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247.398 Aktuelle Fachpublikationen zum Thema Addition

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Experimental mapping of DNA duplex shape enabled by global lineshape analyses of a nucleotide-independent nitroxide probe

01.02.2015 | Yuan Ding; Xiaojun Zhang; Kenneth W. Tham; Peter Z. Qin, Nucleic Acids Research, 2015

Sequence-dependent variation in structure and dynamics of a DNA duplex, collectively referred to as ‘DNA shape’, critically impacts interactions between DNA and proteins. Here, a method based on the technique of site-directed spin labeling was developed to experimentally map shapes of two DNA ...


Mechanism of allosteric inhibition of HIV-1 reverse transcriptase revealed by single-molecule and ensemble fluorescence

01.02.2015 | Grant D. Schauer; Kelly D. Huber; Sanford H. Leuba; Nicolas Sluis-Cremer, Nucleic Acids Research, 2015

Non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs) are routinely used to treat HIV-1 infection, yet their mechanism of action remains unclear despite intensive investigation. In this study, we developed complementary single-molecule fluorescence and ensemble fluorescence anisotropy ...


The multidrug ABC transporter BmrC/BmrD of Bacillus subtilis is regulated via a ribosome-mediated transcriptional attenuation mechanism

01.02.2015 | Ewoud Reilman; Ruben A. T. Mars; Jan Maarten van Dijl; Emma L. Denham, Nucleic Acids Research, 2015

Expression of particular drug transporters in response to antibiotic pressure is a critical element in the development of bacterial multidrug resistance, and represents a serious concern for human health. To obtain a better understanding of underlying regulatory mechanisms, we have dissected the ...


The RIG-I ATPase core has evolved a functional requirement for allosteric stabilization by the Pincer domain

01.02.2015 | David C. Rawling; Andrew S. Kohlway; Dahai Luo; Steve C. Ding; Anna Marie Pyle, Nucleic Acids Research, 2015

Retinoic acid-inducible gene I (RIG-I) is a pattern recognition receptor expressed in metazoan cells that is responsible for eliciting the production of type I interferons and pro-inflammatory cytokines upon detection of intracellular, non-self RNA. Structural studies of RIG-I have identified a ...


sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software

01.02.2015 | Atul Kakrana; Reza Hammond; Parth Patel; Mayumi Nakano; Blake C. Meyers, Nucleic Acids Research, 2015

Parallel analysis of RNA ends (PARE) is a technique utilizing high-throughput sequencing to profile uncapped, mRNA cleavage or decay products on a genome-wide basis. Tools currently available to validate miRNA targets using PARE data employ only annotated genes, whereas important targets may be ...


Simultaneous binding to the tracking strand, displaced strand and the duplex of a DNA fork enhances unwinding by Dda helicase

01.02.2015 | Suja Aarattuthodiyil; Alicia K. Byrd; Kevin D. Raney, Nucleic Acids Research, 2015

Interactions between helicases and the tracking strand of a DNA substrate are well-characterized; however, the role of the displaced strand is a less understood characteristic of DNA unwinding. Dda helicase exhibited greater processivity when unwinding a DNA fork compared to a ss/ds DNA junction ...


Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA

01.02.2015 | Pablo Daniel Dans; Ignacio Faustino; Federica Battistini; Krystyna Zakrzewska; Richard Lavery; Modesto Orozco, Nucleic Acids Research, 2015

We have made a detailed study of one of the most surprising sources of polymorphism in B-DNA: the high twist/low twist (HT/LT) conformational change in the d(CpG) base pair step. Using extensive computations, complemented with database analysis, we were able to characterize the twist polymorphism ...


Dynamics of RNA modification by a multi-site-specific tRNA methyltransferase

01.02.2015 | Djemel Hamdane; Amandine Guelorget; Vincent Guérineau; Béatrice Golinelli-Pimpaneau, Nucleic Acids Research, 2015

In most organisms, the widely conserved 1-methyl-adenosine58 (m1A58) tRNA modification is catalyzed by an S-adenosyl-L-methionine (SAM)-dependent, site-specific enzyme TrmI. In archaea, TrmI also methylates the adjacent adenine 57, m1A57 being an obligatory intermediate of 1-methyl-inosine57 ...


A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions

01.02.2015 | Jonas Paulsen; Einar A. Rødland; Lars Holden; Marit Holden; Eivind Hovig, Nucleic Acids Research, 2015

Identification of three-dimensional (3D) interactions between regulatory elements across the genome is crucial to unravel the complex regulatory machinery that orchestrates proliferation and differentiation of cells. ChIA-PET is a novel method to identify such interactions, where physical ...


Monomeric nature of dengue virus NS3 helicase and thermodynamic analysis of the interaction with single-stranded RNA

01.02.2015 | Leopoldo G. Gebhard; J. Jeremías Incicco; Clara Smal; Mariana Gallo; Andrea V. Gamarnik; Sergio B. Kaufman, Nucleic Acids Research, 2015

Dengue virus nonstructural protein 3 (NS3) is a multifunctional protein formed by a superfamily-2 RNA helicase linked to a protease domain. In this work, we report results from in vitro experiments designed to determine the oligomeric state of dengue virus NS3 helicase (NS3h) and to characterize ...


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