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Nucleic Acids Res

@NAR_Open

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NAR is an open access journal publishing the latest in nucleic acids research. An Oxford University Press journal.

https://t.co/Q5Dn9luqDB
Joined March 2015
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@NAR_Open
Nucleic Acids Res
@NAR_Open
11 months
DDMut: predicting effects of mutations on protein stability using deep learning
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1 year
PlasMapper 3.0—a web server for generating, editing, annotating and visualizing publication quality plasmid maps
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Nucleic Acids Res
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3 years
Visualization and characterization of RNA–protein interactions in living cells
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5 months
A modular dCas9-based recruitment platform for combinatorial epigenome editing
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An atlas of posttranslational modifications on RNA binding proteins
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3 years
The nuclear periphery is a scaffold for tissue-specific enhancers
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2 years
Breakthrough**RNase H is an exo- and endoribonuclease with asymmetric directionality, depending on the binding mode to the structural variants of RNA:DNA hybrids
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3 months
EquiPNAS: improved protein–nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks
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2 years
Breakthrough**AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
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3 months
The levels of p53 govern the hierarchy of DNA damage tolerance pathway usage
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1 year
Breakthrough**Negatively charged, intrinsically disordered regions can accelerate target search by DNA-binding proteins
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2 years
Breakthrough**A phage parasite deploys a nicking nuclease effector to inhibit viral host replication
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2 years
Deficiency of ribosomal proteins reshapes the transcriptional and translational landscape in human cells
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2 years
Breakthrough**Membrane-dependent relief of translation elongation arrest on pseudouridine- and N1-methyl-pseudouridine-modified mRNAs
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2 years
Critical review**Reexamining assumptions about miRNA-guided gene silencing
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1 year
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution
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Nucleic Acids Res
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4 months
Editorial**Fifty years of Nucleic Acids Research
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Fifty years of Nucleic Acids Research

This month marks the 50th anniversary of Nucleic Acids Research (‘NAR’). Led by a team of three founding editors (Richard T. Walker and A. Stanley Jones at

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2 years
CRISPR-RNAa: targeted activation of translation using dCas13 fusions to translation initiation factors
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2 years
Inert Pepper aptamer-mediated endogenous mRNA recognition and imaging in living cells
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Nucleic Acids Res
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6 months
Decoding dissociation of sequence-specific protein–DNA complexes with non-equilibrium simulations
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9 months
Breakthrough**Genome-wide mapping of i-motifs reveals their association with transcription regulation in live human cells
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9 months
Capturing heterogeneous conformers of cobalamin riboswitch by cryo-EM
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1 year
Fitness functions for RNA structure design
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1 year
When translation elongation is impaired, the mRNA is uniformly destabilized by the RNA degradosome, while the concentration of mRNA is altered along the molecule
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3 months
Breakthrough**Gene-to-gene coordinated regulation of transcription and alternative splicing by 3D chromatin remodeling upon NF-κB activation @f_mortreux @Lyon_LBMC @Inserm @ENSdeLyon
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2 years
Repurposing CRISPR RNA-guided integrases system for one-step, efficient genomic integration of ultra-long DNA sequences
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3 years
Breakthrough**Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences
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1 year
RNAcanvas: interactive drawing and exploration of nucleic acid structures
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1 year
The nucleosome unwrapping free energy landscape defines distinct regions of transcription factor accessibility and kinetics
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9 months
Crystal structure of a cap-independent translation enhancer RNA
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1 year
Targeted bacterial conjugation mediated by synthetic cell-to-cell adhesions
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3 years
Breakthrough**Directed evolution of orthogonal RNA–RBP pairs through library-vs-library in vitro selection
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3 years
Breakthrough**Adenovirus prevents dsRNA formation by promoting efficient splicing of viral RNA
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1 year
Versatile strategy using vaccinia virus-capping enzyme to synthesize functional 5′ cap-modified mRNAs
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2 years
ProteinsPlus: a comprehensive collection of web-based molecular modeling tools
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2 years
Breakthrough**RNA marker modifications reveal the necessity for rigorous preparation protocols to avoid artifacts in epitranscriptomic analysis
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3 years
Breakthrough**Pathways of thymidine hypermodification
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3 years
Small circular interfering RNAs (sciRNAs) as a potent therapeutic platform for gene-silencing
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5 months
Quantitative, titratable and high-throughput reporter assays to measure DNA double strand break repair activity in cells
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1 year
Breakthrough**DeepBIO: an automated and interpretable deep-learning platform for high-throughput biological sequence prediction, functional annotation and visualization analysis
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2 years
DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases
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1 year
Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin
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1 year
Methods**Synthetic circular RNA switches and circuits that control protein expression in mammalian cells
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11 months
Breakthrough**Enhanced nonenzymatic RNA copying with in-situ activation of short oligonucleotides
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1 year
Breakthrough**Structure, substrate binding and activity of a unique AAA+ protein: the BrxL phage restriction factor
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3 years
PE-Designer and PE-Analyzer: web-based design and analysis tools for CRISPR prime editing
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1 year
Breakthrough**Cryo-EM structure of the fully assembled Elongator complex @GlattSebastian @MCB_UJ @Struc_biol_PL @SOLARIS_science @JagiellonskiUni
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Nucleic Acids Res
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9 months
Click display: a rapid and efficient in vitro protein display method for directed evolution
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3 years
Discovery of a pre-mRNA structural scaffold as a contributor to the mammalian splicing code
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2 years
Inducible directed evolution of complex phenotypes in bacteria
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3 years
Breakthrough**Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy
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1 year
Restoration of mitochondrial function through activation of hypomodified tRNAs with pathogenic mutations associated with mitochondrial diseases
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1 year
Breakthrough**Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation
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7 months
Nobel Prize winning science at NAR**Incorporation of pseudouridine into mRNA enhances translation by diminishing PKR activation @kkariko @weissmanlab Congratulations to Katalin Karikó and Drew Weissman, fully deserved!
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Incorporation of pseudouridine into mRNA enhances translation by diminishing PKR activation

Abstract. Previous studies have shown that the translation level of in vitro transcribed messenger RNA (mRNA) is enhanced when its uridines are replaced wi

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@NobelPrize
The Nobel Prize
@NobelPrize
7 months
BREAKING NEWS The 2023 #NobelPrize in Physiology or Medicine has been awarded to Katalin Karikó and Drew Weissman for their discoveries concerning nucleoside base modifications that enabled the development of effective mRNA vaccines against COVID-19.
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4 months
Less-is-more: selecting transcription factor binding regions informative
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1 year
Breakthrough**Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart
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2 years
Breakthrough**De novo sequencing, diploid assembly, and annotation of the black carpenter ant, Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing
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11 months
Cas1–Cas2 physically and functionally interacts with DnaK to modulate CRISPR Adaptation
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2 years
Breakthrough**Tissue-specific regulation of translational readthrough tunes functions of the traffic jam transcription factor
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6 months
The proofreading exonuclease of leading-strand DNA polymerase epsilon prevents replication fork collapse at broken template strands
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2 years
G-quadruplex-guided RNA engineering to modulate CRISPR-based genomic regulation
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2 years
CRISPR–Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells
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8 months
Breakthrough**Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome
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2 years
DNA methylation cues in nucleosome geometry, stability and unwrapping
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2 years
Ribocentre: a database of ribozymes
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8 months
A comprehensive analysis of translational misdecoding pattern and its implication on genetic code evolution
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3 years
Breakthrough**Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements
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2 years
Synthesis of point-modified mRNA
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8 months
Stability and mechanism of threose nucleic acid toward acid-mediated degradation
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1 year
Breakthrough**The FANCC–FANCE–FANCF complex is evolutionarily conserved and regulates meiotic recombination
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4 years
New technique**Single molecule mass photometry of nucleic acids
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10 months
G-quadruplex DNA contributes to RNA polymerase II-mediated 3D chromatin architecture
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7 months
High-resolution structure of stem-loop 4 from the 5′-UTR of SARS-CoV-2 solved by solution state NMR
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4 years
Crystal structure of an atypical cobalamin riboswitch reveals RNA structural adaptability as basis for promiscuous ligand binding
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3 months
Single-cell evidence for plasmid addiction mediated by toxin–antitoxin systems
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3 years
An RNA tagging approach for system-wide RNA-binding proteome profiling and dynamics investigation upon transcription inhibition
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4 years
Breakthrough** 5′-fluoro(di)phosphate-labeled oligonucleotides are versatile molecular probes for studying nucleic acid secondary structure and interactions by 19F NMR
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3 years
Breakthrough**Engineering large-scale chromosomal deletions by CRISPR-Cas9
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1 year
A large-scale benchmark study of tools for the classification of protein-coding and non-coding RNAs
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2 years
Twisting DNA by salt
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9 months
Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide
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11 months
Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS
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5 months
Breakthrough**tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut @puglisilab @jeffery_tharp @SergeyVMelniko1 @trushar_7 @NatalieKrahn13 @YaleMBB @CryoStanford
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1 year
The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection now available online
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6 months
In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells
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2 years
Breakthrough**Using a quadruplet codon to expand the genetic code of an animal
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6 months
Functionally comparable but evolutionarily distinct nucleotide-targeting effectors help identify conserved paradigms across diverse immune systems
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1 year
Protection of the human gene research literature from contract cheating organizations known as research paper mills
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1 year
Breakthrough**CRISPR-Cas9 recognition of enzymatically synthesized base-modified nucleic acids
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1 year
Crystal structures and fragment screening of SARS-CoV-2 NSP14 reveal details of exoribonuclease activation and mRNA capping and provide starting points for antiviral drug development
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8 months
When will RNA get its AlphaFold moment?
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6 months
Synthesis of peptide–siRNA conjugates via internal sulfonylphosphoramidate modifications and evaluation of their in vitro activity
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3 years
The effect of hairpin loop on the structure and gene expression activity of the long-loop G-quadruplex
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3 years
Breakthrough** Tandem RNA binding sites induce self-association of the stress granule marker protein TIA-1
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2 years
Breakthrough**Construction of a cross-species cell landscape at single-cell level
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2 years
Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures
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3 years
Survey and summary**G-Quadruplexes as pathogenic drivers in neurodegenerative disorders
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5 months
Quantification of all 12 canonical ribonucleotides by real-time fluorogenic in vitro transcription
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4 years
Duplex formation in a G-quadruplex bulge
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1 year
Mechanism of strand displacement DNA synthesis by the coordinated activities of human mitochondrial DNA polymerase and SSB
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