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7,976 Newest Publications in nucleic acids research


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Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species

16-May-2018 | Lui L, Uzilov A, Bernick D, et al., Nucleic Acids Research, 2018

Abstract Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2′-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene ...


Cell penetrating thiazole peptides inhibit c-MYC expression via site-specific targeting of c-MYC G-quadruplex

14-May-2018 | Dutta D, Debnath M, Müller D, et al., Nucleic Acids Research, 2018

Abstract The structural differences among different G-quadruplexes provide an opportunity for site-specific targeting of a particular G-quadruplex structure. However, majority of G-quadruplex ligands described thus far show little selectivity among different G-quadruplexes. In this work, we ...


Microprocessor depends on hemin to recognize the apical loop of primary microRNA

10-May-2018 | Nguyen T, Park J, Dang T, et al., Nucleic Acids Research, 2018

Abstract Microprocessor, which consists of a ribonuclease III DROSHA and its cofactor DGCR8, initiates microRNA (miRNA) maturation by cleaving primary miRNA transcripts (pri-miRNAs). We recently demonstrated that the DGCR8 dimer recognizes the apical elements of pri-miRNAs, including the UGU ...


bpRNA: large-scale automated annotation and analysis of RNA secondary structure

09-May-2018 | Danaee P, Rouches M, Wiley M, et al., Nucleic Acids Research, 2018

Abstract While RNA secondary structure prediction from sequence data has made remarkable progress, there is a need for improved strategies for annotating the features of RNA secondary structures. Here, we present bpRNA, a novel annotation tool capable of parsing RNA structures, including complex ...


Translational control plays an important role in the adaptive heat-shock response of Streptomyces coelicolor

09-May-2018 | Bucca G, Pothi R, Hesketh A, et al., Nucleic Acids Research, 2018

Abstract Stress-induced adaptations require multiple levels of regulation in all organisms to repair cellular damage. In the present study we evaluated the genome-wide transcriptional and translational changes following heat stress exposure in the soil-dwelling model actinomycete bacterium, ...


Chromatin assembly factor-1 (CAF-1) chaperone regulates Cse4 deposition into chromatin in budding yeast

04-May-2018 | Hewawasam G, Dhatchinamoorthy K, Mattingly M, et al., Nucleic Acids Research, 2018

Nucleic Acids Research, gky169,


PRMT5-mediated arginine methylation of TDP1 for the repair of topoisomerase I covalent complexes

30-Apr-2018 | Rehman I, Basu S, Das S, et al., Nucleic Acids Research, 2018

Abstract Human tyrosyl-DNA phosphodiesterases (TDP) hydrolyze the phosphodiester bond between DNA and the catalytic tyrosine of Top1 to excise topoisomerase I cleavage complexes (Top1cc) that are trapped by camptothecin (CPT) and by genotoxic DNA alterations. Here we show that the protein ...


Visualizing structure-mediated interactions in supercoiled DNA molecules

19-Apr-2018 | Scott S, Xu Z, Kouzine F, et al., Nucleic Acids Research, 2018

Abstract We directly visualize the topology-mediated interactions between an unwinding site on a supercoiled DNA plasmid and a specific probe molecule designed to bind to this site, as a function of DNA supercoiling and temperature. The visualization relies on containing the DNA molecules within ...


Crystal structures of thrombin in complex with chemically modified thrombin DNA aptamers reveal the origins of enhanced affinity

19-Apr-2018 | Dolot R, Lam C, Sierant M, et al., Nucleic Acids Research, 2018

Abstract Thrombin-binding aptamer (TBA) is a DNA 15-mer of sequence 5′-GGT TGG TGT GGT TGG-3′ that folds into a G-quadruplex structure linked by two T-T loops located on one side and a T-G-T loop on the other. These loops are critical for post-SELEX modification to improve TBA target affinity. ...


The number of titrated microRNA species dictates ceRNA regulation

19-Apr-2018 | Chiu H, Martínez M, . Komissarova E, et al., Nucleic Acids Research, 2018

Abstract microRNAs (miRNAs) play key roles in cancer, but their propensity to couple their targets as competing endogenous RNAs (ceRNAs) has only recently emerged. Multiple models have studied ceRNA regulation, but these models did not account for the effects of co-regulation by miRNAs with many ...


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