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252,202 Newest Publications about the topic green biotechnology

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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 ...

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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 ...

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Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex

01-02-2015 | Ali A. Almaqwashi; Thayaparan Paramanathan; Per Lincoln; Ioulia Rouzina; Fredrik Westerlund; Mark C. Williams, Nucleic Acids Research, 2015

DNA intercalation by threading is expected to yield high affinity and slow dissociation, properties desirable for DNA-targeted therapeutics. To measure these properties, we utilize single molecule DNA stretching to quantify both the binding affinity and the force-dependent threading intercalation ...

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The cytoplasmic poly(A) polymerases GLD-2 and GLD-4 promote general gene expression via distinct mechanisms

01-02-2015 | Marco Nousch; Assa Yeroslaviz; Bianca Habermann; Christian R. Eckmann, Nucleic Acids Research, 2015

Post-transcriptional gene regulation mechanisms decide on cellular mRNA activities. Essential gatekeepers of post-transcriptional mRNA regulation are broadly conserved mRNA-modifying enzymes, such as cytoplasmic poly(A) polymerases (cytoPAPs). Although these non-canonical nucleotidyltransferases ...

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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 ...

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Single-molecule analysis uncovers the difference between the kinetics of DNA decatenation by bacterial topoisomerases I and III

01-02-2015 | Ksenia Terekhova; John F. Marko; Alfonso Mondragón, Nucleic Acids Research, 2015

Escherichia coli topoisomerases I and III can decatenate double-stranded DNA (dsDNA) molecules containing single-stranded DNA regions or nicks as well as relax negatively supercoiled DNA. Although the proteins share a mechanism of action and have similar structures, they participate in different ...

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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 ...

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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 ...

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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 ...

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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 ...

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