Subject: New issue: Nucleic Acids Research, Volume 53, Issue 12, 8 July 2025

Volume 53, Issue 12, 8 July 2025

View issue

In 2005 Nucleic Acids Research (NAR) transitioned from a subscription-based publishing model to an open access model. Now, 20 years later, NAR proudly stands as a leading journal in the field of biological sciences, providing barrier-free access to groundbreaking research.

To celebrate this milestone, we have created collection featuring the most cited paper (from standard article types) from each year since 2005. This collection showcases the research excellence that NAR fosters and demonstrates the impact of open access publishing.

Browse the papers

NAR Breakthrough Article

Cells resist starvation through a nutrient stress splice switch

Julie Parenteau and others

Critical Reviews and Perspectives

What makes a small RNA work?

Saleh Alquethamy and others

A comprehensive review of spatial transcriptomics data alignment and integration

Muiz Khan and others

Chemical Biology and Nucleic Acid Chemistry

A rational engineering strategy for structural dynamics modulation enables target specificity enhancement of the Cas9 nuclease

Keewon Sung and others

Systematic analysis of siRNA and mRNA features impacting fully chemically modified siRNA efficacy

Sarah M Davis and others

PAM-free hairpin target binding activates trans-cleavage activity of Cas12a

Xiaolong Li and others

Mechanistic studies of small molecule ligands selective to RNA single G bulges

Shalakha Hegde and others

Pyridine-bis(benzimidazole) induces DNA damage at G-quadruplex loci and promotes synthetic lethality with DNA repair inhibition

Jiangyu Yan and others

i-Motif DNA molecular beacon for microRNA detection

Tengshuo Luo and others

Twisting tetraplex DNA: A strand dynamics regulating i-motif function in diverse molecular crowding environments

Shuntaro Takahashi and others

Manipulating DNA and RNA structures via click-to-release caged nucleic acids for biological and biomedical applications

Shiyu Wang and others

Computational Biology

Building a neural network model to define DNA sequence specificity in V(D)J recombination

Justin C Harris and others

Characterization of bacterial intrinsic transcription terminators identified with TERMITe'a novel method for comprehensive analysis of Term-seq data

Jan Grzegorz KosiÅ"ski and others

Gene Regulation, Chromatin and Epigenetics

The lincRNA Pantr1 is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1

Fabian Gather and others

Oxidative stress elicited by phage infection induces Staphylococcal type III-A CRISPR'Cas system

Yang Li and others

Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers

Ning Qing Liu and others

The quantitative impact of 3²UTRs on gene expression

Jessica D West and others

Differential oligomerization regulates PHF13 chromatin affinity and function

Francesca Rossi and others

EBNA leader protein orchestrates chromatin architecture remodeling during Epstein-Barr virus-induced B cell transformation

Davide Maestri and others

CTCF binding landscape is shaped by the epigenetic state of the N-terminal nucleosome in relation to CTCF motif orientation

Md Tajmul and others

Synergistic DNA and RNA binding of the Hox transcription factor Ultrabithorax coordinates splicing and shapes in vivo homeotic functions

Constanza Blanco and others

Genome Integrity, Repair and Replication

USP37 counteracts HLTF to protect damaged replication forks and promote survival of BRCA1-deficient cells and PARP inhibitor resistance

Mengfan Tang and others

The DNA-PKcs/JNK/p53 pathway underlies changes in cell fate decision toward death during DNA replication catastrophe

Jinal A Patel and others

Loss of DHX36/G4R1, a G4 resolvase, drives genome instability and regulates innate immune gene expression in cancer cells

Anna R Bartosik and others

The inflammasome sensor NLRP3 interacts with REV7 to maintain genome integrity through homologous recombination

Delphine Burlet and others

TRIP12's role in the governance of DNA polymerase beta involvement in DNA damage response and repair

Burcu Inanc and others

Depletion of BRD9-mediated R-loop accumulation inhibits leukemia cell growth via transcription'replication conflict

Seo Yun Lee and others

Genomics

The origin of mirror repeats in the human genome

Ryan McGinty and others

Molecular and Structural Biology

Catalytic-state structure of Candidatus Hydrogenedentes Cas12b revealed by cryo-EM studies

Ye Li and others

PglZ from Type I BREX phage defence systems is a metal-dependent nuclease that forms a sub-complex with BrxB

Jennifer J Readshaw and others

Identification of a minimal Alu domain required for retrotransposition

John B Moldovan and others

Mutational analysis of the F plasmid partitioning protein ParA reveals residues required for oligomerization and plasmid maintenance

Nivedita Mitra and others

Unique conformational dynamics and protein recognition of A-to-I hyper-edited dsRNA

Christoph MÃ¼ller-Hermes and others

Structural and functional studies of the main replication protein NS1 of human parvovirus B19

Yixi Zhang and others

An archaeal chronic virus escapes the immunity of prokaryotic Argonaute

Yu Chen and others

G-quadruplex topologies determine the functional outcome of guanine-rich bioactive oligonucleotides

Prakash Kharel and others

Rewiring of cell morphology by Small protein B enhances stress tolerance and colonization in Aeromonas veronii under adverse conditions

Zucheng Wang and others

Structural heterogeneity and dynamics in the apical stem loop of s2m from SARS-CoV-2 Delta by an integrative NMR spectroscopy and MD simulation approach

Maria A Wirtz Martin and others

Tiny but multi-stable: four distinct conformational states govern the ligand-free state of the preQ₁ riboswitch from a thermophilic bacterium

Stefanie RÃ¼ckriegel and others

Significance of the CTP-binding motif for the interactions of S. coelicolor ParB with DNA, chromosome segregation, and sporogenic hyphal growth

Justyna Szymczak and others

DnaB and DciA: mechanisms of helicase loading and translocation on ssDNA

Nicholas Gao and others

Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer

Shea H Siwik and others

Mechanistic insights into direct DNA and RNA strand transfer and dynamic protein exchange of SSB and RPA

Tapas Paul and others

Structural basis of a dual-function type II-B CRISPR'Cas9

Grace N Hibshman and David W Taylor

Elucidation of multiple high-resolution states of human MutSbeta by cryo-EM reveals interplay between ATP/ADP binding and heteroduplex DNA recognition

Jung-Hoon Lee and others

Nucleic Acid Enzymes

A four-in-one replicase integrating key enzymatic activities for DNA replication

Yuxin Zhang and others

In vitro programmable DNA cleavage by a eukaryotic Argonaute

Guangbo Yan and others

Nonredundant roles of topoisomerase 2alpha and 2beta in the cytosolic replication of vaccinia virus

Ilaria Dalla Rosa and others

Directed assembly of single-stranded DNA fragments for data storage via protein-free catalytic splint ligation

Gemma Mendonsa and others

CARF-dependent preferential RNA cleavage by Csm6 increases drug susceptibility of mycobacteria

Wenping Wei and others

Nucleic Acid Therapeutics

An engineered glutamic acid tRNA for efficient suppression of pathogenic nonsense mutations

Caitlin Specht and others

Novel telomere-targeting dual-pharmacophore dinucleotide prodrugs for anticancer therapy

Ilgen Mender and others

Elucidating brain transport pathways and cell type-dependent gene silencing of a durable lipid'siRNA conjugate administered into cerebrospinal fluid

Alexander G Sorets and others

RNA and RNA-protein complexes

Analysis of natural structures and chemical mapping data reveals local stability compensation in RNA

Robert L Cornwell-Arquitt and others

ERH regulates type II interferon immune signaling through post-transcriptional regulation of JAK2 mRNA

Adrian Soderholm and others

A-to-I mRNA editing in bacteria can affect protein sequence, disulfide bond formation, and function

Liron Didi and others

Structural integrity and side-chain interaction at the loop region of the bridge helix modulate Cas9 substrate discrimination

Difei Wu and others

Mutation-driven RRE stem-loop II conformational change induces HIV-1 nuclear export dysfunction

Manju Ojha and others

The Epstein-Barr virus EBNA1 protein binds to G-quadruplexes in its own mRNA hence controlling its expression and immune evasion of the virus

Van-Trang Dinh and others

Synthetic Biology and Bioengineering

Switchable RNA motifs for dynamic transcriptional control of RNA condensates

Anli A Tang and others

A solid-phase enzymatic synthesis platform for the facile production of 2²-fluoroarabinonucleic acid (FANA) and chimeric XNA oligonucleotides using an evolved XNA polymerase

Binliang Zhang and others

SELECT: high-precision genome editing strategy via integration of CRISPR'Cas and DNA damage response for cross-species applications

Xiaohang Liu and others

Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research

Jeannette Gebel and others

Ligation-induced DNA self-assembly

Qishu Zhang and others

De novo design of insulated cis-regulatory elements based on deep learning-predicted fitness landscape

Haochen Wang and others

Methods

Linkage-based ortholog refinement in bacterial pangenomes with CLARC

Indra GonzÃ¡lez Ojeda and others

UniClo: scarless hierarchical DNA assembly without sequence constraint

Carol N Flores-FernÃ¡ndez and others

Unwinding process of DNA/RNA quadruplexes by proteins under label-free nanopore monitoring

Meili Ren and others

MEBOCOST maps metabolite-mediated intercellular communications using single-cell RNA-seq

Rongbin Zheng and others

A high-throughput single-molecule platform to study DNA supercoiling effect on protein'DNA interactions

Huijin Lee and others

Identification and correction of time-series transcriptomic anomalies

Sophia A Campione and others

Novel enzyme-based reduced representation method for DNA methylation profiling with low inputs

Qianli Liu and others

Characterizing DNA recognition preferences of transcription factors using global couplings and high-throughput sequencing

Qin Zhou and others

Toward optimizing diversifying base editors for high-throughput mutational scanning studies

Carley I Schwartz and others

Corrections

Correction to ˜Novel alternative ribonucleotide excision repair pathways in human cells by DDX3X and specialized DNA polymerases'

Correction to ˜Pathogen-encoded Rum DNA polymerase drives rapid bacterial drug resistance'

Correction to ˜Delineation of pentatricopeptide repeat codes for target RNA prediction'

Correction to ˜Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome'

Correction to ˜GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome'

This email is intended for bionet@evol.mcmaster.ca.