Squaring theory with practice in RNA design.

[1]  B. Ganem RNA world , 1987, Nature.

[2]  P. S. Kim,et al.  A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. , 1993, Science.

[3]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[4]  D. Turner,et al.  Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. , 1998, Biochemistry.

[5]  E. Westhof,et al.  TectoRNA: modular assembly units for the construction of RNA nano-objects. , 2001, Nucleic acids research.

[6]  Steven E. Brenner,et al.  SCOR: a Structural Classification of RNA database , 2002, Nucleic Acids Res..

[7]  Eduardo A. Fierro Structures , 2003, Composite Architecture.

[8]  D. Baker,et al.  Design of a Novel Globular Protein Fold with Atomic-Level Accuracy , 2003, Science.

[9]  Anne Condon,et al.  A new algorithm for RNA secondary structure design. , 2004, Journal of molecular biology.

[10]  R. D'Amato,et al.  Exogenous control of mammalian gene expression through modulation of RNA self-cleavage , 2004, Nature.

[11]  Lauren Ancel Meyers,et al.  Aptamer Database , 2004, Nucleic Acids Res..

[12]  Onnop Srivannavit,et al.  Microfluidic PicoArray synthesis of oligodeoxynucleotides and simultaneous assembling of multiple DNA sequences. , 2004, Nucleic acids research.

[13]  C. Mao,et al.  Bottom-up Assembly of RNA Arrays and Superstructures as Potential Parts in Nanotechnology. , 2004, Nano letters.

[14]  D. Turner,et al.  Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[15]  H. Hansma,et al.  Building Programmable Jigsaw Puzzles with RNA , 2004, Science.

[16]  Luc Jaeger,et al.  Controlled spacing of cationic gold nanoparticles by nanocrown RNA. , 2005, Journal of the American Chemical Society.

[17]  Alain Xayaphoummine,et al.  Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots , 2005, Nucleic Acids Res..

[18]  Rolf Backofen,et al.  INFO-RNA - a fast approach to inverse RNA folding , 2006, Bioinform..

[19]  N. Leontis,et al.  Controlling RNA self-assembly to form filaments , 2006, Nucleic acids research.

[20]  H. Schwalbe,et al.  Conformational dynamics of bistable RNAs studied by time-resolved NMR spectroscopy. , 2007, Journal of the American Chemical Society.

[21]  Charles K. Fisher,et al.  Visualizing spatially correlated dynamics that directs RNA conformational transitions , 2007, Nature.

[22]  V. Viasnoff,et al.  Encoding folding paths of RNA switches , 2006, Nucleic acids research.

[23]  Michael Zuker,et al.  UNAFold: software for nucleic acid folding and hybridization. , 2008, Methods in molecular biology.

[24]  Bruce A Shapiro,et al.  Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler. , 2008, Journal of molecular graphics & modelling.

[25]  P. A. Thompson,et al.  Electronic Reprint Biological Crystallography Structure of Hepatitis C Virus Ires Subdomain Iia Biological Crystallography Structure of Hepatitis C Virus Ires Subdomain Iia , 2022 .

[26]  Eckart Bindewald,et al.  RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign , 2007, Nucleic Acids Res..

[27]  Helen M Berman,et al.  RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). , 2008, RNA.

[28]  Cody W. Geary,et al.  Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors , 2007, Nucleic acids research.

[29]  M. Win,et al.  Higher-Order Cellular Information Processing with Synthetic RNA Devices , 2008, Science.

[30]  Weston R. Whitaker,et al.  Toward scalable parts families for predictable design of biological circuits. , 2008, Current opinion in microbiology.

[31]  Eric Westhof,et al.  The Dynamic Landscapes of RNA Architecture , 2009, Cell.

[32]  David H. Mathews,et al.  RNAstructure: software for RNA secondary structure prediction and analysis , 2010, BMC Bioinformatics.

[33]  Hirohide Saito,et al.  Coordinated control of a designed trans‐acting ligase ribozyme by a loop–receptor interaction , 2009, FEBS letters.

[34]  Maung Nyan Win,et al.  Raw Data, Win MN, Smolke CD. 2008. Higher-order cellular information processing with synthetic RNA devices. Science. 322: 456-60. DOI: 10.1126/science.1160311 , 2009 .

[35]  Christina D Smolke,et al.  Building outside of the box: iGEM and the BioBricks Foundation , 2009, Nature Biotechnology.

[36]  Eric Westhof,et al.  Frequency and isostericity of RNA base pairs , 2009, Nucleic acids research.

[37]  Cody W. Geary,et al.  Square-shaped RNA particles from different RNA folds. , 2009, Nano letters.

[38]  A designed RNA selection: establishment of a stable complex between a target and selectant RNA via two coordinated interactions , 2009, Nucleic acids research.

[39]  Ralph Bock,et al.  Designing and using synthetic RNA thermometers for temperature-controlled gene expression in bacteria , 2009, Nature Protocols.

[40]  Shi-Jie Chen,et al.  Predicting structures and stabilities for H-type pseudoknots with interhelix loops. , 2009, RNA.

[41]  Hervé Isambert,et al.  A nanostructure made of a bacterial noncoding RNA. , 2009, Journal of the American Chemical Society.

[42]  H. Isambert,et al.  RNA synthetic biology inspired from bacteria: construction of transcription attenuators under antisense regulation , 2009, Physical biology.

[43]  J. Šponer,et al.  Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In , 2009, Accounts of chemical research.

[44]  Amber R. Davis,et al.  Thermodynamic characterization of naturally occurring RNA tetraloops. , 2010, RNA.

[45]  A. Ferré-D’Amaré,et al.  Rapid Construction of Empirical RNA Fitness Landscapes , 2010, Science.

[46]  A. Laederach,et al.  Evaluation of the information content of RNA structure mapping data for secondary structure prediction. , 2010, RNA.

[47]  Le A. Trinh,et al.  Programmable in situ amplification for multiplexed imaging of mRNA expression , 2010, Nature Biotechnology.

[48]  Brent M. Znosko,et al.  Thermodynamic characterization of RNA triloops. , 2010, Biochemistry.

[49]  David Baker,et al.  Origins of catalysis by computationally designed retroaldolase enzymes , 2010, Proceedings of the National Academy of Sciences.

[50]  L. Jaeger,et al.  In vitro Assembly of Cubic RNA-Based Scaffolds Designed in silico , 2010, Nature nanotechnology.

[51]  Robert M. Dirks,et al.  Selective cell death mediated by small conditional RNAs , 2010, Proceedings of the National Academy of Sciences.

[52]  Farren J. Isaacs,et al.  Tracking, tuning, and terminating microbial physiology using synthetic riboregulators , 2010, Proceedings of the National Academy of Sciences.

[53]  Folding kinetics for the conformational switch between alternative RNA structures. , 2010, The journal of physical chemistry. B.

[54]  Emily M. LeProust,et al.  Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process , 2010, Nucleic acids research.

[55]  Amber R. Davis,et al.  Positional and neighboring base pair effects on the thermodynamic stability of RNA single mismatches. , 2010, Biochemistry.

[56]  Cody W. Geary,et al.  A polyhedron made of tRNAs , 2010, Nature chemistry.

[57]  Anton I. Petrov,et al.  Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities? , 2010, The journal of physical chemistry. B.

[58]  Eckart Bindewald,et al.  CyloFold: secondary structure prediction including pseudoknots , 2010, Nucleic Acids Res..

[59]  Eric Westhof,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[60]  Joy Sinha,et al.  Reprogramming Bacteria to Seek and Destroy a Herbicide , 2010, Nature chemical biology.

[61]  Harry A. Stern,et al.  Reparameterization of RNA χ Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine , 2010, Journal of chemical theory and computation.

[62]  David H. Mathews,et al.  NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure , 2009, Nucleic Acids Res..

[63]  K. Weeks Advances in RNA structure analysis by chemical probing. , 2010, Current opinion in structural biology.

[64]  Christina D Smolke,et al.  Reprogramming Cellular Behavior with RNA Controllers Responsive to Endogenous Proteins , 2010, Science.

[65]  D. Baker,et al.  Atomic accuracy in predicting and designing non-canonical RNA structure , 2010, Nature Methods.

[66]  Hebing Chen,et al.  ARDesigner: a web-based system for allosteric RNA design. , 2010, Journal of biotechnology.

[67]  Rhiju Das,et al.  Understanding the errors of SHAPE-directed RNA structure modeling. , 2011, Biochemistry.

[68]  D. Turner,et al.  Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for Single-Stranded r(GACC) Are Improved by Revised χ Torsions , 2011, The journal of physical chemistry. B.

[69]  Faisal A. Aldaye,et al.  Organization of Intracellular Reactions with Rationally Designed RNA Assemblies , 2011, Science.

[70]  Cole Trapnell,et al.  Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) , 2011, Proceedings of the National Academy of Sciences.

[71]  Akito Taneda,et al.  MODENA: a multi-objective RNA inverse folding , 2010, Advances and applications in bioinformatics and chemistry : AABC.

[72]  Paul J Jardine,et al.  Structure and assembly of the essential RNA ring component of a viral DNA packaging motor , 2011, Proceedings of the National Academy of Sciences.

[73]  S. Yoshimura,et al.  Synthetic RNA-protein complex shaped like an equilateral triangle. , 2011, Nature nanotechnology.

[74]  Yoshihiro Ito,et al.  Branched RNA nanostructures for RNA interference. , 2011, Chemical communications.

[75]  R. Weiss,et al.  Cancer Cells Multi-Input RNAi-Based Logic Circuit for Identification of Specific , 2011 .

[76]  Craig L. Zirbel,et al.  Sharing and archiving nucleic acid structure mapping data. , 2011, RNA.

[77]  Wade W Grabow,et al.  Self-assembling RNA nanorings based on RNAI/II inverse kissing complexes. , 2011, Nano letters.

[78]  Anton I. Petrov,et al.  WebFR3D—a server for finding, aligning and analyzing recurrent RNA 3D motifs , 2011, Nucleic Acids Res..

[79]  Rhiju Das,et al.  An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling , 2011, Proceedings of the National Academy of Sciences.

[80]  Jens Meiler,et al.  ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. , 2011, Methods in enzymology.

[81]  Scott D Kennedy,et al.  Molecular Mechanics Investigation of an Adenine-Adenine Non-Canonical Pair Conformational Change. , 2011, Journal of chemical theory and computation.

[82]  Tae-Jin Kim,et al.  Use of RNA structure flexibility data in nanostructure modeling. , 2011, Methods.

[83]  Hirohide Saito,et al.  Synthetic human cell fate regulation by protein-driven RNA switches , 2011, Nature Communications.

[84]  Rhiju Das,et al.  A two-dimensional mutate-and-map strategy for non-coding RNA structure. , 2011, Nature chemistry.

[85]  Niles A. Pierce,et al.  Nucleic acid sequence design via efficient ensemble defect optimization , 2011, J. Comput. Chem..

[86]  Adam P Arkin,et al.  Versatile RNA-sensing transcriptional regulators for engineering genetic networks , 2011, Proceedings of the National Academy of Sciences.

[87]  L. Jaeger,et al.  Multistrand RNA secondary structure prediction and nanostructure design including pseudoknots. , 2011, ACS nano.

[88]  Joe C. Liang,et al.  Engineering biological systems with synthetic RNA molecules. , 2011, Molecular cell.

[89]  T. Hermann,et al.  Self-assembling RNA square , 2011, Proceedings of the National Academy of Sciences.

[90]  Hao Yan,et al.  Challenges and opportunities for structural DNA nanotechnology. , 2011, Nature nanotechnology.

[91]  J. Šponer,et al.  Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles , 2011, Journal of chemical theory and computation.

[92]  J. M. Diamond,et al.  Fluorescence Competition and Optical Melting Measurements of RNA Three-Way Multibranch Loops Provide a Revised Model for Thermodynamic Parameters† , 2010, Biochemistry.

[93]  Peter F. Stadler,et al.  ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.

[94]  Conrad Steenberg,et al.  NUPACK: Analysis and design of nucleic acid systems , 2011, J. Comput. Chem..

[95]  D. Turner,et al.  NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions. , 2011, RNA.

[96]  Jay D Keasling,et al.  Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression , 2011, Science.

[97]  Klaus-Peter Zauner,et al.  Design of interacting multi-stable nucleic acids for molecular information processing , 2011, Biosyst..

[98]  B. Shapiro,et al.  Correlating SHAPE signatures with three-dimensional RNA structures. , 2011, RNA.

[99]  Harry A. Stern,et al.  Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs , 2011, Journal of chemical theory and computation.

[100]  Daniel Herschlag,et al.  Robust design and optimization of retroaldol enzymes , 2012, Protein science : a publication of the Protein Society.

[101]  Feng Ding,et al.  RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. , 2012, RNA.

[102]  Pamela L. Vanegas,et al.  RNA CoSSMos: Characterization of Secondary Structure Motifs—a searchable database of secondary structure motifs in RNA three-dimensional structures , 2011, Nucleic Acids Res..

[103]  Eric Westhof,et al.  RNA 3D Structure Analysis and Prediction , 2012, Nucleic Acids and Molecular Biology.

[104]  Effects of non-nearest neighbors on the thermodynamic stability of RNA GNRA hairpin tetraloops. , 2012, Biochemistry.

[105]  Manolis Kellis,et al.  RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction , 2012, Nucleic acids research.

[106]  Yaakov Benenson,et al.  Synthetic biology with RNA: progress report. , 2012, Current opinion in chemical biology.

[107]  Markus Wieland,et al.  Programmable single-cell mammalian biocomputers , 2012, Nature.

[108]  Julius B. Lucks,et al.  Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals , 2012, Nucleic acids research.