Works matching IS 03051048 AND DT 2025 AND VI 53 AND IP 3

Results: 67

A gate-clamp mechanism for ssDNA translocation by DdmD in Vibrio cholerae plasmid defense.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf064

By:

Li, Ruoyu;
Liu, Yusong;
Gao, Haishan;
Lin, Zhonghui

Publication type:

Article

Antagonistic roles by the conserved nuclear poly(A)-binding proteins PABPN1 and ZC3H14 in nuclear RNA surveillance.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf060

By:

Latour, Mélodie;
Kwiatek, Lauren;
Landry-Voyer, Anne-Marie;
Bachand, François

Publication type:

Article

Structural and mechanistic insights into the activation of a short prokaryotic argonaute system from archaeon Sulfolobus islandicus.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf059

By:

Dai, Zhikang;
Chen, Yu;
Guan, Zeyuan;
Chen, Xueting;
Tan, Keyi;
Yang, Kaiyue;
Yan, Xuhui;
Liu, Yidong;
Gong, Zhou;
Han, Wenyuan;
Zou, Tingting

Publication type:

Article

The membrane-targeting-sequence motif is required for exhibition of recessive resurrection in Escherichia coli RNase E.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf055

By:

Basak, Papri;
Ekka, Manjula;
Pandiyan, Apuratha;
Tandon, Smriti;
Gowrishankar, Jayaraman

Publication type:

Article

Identification of an enzyme with strong single-stranded DNA ligation activity and its application for sequencing.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf054

By:

Miura, Fumihito;
Shibata, Yukiko;
Miura, Miki;
Inatomi, Kazune;
Suzuki, Yutaka;
Ito, Takashi

Publication type:

Article

The short conserved region-2 of LARP4 interacts with ribosome-associated RACK1 and promotes translation.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf053

By:

Ranjan, Amitabh;
Mattijssen, Sandy;
Charlly, Nithin;
Gallardo, Isabel Cruz;
Pitman, Leah F;
Coleman, Jennifer C;
Conte, Maria R;
Maraia, Richard J

Publication type:

Article

Local structural dynamics of Rad51 protomers revealed by cryo-electron microscopy of Rad51-ssDNA filaments.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf052

By:

Liu, Jie;
Gore, Steven K;
Heyer, Wolf-Dietrich

Publication type:

Article

An evolved, orthogonal ssDNA generator for targeted hypermutation of multiple genomic loci.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf051

By:

Chu, Weiran;
Tian, Rongzhen;
Guo, Yaxin;
Wu, Yaokang;
Rehm, Fabian B H;
Liu, Long;
Li, Jianghua;
Du, Guocheng;
Chen, Jian;
Liu, Yanfeng

Publication type:

Article

Large serine integrases utilise scavenged phage proteins as directionality cofactors.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf050

By:

Alsaleh, Abdulrazak;
Holland, Alexandria;
Shin, Heewhan;
Reyes, Tania Pena;
Baksh, Aron;
Taiwo-Aiyerin, Oluwateniola T;
Pigli, Ying;
Rice, Phoebe A;
Olorunniji, Femi J

Publication type:

Article

Site-specific free energy surface parameters from single-molecule fluorescence measurements of exciton-coupled (iCy3)<sub>2</sub> dimer probes positioned at DNA replication fork junctions.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf047

By:

Maurer, Jack;
Albrecht, Claire S;
von Hippel, Peter H;
Marcus, Andrew H

Publication type:

Article

Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf046

By:

Bibel, Brianna;
Raskar, Tushar;
Couvillion, Mary;
Lee, Muhoon;
Kleinman, Jordan I;
Takeuchi-Tomita, Nono;
Churchman, L Stirling;
Fraser, James S;
Fujimori, Danica Galonić

Publication type:

Article

zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf045

By:

Salamzade, Rauf;
Tran, Patricia Q;
Martin, Cody;
Manson, Abigail L;
Gilmore, Michael S;
Earl, Ashlee M;
Anantharaman, Karthik;
Kalan, Lindsay R

Publication type:

Article

mRNA-LM: full-length integrated SLM for mRNA analysis.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf044

By:

Li, Sizhen;
Noroozizadeh, Shahriar;
Moayedpour, Saeed;
Kogler-Anele, Lorenzo;
Xue, Zexin;
Zheng, Dinghai;
Montoya, Fernando Ulloa;
Agarwal, Vikram;
Bar-Joseph, Ziv;
Jager, Sven

Publication type:

Article

Early events in G-quadruplex folding captured by time-resolved small-angle X-ray scattering.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf043

By:

Monsen, Robert C;
Sabo, T Michael;
Gray, Robert;
Hopkins, Jesse B;
Chaires, Jonathan B

Publication type:

Article

G-quadruplex structures in 16S rRNA regions correlate with thermal adaptation in prokaryotes.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf042

By:

Lyu, Bo;
Niu, Kangkang;
Anderson, Deborah;
Feng, Qili;
Song, Qisheng

Publication type:

Article

Inhibition of HMGA2 binding to AT-rich DNA by its negatively charged C-terminus.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf035

By:

Su, Linjia;
Deng, Zifang;
Santos-Fernandez, Miguel;
Jeanne Dit Fouque, Kevin;
Chapagain, Prem P;
Chambers, Jeremy W;
Fernandez-Lima, Francisco;
Leng, Fenfei

Publication type:

Article

Direct repeat region 3′ end modifications regulate Cas12a activity and expand its applications.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf040

By:

Zhang, Wei;
Zhong, Yinyin;
Wang, Jiaqi;
Zou, Guangrong;
Chen, Qiaozhen;
Liu, Chaoxing

Publication type:

Article

RNA G-quadruplex structure-based PROTACs for targeted DHX36 protein degradation and gene activity modulation in mammalian cells.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf039

By:

Zhang, Kun;
Nie, Qichang;
Li, Maolin;
Chen, Xiaona;
Zhong, Liting;
Dai, Tianle;
Guo, Xiaofan;
Zhao, Haizhou;
Lau, Terrence Chi-Kong;
Wang, Huating;
Chen, Shuo-Bin;
Kwok, Chun Kit

Publication type:

Article

Measuring XNA polymerase fidelity in a hydrogel particle format.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf038

By:

Medina, Esau L;
Chaput, John C

Publication type:

Article

The ortholog of human DNAJC9 promotes histone H3–H4 degradation and is counteracted by Asf1 in fission yeast.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf036

By:

Ding, Yan;
Li, Jun;
Jiang, He-Li;
Suo, Fang;
Shao, Guang-Can;
Zhang, Xiao-Ran;
Dong, Meng-Qiu;
Liu, Chao-Pei;
Xu, Rui-Ming;
Du, Li-Lin

Publication type:

Article

Two temperature-responsive RNAs act in concert: the small RNA CyaR and the mRNA ompX.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf041

By:

Guanzon, David A;
Pienkoß, Stephan;
Brandenburg, Vivian B;
Röder, Jennifer;
Scheller, Daniel;
Dietze, Alisa;
Wimbert, Andrea;
Twittenhoff, Christian;
Narberhaus, Franz

Publication type:

Article

A novel ADP-directed chaperone function facilitates the ATP-driven motor activity of SARS-CoV helicase.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf034

By:

Yu, Jeongmin;
Im, Hyeryeon;
Cho, HyeokJin;
Jeon, Yongmoon;
Lee, Jong-Bong;
Lee, Gwangrog

Publication type:

Article

Cryo-EM structure of AAV2 Rep68 bound to integration site AAVS1: insights into the mechanism of DNA melting.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf033

By:

Jaiswal, Rahul;
Braud, Brandon;
Hernandez-Ramirez, Karen C;
Santosh, Vishaka;
Washington, Alexander;
Escalante, Carlos R

Publication type:

Article

Telomemore enables single-cell analysis of cell cycle and chromatin condensation.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf031

By:

Yakovenko, Iryna;
Mihai, Ionut Sebastian;
Selinger, Martin;
Rosenbaum, William;
Dernstedt, Andy;
Gröning, Remigius;
Trygg, Johan;
Carroll, Laura;
Forsell, Mattias;
Henriksson, Johan

Publication type:

Article

A high-resolution view of RNA endonuclease cleavage in Bacillus subtilis.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf030

By:

Taggart, James C;
Dierksheide, Kathryn Julia;
LeBlanc, Hannah J;
Lalanne, Jean-Benoît;
Durand, Sylvain;
Braun, Frédérique;
Condon, Ciarán;
Li, Gene-Wei

Publication type:

Article

Editor's Note on 'MicroRNA-296 is enriched in cancer cells and downregulates p21WAF1 mRNA expression via interaction with its 3′ untranslated region'.

Published in:: 2025
Publication type:: Correction Notice

5′ terminal nucleotide determines the immunogenicity of IVT RNAs.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkae1252

By:

Wolczyk, Magdalena;
Szymanski, Jacek;
Trus, Ivan;
Naz, Zara;
Tame, Tola;
Bolembach, Agnieszka;
Choudhury, Nila Roy;
Kasztelan, Karolina;
Rappsilber, Juri;
Dziembowski, Andrzej;
Michlewski, Gracjan

Publication type:

Article

Influenza A virus NS2 protein acts on vRNA-resident polymerase to drive the transcription to replication switch.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf027

By:

Zhang, Lei;
Yang, Qiuxian;
Shao, Yuekun;
Ding, Shenyang;
Guo, Jiamei;
Gao, George F;
Deng, Tao

Publication type:

Article

Correction to 'ECBD: European chemical biology database'.

Published in:: 2025
Publication type:: Correction Notice

Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf025

By:

Chernigovskaya, Maria;
Pavlović, Milena;
Kanduri, Chakravarthi;
Gielis, Sofie;
Robert, Philippe A;
Scheffer, Lonneke;
Slabodkin, Andrei;
Haff, Ingrid Hobæk;
Meysman, Pieter;
Yaari, Gur;
Sandve, Geir Kjetil;
Greiff, Victor

Publication type:

Article

The ATPase activity of yeast chromosome axis protein Hop1 affects the frequency of meiotic crossovers.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkae1264

By:

Dhyani, Kshitiza M;
Dash, Suman;
Joshi, Sameer;
Garg, Aditi;
Pal, Debnath;
Nishant, Koodali T;
Muniyappa, Kalappa

Publication type:

Article

methylGrapher: genome-graph-based processing of DNA methylation data from whole genome bisulfite sequencing.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf028

By:

Zhang, Wenjin;
Macias-Velasco, Juan F;
Zhuo, Xiaoyu;
Belter, Edward A;
Tomlinson, Chad;
Garza, John;
Tekkey, Nina;
Li, Daofeng;
Wang, Ting

Publication type:

Article

Genome-wide identification of bacterial genes contributing to nucleus-forming jumbo phage infection.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkae1194

By:

Harding, Kate R;
Malone, Lucia M;
Kyte, Natalie A P;
Jackson, Simon A;
Smith, Leah M;
Fineran, Peter C

Publication type:

Article

Improving the generalization of protein expression models with mechanistic sequence information.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf020

By:

Shen, Yuxin;
Kudla, Grzegorz;
Oyarzún, Diego A

Publication type:

Article

Correction to 'DNA target binding-induced pre-crRNA processing in type II and V CRISPR-Cas systems'.

Published in:: 2025
Publication type:: Correction Notice

Diversity and evolution of viroids and viroid-like agents with circular RNA genomes revealed by metatranscriptome mining.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkae1278

By:

Koonin, Eugene V;
Lee, Benjamin D

Publication type:

Article

Fam170a deficiency causes male infertility by impairing histone-to-protamine exchange during mouse spermiogenesis.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf023

By:

Cheng, Jinmei;
Gu, Yimin;
Wang, Yueming;
Xun, Junjie;
Wang, Guishuan;
Wang, Yu;
Wang, Jianyu;
Li, Yinchuan;
Sun, Fei

Publication type:

Article

Methyl-dependent auto-regulation of the DNA N<sup>6</sup>-adenine methyltransferase AMT1 in the unicellular eukaryote Tetrahymena thermophila.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf022

By:

Duan, Lili;
Li, Haicheng;
Ju, Aili;
Zhang, Zhe;
Niu, Junhua;
Zhang, Yumiao;
Diao, Jinghan;
Liu, Yongqiang;
Song, Ni;
Ma, Honggang;
Kataoka, Kensuke;
Gao, Shan;
Wang, Yuanyuan

Publication type:

Article

Selection of initiator tRNA and start codon by mammalian mitochondrial initiation factor 3 in leaderless mRNA translation.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf021

By:

Lee, Muhoon;
Wakigawa, Taisei;
Jia, Qimin;
Liu, Chang;
Huang, Ruiyuan;
Huang, Shuai;
Nagao, Asuteka;
Suzuki, Tsutomu;
Tomita, Kozo;
Iwasaki, Shintaro;
Takeuchi-Tomita, Nono

Publication type:

Article

Transcriptome-scale analysis uncovers conserved residues in the hydrophobic core of the bacterial RNA chaperone Hfq required for small regulatory RNA stability.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf019

By:

McQuail, Josh;
Krepl, Miroslav;
Katsuya-Gaviria, Kai;
Tabib-Salazar, Aline;
Burchell, Lynn;
Bischler, Thorsten;
Gräfenhan, Tom;
Brear, Paul;
Šponer, Jiří;
Luisi, Ben F;
Wigneshweraraj, Sivaramesh

Publication type:

Article

Proximity-activated guide RNA of CRISPR–Cas12a for programmable diagnostic detection and gene regulation.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf017

By:

Hu, Zhian;
Ling, Shen;
Duan, Jialin;
Yu, Zixiao;
Che, Yanfei;
Wang, Song;
Zhang, Sichun;
Zhang, Xinrong;
Li, Zhengping

Publication type:

Article

Genomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at super-enhancers.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf015

By:

Wang, Shengyuan;
Wang, Zhenjia;
Zang, Chongzhi

Publication type:

Article

Transcription near arrested DNA replication forks triggers ribosomal DNA copy number changes.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf014

By:

Sasaki, Mariko;
Kobayashi, Takehiko

Publication type:

Article

AAV vector transduction restriction and attenuated toxicity in hESCs via a rationally designed inverted terminal repeat.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf013

By:

Song, Liujiang;
Hasegawa, Tomoko;
Brown, Nolan J;
Bower, Jacquelyn J;
Samulski, Richard J;
Hirsch, Matthew L

Publication type:

Article

ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf009

By:

Park, Joon Young;
Jang, Minchang;
Choi, Eunna;
Lee, Sang-Mok;
Bang, Ina;
Woo, Jihoon;
Kim, Seonggyu;
Lee, Eun-Jin;
Kim, Donghyuk

Publication type:

Article

Chromatin remodeler CHD4 establishes chromatin states required for ovarian reserve formation, maintenance and male germ cell survival.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf008

By:

Munakata, Yasuhisa;
Hu, Mengwen;
Kitamura, Yuka;
Dani, Raissa G;
Bynder, Adam L;
Fritz, Amelia S;
Schultz, Richard M;
Namekawa, Satoshi H

Publication type:

Article

Dual DNA replication modes: varying fork speeds and initiation rates within the spatial replication program in Xenopus.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf007

By:

Ciardo, Diletta;
Haccard, Olivier;
de Carli, Francesco;
Hyrien, Olivier;
Goldar, Arach;
Marheineke, Kathrin

Publication type:

Article

c-JUN: a chromatin repressor that limits mesoderm differentiation in human pluripotent stem cells.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkaf001

By:

Zhang, Ran;
Li, Guihuan;
Zhang, Qi;
Wang, Zhenhua;
Xiang, Dan;
Zhang, Xiaofei;
Chen, Jiekai;
Hutchins, Andrew P;
Qin, Dajiang;
Su, Huanxing;
Pei, Duanqing;
Li, Dongwei

Publication type:

Article

WBSCR16 is essential for mitochondrial 16S rRNA processing in mammals.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkae1325

By:

Zhang, Shengjie;
Dong, Zi;
Feng, Yang;
Guo, Wei;
Zhang, Chen;
Shi, Yifan;
Zhao, Zhiyun;
Wang, Jiqiu;
Ning, Guang;
Huang, Guorui

Publication type:

Article

Neutrophil extracellular traps have active DNAzymes that promote bactericidal activity.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 3, p. 1, doi. 10.1093/nar/gkae1262

By:

Ku, Ti-Hsuan;
Ram-Mohan, Nikhil;
Zudock, Elizabeth J;
Abe, Ryuichiro;
Yang, Samuel

Publication type:

Article