Works matching IS 03051048 AND DT 2022 AND VI 50 AND IP 2

Results: 47

Dissection of nanoconfinement and proximity effects on the binding events in DNA origami nanocavity.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 697, doi. 10.1093/nar/gkab1298

By:

Jonchhe, Sagun;
Pandey, Shankar;
Beneze, Christian;
Emura, Tomoko;
Sugiyama, Hiroshi;
Endo, Masayuki;
Mao, Hanbin

Publication type:

Article

"Bind, cleave and leave": multiple turnover catalysis of RNA cleavage by bulge–loop inducing supramolecular conjugates.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 651, doi. 10.1093/nar/gkab1273

By:

Amirloo, Bahareh;
Staroseletz, Yaroslav;
Yousaf, Sameen;
Clarke, David J;
Brown, Tom;
Aojula, Harmesh;
Zenkova, Marina A;
Bichenkova, Elena V

Publication type:

Article

Genomic landscape of single-stranded DNA gapped intermediates in Escherichia coli.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 937, doi. 10.1093/nar/gkab1269

By:

Pham, Phuong;
Shao, Yijun;
Cox, Michael M;
Goodman, Myron F

Publication type:

Article

Comprehensive analysis of prime editing outcomes in human embryonic stem cells.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 1187, doi. 10.1093/nar/gkab1295

By:

Habib, Omer;
Habib, Gizem;
Hwang, Gue-Ho;
Bae, Sangsu

Publication type:

Article

Ribosomal leaky scanning through a translated uORF requires eIF4G2.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 1111, doi. 10.1093/nar/gkab1286

By:

Smirnova, Victoria V;
Shestakova, Ekaterina D;
Nogina, Daria S;
Mishchenko, Polina A;
Prikazchikova, Tatiana A;
Zatsepin, Timofei S;
Kulakovskiy, Ivan V;
Shatsky, Ivan N;
Terenin, Ilya M

Publication type:

Article

HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. e10, doi. 10.1093/nar/gkab993

By:

Rashid, Fatema-Zahra M;
Mahlandt, Eike;
van der Vaart, Michiel;
Boer, Daphne E C;
Varela Alvarez, Monica;
Henneman, Bram;
Brocken, Daan J W;
Voskamp, Patrick;
Blok, Anneloes J;
Shimizu, Thomas S;
Meijer, Annemarie H;
Luijsterburg, Martijn S;
Goedhart, Joachim;
Crémazy, Frédéric G E;
Dame, Remus T

Publication type:

Article

High-Throughput-Methyl-Reading (HTMR) assay: a solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. e9, doi. 10.1093/nar/gkab989

By:

Xiao, Senhao;
Guo, Siqi;
Han, Jie;
Sun, Yanli;
Wang, Mingchen;
Chen, Yantao;
Fang, Xueyu;
Yang, Feng;
Mu, Yajuan;
Zhang, Liang;
Ding, Yiluan;
Zhang, Naixia;
Jiang, Hualiang;
Chen, Kaixian;
Zhao, Kehao;
Luo, Cheng;
Chen, Shijie

Publication type:

Article

Integration of single cell data by disentangled representation learning.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. e8, doi. 10.1093/nar/gkab978

By:

Guo, Tiantian;
Chen, Yang;
Shi, Minglei;
Li, Xiangyu;
Zhang, Michael Q

Publication type:

Article

scMRMA: single cell multiresolution marker-based annotation.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. e7, doi. 10.1093/nar/gkab931

By:

Li, Jia;
Sheng, Quanhu;
Shyr, Yu;
Liu, Qi

Publication type:

Article

Directed evolution of orthogonal RNA–RBP pairs through library-vs-library in vitro selection.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 601, doi. 10.1093/nar/gkab527

By:

Fukunaga, Keisuke;
Yokobayashi, Yohei

Publication type:

Article

Crystal structures of alphavirus nonstructural protein 4 (nsP4) reveal an intrinsically dynamic RNA-dependent RNA polymerase fold.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 1000, doi. 10.1093/nar/gkab1302

By:

Tan, Yaw Bia;
Lello, Laura Sandra;
Liu, Xin;
Law, Yee-Song;
Kang, Congbao;
Lescar, Julien;
Zheng, Jie;
Merits, Andres;
Luo, Dahai

Publication type:

Article

Structure–activity relationships at a nucleobase-stacking tryptophan required for chemomechanical coupling in the DNA resecting motor-nuclease AdnAB.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 952, doi. 10.1093/nar/gkab1270

By:

Warren, Garrett M;
Meir, Aviv;
Wang, Juncheng;
Patel, Dinshaw J;
Greene, Eric C;
Shuman, Stewart

Publication type:

Article

Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 820, doi. 10.1093/nar/gkab1268

By:

Ryu, Je-Kyung;
Rah, Sang-Hyun;
Janissen, Richard;
Kerssemakers, Jacob W J;
Bonato, Andrea;
Michieletto, Davide;
Dekker, Cees

Publication type:

Article

Editorial Expression of Concern on 'Protein kinase CK2 phosphorylation regulates the interaction of Kaposi's sarcoma-associated herpesvirus regulatory protein ORF57 with its multifunctional partner hnRNP K'.

Published in:: Nucleic Acids Research, 2022, v. 50, n. 2, p. 1200, doi. 10.1093/nar/gkab1294
Publication type:: Article

Correction to 'Fail-safe genetic codes designed to intrinsically contain engineered organisms'.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 1199, doi. 10.1093/nar/gkab1285

By:

Calles, Jonathan;
Justice, Isaac;
Brinkley, Detravious;
Garcia, Alexa;
Endy, Drew

Publication type:

Article

Correction to 'MoiRNAiFold: a novel tool for complex in silico RNA design'.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 1198, doi. 10.1093/nar/gkab1284

By:

Minuesa, Gerard;
Alsina, Cristina;
Garcia-Martin, Juan Antonio;
Oliveros, Juan Carlos;
Dotu, Ivan

Publication type:

Article

Nonalternating purine pyrimidine sequences can form stable left-handed DNA duplex by strong topological constraint.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 684, doi. 10.1093/nar/gkab1283

By:

Li, Lin;
Zhang, Yaping;
Ma, Wanzhi;
Chen, Hui;
Liu, Mengqin;
An, Ran;
Cheng, Bingxiao;
Liang, Xingguo

Publication type:

Article

nucleotide messenger (p)ppGpp is an anti-inducer of the purine synthesis transcription regulator PurR in Bacillus.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 847, doi. 10.1093/nar/gkab1281

By:

Anderson, Brent W;
Schumacher, Maria A;
Yang, Jin;
Turdiev, Asan;
Turdiev, Husan;
Schroeder, Jeremy W;
He, Qixiang;
Lee, Vincent T;
Brennan, Richard G;
Wang, Jue D

Publication type:

Article

Systematic characterization of short intronic splicing-regulatory elements in SMN2 pre-mRNA.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 731, doi. 10.1093/nar/gkab1280

By:

Gao, Yuan;
Lin, Kuan-Ting;
Jiang, Tao;
Yang, Yang;
Rahman, Mohammad A;
Gong, Shuaishuai;
Bai, Jialin;
Wang, Li;
Sun, Junjie;
Sheng, Lei;
Krainer, Adrian R;
Hua, Yimin

Publication type:

Article

Coronaviral RNA-methyltransferases: function, structure and inhibition.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 635, doi. 10.1093/nar/gkab1279

By:

Nencka, Radim;
Silhan, Jan;
Klima, Martin;
Otava, Tomas;
Kocek, Hugo;
Krafcikova, Petra;
Boura, Evzen

Publication type:

Article

Metallohelix vectors for efficient gene delivery via cationic DNA nanoparticles.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 674, doi. 10.1093/nar/gkab1277

By:

Malina, Jaroslav;
Kostrhunova, Hana;
Novohradsky, Vojtech;
Scott, Peter;
Brabec, Viktor

Publication type:

Article

Structural and biochemical characterization of human Schlafen 5.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 1147, doi. 10.1093/nar/gkab1278

By:

Metzner, Felix J;
Huber, Elisabeth;
Hopfner, Karl-Peter;
Lammens, Katja

Publication type:

Article

H2A mono-ubiquitination differentiates FACT's functions in nucleosome assembly and disassembly.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 833, doi. 10.1093/nar/gkab1271

By:

Wang, Yi-Zhou;
Liu, Cuifang;
Zhao, Jicheng;
Yu, Juan;
Luo, Anfeng;
Xiao, Xue;
Dou, Shuo-Xing;
Ma, Lu;
Wang, Peng-Ye;
Li, Ming;
Li, Guohong;
Yan, Jianbin;
Chen, Ping;
Li, Wei

Publication type:

Article

Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 867, doi. 10.1093/nar/gkab1276

By:

Fefelova, Elena A;
Pleshakova, Irina M;
Mikhaleva, Elena A;
Pirogov, Sergei A;
Poltorachenko, Valentin A;
Abramov, Yuri A;
Romashin, Daniil D;
Shatskikh, Aleksei S;
Blokh, Roman S;
Gvozdev, Vladimir A;
Klenov, Mikhail S

Publication type:

Article

Early rRNA processing is a stress-dependent regulatory event whose inhibition maintains nucleolar integrity.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 1033, doi. 10.1093/nar/gkab1231

By:

Szaflarski, Witold;
Leśniczak-Staszak, Marta;
Sowiński, Mateusz;
Ojha, Sandeep;
Aulas, Anaïs;
Dave, Dhwani;
Malla, Sulochan;
Anderson, Paul;
Ivanov, Pavel;
Lyons, Shawn M

Publication type:

Article

Stimulation of adaptive gene amplification by origin firing under replication fork constraint.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 915, doi. 10.1093/nar/gkab1257

By:

Whale, Alex J;
King, Michelle;
Hull, Ryan M;
Krueger, Felix;
Houseley, Jonathan

Publication type:

Article

Probing the mechanisms of two exonuclease domain mutators of DNA polymerase ϵ.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 962, doi. 10.1093/nar/gkab1255

By:

Dahl, Joseph M;
Thomas, Natalie;
Tracy, Maxwell A;
Hearn, Brady L;
Perera, Lalith;
Kennedy, Scott R;
Herr, Alan J;
Kunkel, Thomas A

Publication type:

Article

CryoEM of RUVBL1–RUVBL2–ZNHIT2, a complex that interacts with pre-mRNA-processing-splicing factor 8.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 1128, doi. 10.1093/nar/gkab1267

By:

Serna, Marina;
González-Corpas, Ana;
Cabezudo, Sofía;
López-Perrote, Andrés;
Degliesposti, Gianluca;
Zarzuela, Eduardo;
Skehel, J Mark;
Muñoz, Javier;
Llorca, Oscar

Publication type:

Article

Determinants of the temperature adaptation of mRNA degradation.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 1092, doi. 10.1093/nar/gkab1261

By:

Jaquet, Vincent;
Wallerich, Sandrine;
Voegeli, Sylvia;
Túrós, Demeter;
Viloria, Eduardo C;
Becskei, Attila

Publication type:

Article

CCPE: cell cycle pseudotime estimation for single cell RNA-seq data.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 704, doi. 10.1093/nar/gkab1236

By:

Liu, Jiajia;
Yang, Mengyuan;
Zhao, Weiling;
Zhou, Xiaobo

Publication type:

Article

Genetic screen for suppression of transcriptional interference reveals fission yeast 14–3–3 protein Rad24 as an antagonist of precocious Pol2 transcription termination.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 803, doi. 10.1093/nar/gkab1263

By:

Garg, Angad;
Shuman, Stewart;
Schwer, Beate

Publication type:

Article

interaction between the Spt6-tSH2 domain and Rpb1 affects multiple functions of RNA Polymerase II.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 784, doi. 10.1093/nar/gkab1262

By:

Connell, Zaily;
Parnell, Timothy J;
McCullough, Laura L;
Hill, Christopher P;
Formosa, Tim

Publication type:

Article

Reexamining assumptions about miRNA-guided gene silencing.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 617, doi. 10.1093/nar/gkab1256

By:

Kilikevicius, Audrius;
Meister, Gunter;
Corey, David R

Publication type:

Article

Ribonucleotides embedded in template DNA impair mitochondrial RNA polymerase progression.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 989, doi. 10.1093/nar/gkab1251

By:

Singh, Meenakshi;
Posse, Viktor;
Peter, Bradley;
Falkenberg, Maria;
Gustafsson, Claes M

Publication type:

Article

Redirecting meiotic DNA break hotspot determinant proteins alters localized spatial control of DNA break formation and repair.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 899, doi. 10.1093/nar/gkab1253

By:

Hyppa, Randy W;
Cho, Joshua D;
Nambiar, Mridula;
Smith, Gerald R

Publication type:

Article

Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 763, doi. 10.1093/nar/gkab1250

By:

Carnesecchi, Julie;
Boumpas, Panagiotis;
van Nierop y Sanchez, Patrick;
Domsch, Katrin;
Pinto, Hugo Daniel;
Borges Pinto, Pedro;
Lohmann, Ingrid

Publication type:

Article

Regulation of AR mRNA translation in response to acute AR pathway inhibition.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 1069, doi. 10.1093/nar/gkab1247

By:

Somasekharan, Syam Prakash;
Saxena, Neetu;
Zhang, Fan;
Beraldi, Eliana;
Huang, Jia Ni;
Gentle, Christina;
Fazli, Ladan;
Thi, Marisa;
Sorensen, Poul H;
Gleave, Martin

Publication type:

Article

Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 717, doi. 10.1093/nar/gkab1246

By:

Adendorff, Matthew R;
Tang, Guo Qing;
Millar, David P;
Bathe, Mark;
Bricker, William P

Publication type:

Article

Horizontal gene transfer as a mechanism for the promiscuous acquisition of distinct classes of IRES by avian caliciviruses.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 1052, doi. 10.1093/nar/gkab1243

By:

Arhab, Yani;
Miścicka, Anna;
Pestova, Tatyana V;
Hellen, Christopher U T

Publication type:

Article

Pairing of single mutations yields obligate Cre-type site-specific recombinases.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 1174, doi. 10.1093/nar/gkab1240

By:

Hoersten, Jenna;
Ruiz-Gómez, Gloria;
Lansing, Felix;
Rojo-Romanos, Teresa;
Schmitt, Lukas Theo;
Sonntag, Jan;
Pisabarro, M Teresa;
Buchholz, Frank

Publication type:

Article

Disrupting the Cdk9/Cyclin T1 heterodimer of 7SK snRNP for the Brd4 and AFF1/4 guided reconstitution of active P-TEFb.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 750, doi. 10.1093/nar/gkab1228

By:

Zhou, Kai;
Zhuang, Songkuan;
Liu, Fulong;
Chen, Yanheng;
Li, You;
Wang, Shihui;
Li, Yuxuan;
Wen, Huixin;
Lin, Xiaohua;
Wang, Jie;
Huang, Yue;
He, Cailing;
Xu, Nan;
Li, Zongshu;
Xu, Lang;
Zhang, Zixuan;
Chen, Lin-Feng;
Chen, Ruichuan;
Liu, Min

Publication type:

Article

Efficient target cleavage by Type V Cas12a effectors programmed with split CRISPR RNA.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 1162, doi. 10.1093/nar/gkab1227

By:

Shebanova, Regina;
Nikitchina, Natalia;
Shebanov, Nikita;
Mekler, Vladimir;
Kuznedelov, Konstantin;
Ulashchik, Egor;
Vasilev, Ruslan;
Sharko, Olga;
Shmanai, Vadim;
Tarassov, Ivan;
Severinov, Konstantin;
Entelis, Nina;
Mazunin, Ilya

Publication type:

Article

Highly conserved s2m element of SARS-CoV-2 dimerizes via a kissing complex and interacts with host miRNA-1307-3p.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 1017, doi. 10.1093/nar/gkab1226

By:

Imperatore, Joshua A;
Cunningham, Caylee L;
Pellegrene, Kendy A;
Brinson, Robert G;
Marino, John P;
Evanseck, Jeffrey D;
Mihailescu, Mihaela Rita

Publication type:

Article

Translesion DNA synthesis-driven mutagenesis in very early embryogenesis of fast cleaving embryos.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 885, doi. 10.1093/nar/gkab1223

By:

Lo Furno, Elena;
Busseau, Isabelle;
Aze, Antoine;
Lorenzi, Claudio;
Saghira, Cima;
Danzi, Matt C;
Zuchner, Stephan;
Maiorano, Domenico

Publication type:

Article

epigenetic switch activates bacterial quorum sensing and horizontal transfer of an integrative and conjugative element.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. 975, doi. 10.1093/nar/gkab1217

By:

Ramsay, Joshua P;
Bastholm, Tahlia R;
Verdonk, Callum J;
Tambalo, Dinah D;
Sullivan, John T;
Harold, Liam K;
Panganiban, Beatrice A;
Colombi, Elena;
Perry, Benjamin J;
Jowsey, William;
Morris, Calum;
Hynes, Michael F;
Bond, Charles S;
Cameron, Andrew D S;
Yost, Christopher K;
Ronson, Clive W

Publication type:

Article

Enhancing biological signals and detection rates in single-cell RNA-seq experiments with cDNA library equalization.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. e12, doi. 10.1093/nar/gkab1071

By:

Bacher, Rhonda;
Chu, Li-Fang;
Argus, Cara;
Bolin, Jennifer M;
Knight, Parker;
Thomson, James A;
Stewart, Ron;
Kendziorski, Christina

Publication type:

Article

Uncertainty-aware and interpretable evaluation of Cas9–gRNA and Cas12a–gRNA specificity for fully matched and partially mismatched targets with Deep Kernel Learning.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 2, p. e11, doi. 10.1093/nar/gkab1065

By:

Kirillov, Bogdan;
Savitskaya, Ekaterina;
Panov, Maxim;
Ogurtsov, Aleksey Y;
Shabalina, Svetlana A;
Koonin, Eugene V;
Severinov, Konstantin V

Publication type:

Article