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3,029 Newest Publications in nucleic acids research
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A strategically located serine residue is critical for the mutator activity of DNA polymerase IV from Escherichia coli
01-05-2013 | Amit Sharma; Jithesh Kottur; Naveen Narayanan; Deepak T. Nair, Nucleic Acids Research, 2013
The Y-family DNA polymerase IV or PolIV (Escherichia coli) is the founding member of the DinB family and is known to play an important role in stress-induced mutagenesis. We have determined four crystal structures of this enzyme in its pre-catalytic state in complex with substrate DNA ...
Leucine-specific domain modulates the aminoacylation and proofreading functional cycle of bacterial leucyl-tRNA synthetase
01-05-2013 | Wei Yan; Min Tan; Gilbert Eriani; En-Duo Wang, Nucleic Acids Research, 2013
The leucine-specific domain (LSD) is a compact well-ordered module that participates in positioning of the conserved KMSKS catalytic loop in most leucyl-tRNA synthetases (LeuRSs). However, the LeuRS from Mycoplasma mobile (MmLeuRS) has a tetrapeptide GKDG instead of the LSD. Here, we show ...
A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control
01-05-2013 | Ewald van Dyk; Marcel J.T. Reinders; Lodewyk F.A. Wessels, Nucleic Acids Research, 2013
Tumor formation is partially driven by DNA copy number changes, which are typically measured using array comparative genomic hybridization, SNP arrays and DNA sequencing platforms. Many techniques are available for detecting recurring aberrations across multiple tumor samples, including ...
All three RNA recognition motifs and the hinge region of HuC play distinct roles in the regulation of alternative splicing
01-05-2013 | Melissa N. Hinman; Hua-Lin Zhou; Alok Sharma; Hua Lou, Nucleic Acids Research, 2013
The four Hu [embryonic lethal abnormal vision-like (ELAVL)] protein family members regulate alternative splicing by binding to U-rich sequences surrounding target exons and affecting the interaction of the splicing machinery and/or local chromatin modifications. Each of the Hu proteins ...
The Mediator complex subunit MED25 is targeted by the N-terminal transactivation domain of the PEA3 group members
01-05-2013 | Alexis Verger; Jean-Luc Baert; Kathye Verreman; Frédérique Dewitte; Elisabeth Ferreira; Zoé Lens; Yvan de Launoit; V ..., Nucleic Acids Research, 2013
PEA3, ERM and ER81 belong to the PEA3 subfamily of Ets transcription factors and play important roles in a number of tissue-specific processes. Transcriptional activation by PEA3 subfamily factors requires their characteristic amino-terminal acidic transactivation domain (TAD). However, the ...
Effects of post-transcriptional regulation on phenotypic noise in Escherichia coli
01-05-2013 | Rinat Arbel-Goren; Asaf Tal; Tamar Friedlander; Shiri Meshner; Nina Costantino; Donald L. Court; Joel Stavans, Nucleic Acids Research, 2013
Cell-to-cell variations in protein abundance, called noise, give rise to phenotypic variability between isogenic cells. Studies of noise have focused on stochasticity introduced at transcription, yet the effects of post-transcriptional regulatory processes on noise remain unknown. We study ...
The effect of hybridization-induced secondary structure alterations on RNA detection using backscattering interferometry
01-05-2013 | Nicholas M. Adams; Ian R. Olmsted; Frederick R. Haselton; Darryl J. Bornhop; David W. Wright, Nucleic Acids Research, 2013
Backscattering interferometry (BSI) has been used to successfully monitor molecular interactions without labeling and with high sensitivity. These properties suggest that this approach might be useful for detecting biomarkers of infection. In this report, we identify interactions and ...
CoFold: an RNA secondary structure prediction method that takes co-transcriptional folding into account
01-05-2013 | Jeff R. Proctor; Irmtraud M. Meyer, Nucleic Acids Research, 2013
Existing state-of-the-art methods that take a single RNA sequence and predict the corresponding RNA secondary structure are thermodynamic methods. These aim to predict the most stable RNA structure. There exists by now ample experimental and theoretical evidence that the process of structure ...
LncRNA loc285194 is a p53-regulated tumor suppressor
01-05-2013 | Qian Liu; Jianguo Huang; Nanjiang Zhou; Ziqiang Zhang; Ali Zhang; Zhaohui Lu; Fangting Wu; Yin-Yuan Mo, Nucleic Acids Research, 2013
Protein-coding genes account for only a small part of the human genome, whereas the vast majority of transcripts make up the non-coding RNAs including long non-coding RNAs (lncRNAs). Accumulating evidence indicates that lncRNAs could play a critical role in regulation of cellular processes ...
Spanning high-dimensional expression space using ribosome-binding site combinatorics
01-05-2013 | Lior Zelcbuch; Niv Antonovsky; Arren Bar-Even; Ayelet Levin-Karp; Uri Barenholz; Michal Dayagi; Wolfram Liebermeiste ..., Nucleic Acids Research, 2013
Protein levels are a dominant factor shaping natural and synthetic biological systems. Although proper functioning of metabolic pathways relies on precise control of enzyme levels, the experimental ability to balance the levels of many genes in parallel is a major outstanding challenge. ...
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