Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects

Secondary structure prediction for RNA sequences including N6-methyladenosine

(2022) Elzbieta Kierzek et al.   Nature Communications

RNA secondary structure prediction using deep learning with thermodynamic integration

(2021) Kengo Sato et al.   Nature Communications

Theoretical basis for stabilizing messenger RNA through secondary structure design

(2021) Hannah K Wayment-Steele et al.   NUCLEIC ACIDS RESEARCH

LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2

(2021) Sizhen Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small-molecule targeted recruitment of a nuclease to cleave an oncogenic RNA in a mouse model of metastatic cancer

(2020) Matthew G. Costales et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis

(2020) David C Tack et al.   RNA

Forces maintaining the DNA double helix

(2020) Peter L. Privalov et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities

(2020) He Zhang et al.   BIOINFORMATICS

Probing conformational transitions towards mutagenic Watson–Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion

(2020) Atul Rangadurai et al.   JOURNAL OF BIOMOLECULAR NMR

SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness

(2020) Kizzmekia S. Corbett et al.   NATURE

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

Identification of the initial nucleocapsid recognition element in the HIV-1 RNA packaging signal

(2020) Pengfei Ding et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in Bacillus subtilis

(2020) Laura E Ritchey et al.   RNA

FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds

(2020) Andrew Martin Watkins et al.   STRUCTURE

The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2

(2020) Omer Ziv et al.   MOLECULAR CELL

A general fragment-based approach to identify and optimize bioactive ligands targeting RNA

(2020) Blessy M. Suresh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hachimoji DNA and RNA: A genetic system with eight building blocks

(2019) Shuichi Hoshika et al.   SCIENCE

The multiple flavors of GoU pairs in RNA

(2019) Eric Westhof et al.   JOURNAL OF MOLECULAR RECOGNITION

Precise small-molecule cleavage of an r(CUG) repeat expansion in a myotonic dystrophy mouse model

(2019) Alicia J. Angelbello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating uncertainty in predicted folding free energy changes of RNA secondary structures

(2019) Jeffrey Zuber et al.   RNA

LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search

(2019) Liang Huang et al.   BIOINFORMATICS

Quantitative Studies of an RNA Duplex Electrostatics by Ion Counting

(2019) Magdalena Gebala et al.   BIOPHYSICAL JOURNAL

mRNA structure regulates protein expression through changes in functional half-life

(2019) David M. Mauger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving RNA nearest neighbor parameters for helices by going beyond the two-state model

(2018) Aleksandar Spasic et al.   NUCLEIC ACIDS RESEARCH

Analysis of RNA Nearest Neighbor Parameters Reveals Interdependencies and Quantifies the Uncertainty in RNA Secondary Structure Prediction

(2018) Jeffrey Zuber et al.   RNA

Stability of RNA duplexes containing inosine·cytosine pairs

(2018) Daniel J Wright et al.   NUCLEIC ACIDS RESEARCH

Genome-wide RNA structurome reprogramming by acute heat shock globally regulates mRNA abundance

(2018) Zhao Su et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA targeting with CRISPR–Cas13

(2017) Omar O. Abudayyeh et al.   NATURE

Bridging the gap between in vitro and in vivo RNA folding

(2016) Kathleen A. Leamy et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

(2016) Michael F. Sloma et al.   RNA

Evaluating Hydrogen Bonds and Base Stacking of Single, Tandem and Terminal GU Mismatches in RNA with a Mesoscopic Model

(2015) Tauanne D. Amarante et al.   Journal of Chemical Information and Modeling

Structures and Energetics of Four Adjacent G·U Pairs That Stabilize an RNA Helix

(2015) Xiaobo Gu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The energetic basis of the DNA double helix: a combined microcalorimetric approach

(2015) Paulius Vaitiekunas et al.   NUCLEIC ACIDS RESEARCH

Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures

(2015) Yinghan Fu et al.   PLoS One

Understanding Nucleic Acid–Ion Interactions

(2014) Jan Lipfert et al.   Annual Review of Biochemistry

Secondary Structure of a Conserved Domain in an Intron of Influenza A M1 mRNA

(2014) Tian Jiang et al.   BIOCHEMISTRY

RNAcentral: an international database of ncRNA sequences

(2014)   NUCLEIC ACIDS RESEARCH

A Decade of Riboswitches

(2013) Alexander Serganov et al.   CELL

RNAiFold: a web server for RNA inverse folding and molecular design

(2013) Juan Antonio Garcia-Martin et al.   NUCLEIC ACIDS RESEARCH

Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters

(2012) Jonathan L. Chen et al.   BIOCHEMISTRY

RNA and Its Ionic Cloud: Solution Scattering Experiments and Atomically Detailed Simulations

(2012) Serdal Kirmizialtin et al.   BIOPHYSICAL JOURNAL

Visualizing transient low-populated structures of RNA

(2012) Elizabeth A. Dethoff et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

ViennaRNA Package 2.0

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

Enhanced Base-Pair Opening in the Adenine Tract of a RNA Double Helix

(2011) Yuegao Huang et al.   BIOCHEMISTRY

Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy

(2011) Jameson R Bothe et al.   NATURE METHODS

Consecutive Terminal GU Pairs Stabilize RNA Helices

(2010) Mai-Thao Nguyen et al.   BIOCHEMISTRY

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Nucleic acid sequence design via efficient ensemble defect optimization

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

Direct observation of the temperature-induced melting process of the Salmonella fourU RNA thermometer at base-pair resolution

(2010) Jörg Rinnenthal et al.   NUCLEIC ACIDS RESEARCH

Thermodynamics of RNA melting, one base pair at a time

(2010) E. N. Nikolova et al.   RNA

ProbKnot: Fast prediction of RNA secondary structure including pseudoknots

(2010) S. Bellaousov et al.   RNA

Group II Introns: Mobile Ribozymes that Invade DNA

(2010) A. M. Lambowitz et al.   Cold Spring Harbor Perspectives in Biology

Telomerase: An RNP Enzyme Synthesizes DNA

(2010) E. H. Blackburn et al.   Cold Spring Harbor Perspectives in Biology

Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA

(2009) Suzette A. Pabit 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

Modulation of RNA Metal Binding by Flanking Bases:15N NMR Evaluation of GC, Tandem GU, and Tandem GA Sites

(2009) Weimin Wang et al.   NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS

3′ Terminal Nucleotides Determine Thermodynamic Stabilities of Mismatches at the Ends of RNA Helices†

(2008) Koree Clanton-Arrowood et al.   BIOCHEMISTRY

The Dynamic Structural Basis of Differential Enhancement of Conformational Stability by 5′- and 3′-Dangling Ends in RNA†

(2008) John D. Liu et al.   BIOCHEMISTRY

RNA Folding: Thermodynamic and Molecular Descriptions of the Roles of Ions

(2008) David E. Draper   BIOPHYSICAL JOURNAL

Let Me Count the Ways: Mechanisms of Gene Regulation by miRNAs and siRNAs

(2008) Ligang Wu et al.   MOLECULAR CELL

The impact of target site accessibility on the design of effective siRNAs

(2008) Hakim Tafer et al.   NATURE BIOTECHNOLOGY

Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design

(2008) Z. J. Lu et al.   NUCLEIC ACIDS RESEARCH