediated transcriptional control

(2022) Georgios Pothoulakis et al.   NUCLEIC ACIDS RESEARCH

Synthetic Translational Regulation by Protein-Binding RNA Origami Scaffolds

(2022) Michael T. A. Nguyen et al.   ACS Synthetic Biology

Phage‐free production of artificial ssDNA with Escherichia coli

(2022) Karl L. Behler et al.   BIOTECHNOLOGY AND BIOENGINEERING

Synthetic chromosomes, genomes, viruses, and cells

(2022) J. Craig Venter et al.   CELL

Algorithmic Design of 3D Wireframe RNA Polyhedra

(2022) Antti Elonen et al.   ACS Nano

Multi-micron crisscross structures grown from DNA-origami slats

(2022) Christopher M. Wintersinger et al.   Nature Nanotechnology

An RNA Paranemic Crossover Triangle as A 3D Module for Cotranscriptional Nanoassembly

(2022) Néstor Sampedro Vallina et al.   Small

Super-resolution RNA imaging using a rhodamine-binding aptamer with fast exchange kinetics

(2021) Murat Sunbul et al.   NATURE BIOTECHNOLOGY

RNA origami design tools enable cotranscriptional folding of kilobase-sized nanoscaffolds

(2021) Cody Geary et al.   Nature Chemistry

Multivalent Aptamer‐Functionalized Single‐Strand RNA Origami as Effective, Target‐Specific Anticoagulants with Corresponding Reversal Agents

(2021) Abhichart Krissanaprasit et al.   Advanced Healthcare Materials

Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution

(2021) Di Liu et al.   Science Advances

UFold: fast and accurate RNA secondary structure prediction with deep learning

(2021) Laiyi Fu et al.   NUCLEIC ACIDS RESEARCH

Phase separation in the outer membrane of Escherichia coli

(2021) Georgina Benn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kinetics of RNA and RNA:DNA Hybrid Strand Displacement

(2021) Hao Liu et al.   ACS Synthetic Biology

Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures

(2020) Di Liu et al.   Nature Chemistry

RNA Origami Nanostructures for Potent and Safe Anticancer Immunotherapy

(2020) Xiaodong Qi et al.   ACS Nano

Co-transcriptional folding of a bio-orthogonal fluorescent scaffolded RNA origami

(2020) Emanuela Torelli et al.   ACS Synthetic Biology

Barcoded DNA origami structures for multiplexed optimization and enrichment of DNA-based protein-binding cavities

(2020) Ali Aghebat Rafat et al.   Nature Chemistry

Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution

(2020) Massimo Kube et al.   Nature Communications

Design and Characterization of RNA Nanotubes

(2019) Jaimie Marie Stewart et al.   ACS Nano

Genetically Encoded, Functional Single‐Strand RNA Origami: Anticoagulant

(2019) Abhichart Krissanaprasit et al.   ADVANCED MATERIALS

Highly efficient expression of circular RNA aptamers in cells using autocatalytic transcripts

(2019) Jacob L. Litke et al.   NATURE BIOTECHNOLOGY

Construction of RNA nanotubes

(2019) Hui Li et al.   Nano Research

Computational design of three-dimensional RNA structure and function

(2019) Joseph D. Yesselman et al.   Nature Nanotechnology

RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning

(2019) Jaswinder Singh et al.   Nature Communications

An RNA Origami Octahedron with Intrinsic siRNAs for Potent Gene Knockdown

(2018) Hans Christian Høiberg et al.   Biotechnology Journal

Favorable biodistribution, specific targeting and conditional endosomal escape of RNA nanoparticles in cancer therapy

(2018) Congcong Xu et al.   CANCER LETTERS

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

(2018) Jiří Šponer et al.   CHEMICAL REVIEWS

The Effect of Size and Shape of RNA Nanoparticles on Biodistribution

(2018) Daniel L. Jasinski et al.   MOLECULAR THERAPY

Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography

(2018) Dongsheng Lei et al.   Nature Communications

In vivo production of RNA nanostructures via programmed folding of single-stranded RNAs

(2018) Mo Li et al.   Nature Communications

Development of a genetically encodable FRET system using fluorescent RNA aptamers

(2018) Mette D. E. Jepsen et al.   Nature Communications

An RNA Origami Octahedron with Intrinsic siRNAs for Potent Gene Knockdown

(2018) Hans Christian Høiberg et al.   Biotechnology Journal

Chemical and structural effects of base modifications in messenger RNA

(2017) Emily M. Harcourt et al.   NATURE

Biotechnological mass production of DNA origami

(2017) Florian Praetorius et al.   NATURE

Single-stranded DNA and RNA origami

(2017) Dongran Han et al.   SCIENCE

Protein-driven RNA nanostructured devices that function in vitro and control mammalian cell fate

(2017) Tomonori Shibata et al.   Nature Communications

Size, Shape, and Sequence-Dependent Immunogenicity of RNA Nanoparticles

(2017) Sijin Guo et al.   Molecular Therapy-Nucleic Acids

Controllable Self-Assembly of RNA Tetrahedrons with Precise Shape and Size for Cancer Targeting

(2016) Hui Li et al.   ADVANCED MATERIALS

Controllable self-assembly of RNA dendrimers

(2016) Ashwani Sharma et al.   Nanomedicine-Nanotechnology Biology and Medicine

SimRNAweb: a web server for RNA 3D structure modeling with optional restraints

(2016) Marcin Magnus et al.   NUCLEIC ACIDS RESEARCH

Designer nanoscale DNA assemblies programmed from the top down

(2016) R. Veneziano et al.   SCIENCE

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction

(2015) Michal J. Boniecki et al.   NUCLEIC ACIDS RESEARCH

De novo design of an RNA tile that self-assembles into a homo-octameric nanoprism

(2015) Jinwen Yu et al.   Nature Communications

Directed Self-Assembly of DNA Tiles into Complex Nanocages

(2014) Cheng Tian et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Preparation of Chemically Modified RNA Origami Nanostructures

(2014) Masayuki Endo et al.   CHEMISTRY-A EUROPEAN JOURNAL

A nucleotide-level coarse-grained model of RNA

(2014) Petr Šulc et al.   JOURNAL OF CHEMICAL PHYSICS

A comparison between parallelization approaches in molecular dynamics simulations on GPUs

(2014) Lorenzo Rovigatti et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Coarse Grained Models Reveal Essential Contributions of Topological Constraints to the Conformational Free Energy of RNA Bulges

(2014) Anthony M. Mustoe et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Understanding the Mechanical Properties of DNA Origami Tiles and Controlling the Kinetics of Their Folding and Unfolding Reconfiguration

(2014) Haorong Chen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Multifunctional RNA Nanoparticles

(2014) Kirill A. Afonin et al.   NANO LETTERS

Enhancing immunomodulation on innate immunity by shape transition among RNA triangle, square and pentagon nanovehicles

(2014) Emil F. Khisamutdinov et al.   NUCLEIC ACIDS RESEARCH

A single-stranded architecture for cotranscriptional folding of RNA nanostructures

(2014) C. Geary et al.   SCIENCE

RNA-templated DNA origami structures

(2013) Masayuki Endo et al.   CHEMICAL COMMUNICATIONS

RNA–DNA hybrid origami: folding of a long RNA single strand into complex nanostructures using short DNA helper strands

(2013) Pengfei Wang et al.   CHEMICAL COMMUNICATIONS

Coarse-Grained Model for Predicting RNA Folding Thermodynamics

(2013) Natalia A. Denesyuk et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Imaging living cells surface and quantifying its properties at high resolution using AFM in QI™ mode

(2013) L. Chopinet et al.   MICRON

Fabrication of 14 different RNA nanoparticles for specific tumor targeting without accumulation in normal organs

(2013) Y. Shu et al.   RNA

The Effect of Nanoparticle Size, Shape, and Surface Chemistry on Biological Systems

(2012) Alexandre Albanese et al.   Annual Review of Biomedical Engineering

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

(2012) Kirill A. Afonin et al.   NANO LETTERS

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

(2011) Kengo Sato et al.   BIOINFORMATICS

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Physics-Based De Novo Prediction of RNA 3D Structures

(2011) Song Cao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Assembly of multifunctional phi29 pRNA nanoparticles for specific delivery of siRNA and other therapeutics to targeted cells

(2011) Yi Shu et al.   METHODS

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

(2011) Wade W. Grabow et al.   NANO LETTERS

Design and self-assembly of siRNA-functionalized RNA nanoparticles for use in automated nanomedicine

(2011) Kirill A Afonin et al.   Nature Protocols

Organization of Intracellular Reactions with Rationally Designed RNA Assemblies

(2011) C. J. Delebecque et al.   SCIENCE

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels

(2010) F. Jossinet et al.   BIOINFORMATICS

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

(2010) Pavel Banáš et al.   Journal of Chemical Theory and Computation

NUPACK: Analysis and design of nucleic acid systems

(2010) Joseph N. Zadeh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

HiRE-RNA: A High Resolution Coarse-Grained Energy Model for RNA

(2010) Samuela Pasquali et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Synergistic self-assembly of RNA and DNA molecules

(2010) Seung Hyeon Ko et al.   Nature Chemistry

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

(2010) Kirill A. Afonin et al.   Nature Nanotechnology

ProbKnot: Fast prediction of RNA secondary structure including pseudoknots

(2010) S. Bellaousov et al.   RNA

Surface-Mediated DNA Self-Assembly

(2009) Xuping Sun et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Square-Shaped RNA Particles from Different RNA Folds

(2009) Isil Severcan et al.   NANO LETTERS

Self-assembly of a nanoscale DNA box with a controllable lid

(2009) Ebbe S. Andersen et al.   NATURE

Rapid prototyping of 3D DNA-origami shapes with caDNAno

(2009) Shawn M. Douglas et al.   NUCLEIC ACIDS RESEARCH

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

(2009) Douglas H. Turner et al.   NUCLEIC ACIDS RESEARCH

PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy

(2009) Srinivasa M. Gopal et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler

(2008) Eckart Bindewald et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Specific RNA Self-Assembly with Minimal Paranemic Motifs

(2007) Kirill A. Afonin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY