Ghosh, Anirban Largy, Eric Gabelica, Valérie
Published in
Nucleic Acids Research
G-quadruplex DNA structures have become attractive drug targets, and native mass spectrometry can provide detailed characterization of drug binding stoichiometry and affinity, potentially at high throughput. However, the G-quadruplex DNA polymorphism poses problems for interpreting ligand screening assays. In order to establish standardized MS-base...
Ketkar, Amit Smith, Lane Johnson, Callie Richey, Alyssa Berry, Makayla Hartman, Jessica H Maddukuri, Leena Reed, Megan R Gunderson, Julie E C Leung, Justin W C
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Published in
Nucleic Acids Research
We previously reported that human Rev1 (hRev1) bound to a parallel-stranded G-quadruplex (G4) from the c-MYC promoter with high affinity. We have extended those results to include other G4 motifs, finding that hRev1 exhibited stronger affinity for parallel-stranded G4 than either anti-parallel or hybrid folds. Amino acids in the αE helix of insert-...
Bielskutė, Stasė Plavec, Janez Podbevšek, Peter
Published in
Nucleic Acids Research
Graphical Abstract oxoG influences the fold of a G-quadruplex structure within the human BCL2 promoter and enhances the thermal stability of the G4 structure by forming novel structural elements.
Huesa, Juanjo Giner-Lamia, Joaquín Pucciarelli, M Graciela Paredes-Martínez, Francisco Portillo, Francisco García-del Marina, Alberto Casino, Patricia
Published in
Nucleic Acids Research
RcsB is a transcriptional regulator that controls expression of numerous genes in enteric bacteria. RcsB accomplishes this role alone or in combination with auxiliary transcriptional factors independently or dependently of phosphorylation. To understand the mechanisms by which RcsB regulates such large number of genes, we performed structural studi...
Bonchuk, Artem Boyko, Konstantin Fedotova, Anna Nikolaeva, Alena Lushchekina, Sofya Khrustaleva, Anastasia Popov, Vladimir Georgiev, Pavel
Published in
Nucleic Acids Research
In arthropods, zinc finger-associated domains (ZADs) are found at the N-termini of many DNA-binding proteins with tandem arrays of Cys2-His2 zinc fingers (ZAD-C2H2 proteins). ZAD-C2H2 proteins undergo fast evolutionary lineage-specific expansion and functional diversification. Here, we show that all ZADs from Drosophila melanogaster form homodimers...
Shen, Dan Song, Chengyi Miskey, Csaba Chan, Shuheng Guan, Zhongxia Sang, Yatong Wang, Yali Chen, Cai Wang, Xiaoyan Müller, Ferenc
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Published in
Nucleic Acids Research
New genetic tools and strategies are currently under development to facilitate functional genomics analyses. Here, we describe an active member of the Tc1/mariner transposon superfamily, named ZB , which invaded the zebrafish genome very recently. ZB exhibits high activity in vertebrate cells, in the range of those of the widely used transposons pi...
Volek, Martin Kolesnikova, Sofia Svehlova, Katerina Srb, Pavel Sgallová, Ráchel Streckerová, Tereza Redondo, Juan A Veverka, Václav Curtis, Edward A
Published in
Nucleic Acids Research
G-quadruplexes are noncanonical nucleic acid structures formed by stacked guanine tetrads. They are capable of a range of functions and thought to play widespread biological roles. This diversity raises an important question: what determines the biochemical specificity of G-quadruplex structures? The answer is particularly important from the perspe...
Bezrukov, Fedor Prados, Julien Renzoni, Adriana Panasenko, Olesya O
Published in
Nucleic Acids Research
Graphical Abstract MazF toxin causes alterations in Staphylococcus aureus transcriptome, translatome and proteome that underlie bacterial dormancy.
León, Lina M Park, Allyson E Borges, Adair L Zhang, Jenny Y Bondy-Denomy, Joseph
Published in
Nucleic Acids Research
Bacteria deploy multiple defenses to prevent mobile genetic element (MGEs) invasion. CRISPR–Cas immune systems use RNA-guided nucleases to target MGEs, which counter with anti-CRISPR (Acr) proteins. Our understanding of the biology and co-evolutionary dynamics of the common Type I-C CRISPR–Cas subtype has lagged because it lacks an in vivo phage-ho...
Xu, Yanxin Xi, Jiajie Wang, Guiying Guo, Zhenming Sun, Qiaoyi Lu, Chenqi Ma, Li Wu, Yukang Jia, Wenwen Zhu, Songcheng
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Published in
Nucleic Acids Research
Long noncoding RNAs (lncRNAs) play a wide range of roles in the epigenetic regulation of crucial biological processes, but the functions of lncRNAs in cortical development are poorly understood. Using human embryonic stem cell (hESC)-based 2D neural differentiation approach and 3D cerebral organoid system, we identified that the lncRNA PAUPAR , whi...
