Beggs, Grace A Ayala, Julio C Kavanaugh, Logan G Read, Timothy D Hooks, Grace M Schumacher, Maria A Shafer, William M Brennan, Richard G
Published in
Nucleic acids research
Mutations within the mtrR gene are commonly found amongst multidrug resistant clinical isolates of Neisseria gonorrhoeae, which has been labelled a superbug by the Centers for Disease Control and Prevention. These mutations appear to contribute to antibiotic resistance by interfering with the ability of MtrR to bind to and repress expression of its...
Barberi, Luca Livolant, Françoise Leforestier, Amélie Lenz, Martin
Published in
Nucleic acids research
In viruses and cells, DNA is closely packed and tightly curved thanks to polyvalent cations inducing an effective attraction between its negatively charged filaments. Our understanding of this effective attraction remains very incomplete, partly because experimental data is limited to bulk measurements on large samples of mostly uncurved DNA helice...
Jahnke, Kevin Grubmüller, Helmut Igaev, Maxim Göpfrich, Kerstin
Published in
Nucleic acids research
The ability to dynamically remodel DNA origami structures or functional nanodevices is highly desired in the field of DNA nanotechnology. Concomitantly, the use of fluorophores to track and validate the dynamics of such DNA-based architectures is commonplace and often unavoidable. It is therefore crucial to be aware of the side effects of popular f...
Dai, Yang-Xue Chen, Wei-Fei Liu, Na-Nv Teng, Fang-Yuan Guo, Hai-Lei Hou, Xi-Miao Dou, Shuo-Xing Rety, Stephane Xi, Xu-Guang
Published in
Nucleic acids research
Pif1 is an SF1B helicase that is evolutionarily conserved from bacteria to humans and plays multiple roles in maintaining genome stability in both nucleus and mitochondria. Though highly conserved, Pif1 family harbors a large mechanistic diversity. Here, we report crystal structures of Thermus oshimai Pif1 (ToPif1) alone and complexed with partial ...
Park, Hyojin Kim, Seokhee
Published in
Nucleic acids research
Various in vivo mutagenesis methods have been developed to facilitate fast and efficient continuous evolution of proteins in cells. However, they either modify the DNA region that does not match the target gene, or suffer from low mutation rates. Here, we report a mutator, eMutaT7 (enhanced MutaT7), with very fast in vivo mutation rate and high gen...
Kim, Eunkyeong Kim, Jun Kim, Chuna Lee, Junho
Published in
Nucleic acids research
Karyotype change and subsequent evolution is triggered by chromosome fusion and rearrangement events, which often occur when telomeres become dysfunctional. Telomeres protect linear chromosome ends from DNA damage responses (DDRs), and telomere dysfunction may result in genome instability. However, the complex chromosome end structures and the othe...
Tálas, András Huszár, Krisztina Kulcsár, Péter István Varga, Julia K Varga, Éva Tóth, Eszter Welker, Zsombor Erdős, Gergely Pach, Péter Ferenc Welker, Ágnes
...
Published in
Nucleic acids research
Detailed target-selectivity information and experiment-based efficacy prediction tools are primarily available for Streptococcus pyogenes Cas9 (SpCas9). One obstacle to develop such tools is the rarity of accurate data. Here, we report a method termed 'Self-targeting sgRNA Library Screen' (SLS) for assaying the activity of Cas9 nucleases in bacteri...
Dubey, Ashutosh P Tylec, Brianna L McAdams, Natalie M Sortino, Katherine Read, Laurie K
Published in
Nucleic acids research
Uridine insertion/deletion editing of mitochondrial mRNAs is a characteristic feature of kinetoplastids, including Trypanosoma brucei. Editing is directed by trans-acting gRNAs and catalyzed by related RNA Editing Core Complexes (RECCs). The non-catalytic RNA Editing Substrate Binding Complex (RESC) coordinates interactions between RECC, gRNA and m...
Meldal, Birgit H M Pons, Carles Perfetto, Livia Del-Toro, Noemi Wong, Edith Aloy, Patrick Hermjakob, Henning Orchard, Sandra Porras, Pablo
Published in
Nucleic acids research
The EMBL-EBI Complex Portal is a knowledgebase of macromolecular complexes providing persistent stable identifiers. Entries are linked to literature evidence and provide details of complex membership, function, structure and complex-specific Gene Ontology annotations. Data are freely available and downloadable in HUPO-PSI community standards and mi...
Koulouras, Grigorios Frith, Martin C
Published in
Nucleic acids research
Minimal absent words (MAWs) are minimal-length oligomers absent from a genome or proteome. Although some artificially synthesized MAWs have deleterious effects, there is still a lack of a strategy for the classification of non-occurring sequences as potentially malicious or benign. In this work, by using Markovian models with multiple-testing corre...
