Subject: New issue: Nucleic Acids Research, Volume 53, Issue 20, 11 November 2025

Volume 53, Issue 20, 11 November 2025

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Critical Reviews and Perspectives

From liquid-phase synthesis to chemical ligation: preparation of oligonucleotides and their backbone analogs in solution

Pasi Virta

Histone PARylation factor 1: a review of its role in the DNA damage response

Johannes Rudolph and Karolin Luger

Chemical Biology and Nucleic Acid Chemistry

The Zuo1 C-terminal domain stabilizes DNA guanosine quadruplex (G4) structures located on Chromosome IX in Saccharomyces cerevisiae

Ines Burkhart and others

Affinity-selected peptide ligands specifically bind i-motif DNA and modulate c-Myc gene expression

Dilek Guneri and others

Computational Biology

Near-cognate tRNAs dominate codon decoding times in simulated ribosomes

Fabio Hedayioglu and others

Data Resources and Analyses

Nucleosome context regulates chromatin reader preference

Matthew R Marunde and others

Transcriptional regulatory networks of the human gut symbiont Bacteroides thetaiotaomicron are uncovered using machine learning

Kangsan Kim and others

Gene Regulation, Chromatin and Epigenetics

Cyclic-di-GMP interferes with DNA-MucR-DNA bridging to derepress genes targeted by the xenogeneic silencer MucR

Ning-Ning Liu and others

ERC accumulation depletes Sir2 from rDNA and induces cellular senescence by rDNA destabilization

Yoshio Yamamuro and others

Transcription factor 4 maintains endothelial cell identity by inhibiting endothelial to mesenchymal transition

Gaopeng Xian and others

The stringent response does not influence ribosome pausing in Bacillus subtilis

Yaozu Han and others

The Tip60 acetylome is a hallmark of the proliferative state in Drosophila

Zivkos Apostolou and others

Maf1 cooperates with progesterone receptor to repress RNA polymerase III transcription of select tRNAs

Jessica Finlay-Schultz and others

The harmonized activities of HER2'HER3 heterodimer and deacetylated FOXA1 evade hormone response by regulating FOXA1 chromatin binding

Shixiong Wang and others

Conserved facultative heterochromatin across cell types identify regulatory sequences underpinning cell identity and disease

Enakshi Sinniah and others

Genome Integrity, Repair and Replication

Nuclear poly(A)-binding protein and nucleolin utilize their RNA recognition motifs to read PAR chains

Leilei Shi and others

Chromatin context shapes DNA damage formation and nucleotide excision repair dynamics in Caenorhabditis elegans

Cansu Kose and others

Mei5'Sae3 stabilizes both active and inactive forms of Dmc1 filaments independently of its impact on ATP hydrolysis

Yuen-Ling Chan and others

The stability and unfolding of DNA: RNA hybrid G-quadruplexes

Bo Zhang and others

Molecular and Structural Biology

Solution structure of the Sox2 DNA-binding domain reveals conformational selection in DNA binding

Andrea Orsetti and others

Pooled overexpression screening identifies PIPPI as a novel microprotein involved in the ER stress response

Lorenzo Lafranchi and others

Virion content unpacked by long-read sequencing: stress-induced changes in transmitted staphylococcal mobilome due to phage-satellite interactions

Tibor Botka and others

Structural and functional relevance of the DUF4352 domain in antiviral immunity and physiology of mycobacteria

Sandhya Sharma and Vikas Jain

Molecular mechanism of the type 2 defense-associated reverse transcriptase

Zhikun Liu and others

Organisation and dynamics of individual DNA segments in topologically complex genomes

Saminathan Ramakrishnan and others

Nucleic Acid Enzymes

Proteolytic cleavage activates the mitochondrial isoform of TOP3A

Direnis Erdinc and others

Photocontrolled dissociation and toehold-mediated strand displacement-based synergistic regulation of CRISPR-Cas12a

Jia-ni Wu and others

Nucleic Acid Therapeutics

Discovery of long-acting APOC3 siRNA for treating patients with hypertriglyceridemia

Thazha P Prakash and others

Improved targeted delivery of antisense oligonucleotide with an antibody mask

Hung-En Hsia and others

Modulating NLRP3 splicing with antisense oligonucleotides to control pathological inflammation

Roni Klein and others

Therapeutic antisense oligonucleotide mitigates retinal dysfunction in a pig model of CLN3 Batten disease

Matthew P Stratton and others

RNA and RNA-protein complexes

YsxC is a placeholder for ribosomal protein uL2 during 50S ribosomal subunit assembly

Amal Seffouh and others

An autism spectrum disorder mutation in Topoisomerase 3beta causes accumulation of covalent mRNA intermediates by disrupting metal binding within the zinc finger domain

Julia E Warrick and others

Synthetic Biology and Bioengineering

A versatile plug and play bacterial chassis based on a fast-growing Mycoplasma species

Jana InÃ¤bnit and others

Methods

Mirror-synchronized asymmetric CRISPR nanoswitch for single-molecule profiling of multiple circRNAs in different stages of breast cancer

Qian Liu and others

Synthetic closed-loop gene circuit for phenylalanine regulation

Silvia Galvan and others

Development of programmable RNA imaging with RNA-guided GFP via click chemistry

Jun Nakamura and others

GRASP: a modular toolkit for building synthetic pentatricopeptide repeat RNA-binding proteins

Michael Dennis and others

Corrections

Correction to ˜MexR and NalD are pyocyanin-responsive transcriptional repressors of the efflux pump MexAB-OprM in Pseudomonas aeruginosa'

Correction to ˜PAM-interacting domain turn-helix 51 motifs can improve Cas9-SpRY activity'

Correction to ˜Comprehensive profiling of activity and specificity of RNA-guided transposons reveals opportunities to engineer improved variants'

Correction to ˜FASTKD5 processes mitochondrial pre-mRNAs at noncanonical cleavage site'

Correction to ˜The ParB-CTP cycle activates phase separation in bacterial DNA segregation'

Correction to ˜Investigating the origins of the mutational signatures in cancer'

Correction to ˜CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation'

Correction to ˜Fidelity, specialization, and evolution of Paramecium PolX DNA polymerases involved in programmed double-strand break DNA repair'

Correction to ˜DNA-protein Interactions at the Telomeric Repeats of Schizosaccharomyces Pombe'

Correction to ˜Enhanced or reversible RNA N6-methyladenosine editing by red/far-red light induction'

Correction to ˜Unleashing high trans-substrate cleavage kinetics of Cas12a for nucleic acid diagnostics'

Correction to ˜Deep learning guided programmable design of Escherichia coli core promoters from sequence architecture to strength control'

Editor's Note

Editor's Note on ˜R-loop-induced irreparable DNA damage evades checkpoint detection in the C. elegans germline'

Editor's Note on ˜Expanding the repertoire of DNA polymerase substrates: template-instructed incorporation of non-nucleoside triphosphate analogues by DNA polymerases beta and lambda '

Editor's Note on ˜The human insulin receptor mRNA contains a functional internal ribosome entry segment'

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