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Science and Mathematics x Biochemistry x Research Methods in Life Sciences x clear all

3.9 Å structure of the nucleosome core particle determined by phase-plate cryo-EM

Eugene Y.D. Chua, Vinod K. Vogirala, Oviya Inian, Andrew S.W. Wong, Lars Nordenskiöld, Juergen M. Plitzko, Radostin Danev and Sara Sandin.

in Nucleic Acids Research

September 2016; p ublished online August 2016 .

Journal Article. Subjects: Molecular and Cell Biology; Genetics and Genomics; Research Methods in Life Sciences; Proteins; Molecular Biology and Genetics. 3716 words.

The Volta phase plate is a recently developed electron cryo-microscopy (cryo-EM) device that enables contrast enhancement of biological samples. Here we have evaluated the potential of...

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Automated physics-based design of synthetic riboswitches from diverse RNA aptamers

Amin Espah Borujeni, Dennis M. Mishler, Jingzhi Wang, Walker Huso and Howard M. Salis.

in Nucleic Acids Research

January 2016; p ublished online November 2015 .

Journal Article. Subjects: Research Methods in Life Sciences; Bioinformatics and Computational Biology; Proteins; Molecular Biology and Genetics. 8537 words.

Riboswitches are shape-changing regulatory RNAs that bind chemicals and regulate gene expression, directly coupling sensing to cellular actuation. However, it remains unclear how their...

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Comprehensive mutational scanning of a kinase <i>in vivo</i> reveals substrate-dependent fitness landscapes

Alexandre Melnikov, Peter Rogov, Li Wang, Andreas Gnirke and Tarjei S. Mikkelsen.

in Nucleic Acids Research

August 2014; p ublished online June 2014 .

Journal Article. Subjects: Research Methods in Life Sciences; Enzymology; Molecular Biology and Genetics. 4829 words.

Deep mutational scanning has emerged as a promising tool for mapping sequence–activity relationships in proteins, ribonucleic acid and deoxyribonucleic acid. In this approach, diverse...

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Engineering a high-affinity methyl-CpG-binding protein

Helle F. Jørgensen, Karen Adie, Pascal Chaubert and Adrian P. Bird.

in Nucleic Acids Research

August 2006; p ublished online August 2006 .

Journal Article. Subjects: Research Methods in Life Sciences; Proteins; Molecular Biology and Genetics. 4350 words.

Core members of the MBD protein family (MeCP2, MBD1, MBD2 and MBD4) share a methyl-CpG-binding domain that has a specific affinity for methylated CpG sites in double-stranded DNA. By...

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A fluorescence-based helicase assay: application to the screening of G-quadruplex ligands

Oscar Mendoza, Nassima Meriem Gueddouda, Jean-Baptiste Boulé, Anne Bourdoncle and Jean-Louis Mergny.

in Nucleic Acids Research

June 2015; p ublished online March 2015 .

Journal Article. Subjects: Research Methods in Life Sciences; Enzymology; Molecular Biology and Genetics; Proteins. 6241 words.

Helicases, enzymes that unwind DNA or RNA structure, are present in the cell nucleus and in the mitochondrion. Although the majority of the helicases unwind DNA or RNA duplexes, some of...

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Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins

Isaure Chauvot de Beauchene, Sjoerd J. de Vries and Martin Zacharias.

in Nucleic Acids Research

June 2016; p ublished online April 2016 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics; Research Methods in Life Sciences; Bioinformatics and Computational Biology. 11320 words.

Protein-RNA complexes are important for many biological processes. However, structural modeling of such complexes is hampered by the high flexibility of RNA. Particularly challenging is the...

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H1 RNA polymerase III promoter-driven expression of an RNA aptamer leads to high-level inhibition of intracellular protein activity

Jing Mi, Xiuwu Zhang, Zahid N Rabbani, Yingmiao Liu, Zhen Su, Zeljko Vujaskovic, Christopher D. Kontos, Bruce A. Sullenger and Bryan M. Clary.

in Nucleic Acids Research

January 2006; p ublished online January 2006 .

Journal Article. Subjects: Proteins; Research Methods in Life Sciences; Molecular Biology and Genetics. 5506 words.

Aptamers offer advantages over other oligonucleotide-based approaches that artificially interfere with target gene function due to their ability to bind protein products of these genes with...

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High-throughput assay and engineering of self-cleaving ribozymes by sequencing

Shungo Kobori, Yoko Nomura, Anh Miu and Yohei Yokobayashi.

in Nucleic Acids Research

July 2015; p ublished online March 2015 .

Journal Article. Subjects: Enzymology; Research Methods in Life Sciences; Molecular Biology and Genetics. 5349 words.

Self-cleaving ribozymes are found in all domains of life and are believed to play important roles in biology. Additionally, self-cleaving ribozymes have been the subject of extensive...

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Identification of the CRP regulon using <i>in vitro</i> and <i>in vivo</i> transcriptional profiling

Dongling Zheng, Chrystala Constantinidou, Jon L. Hobman and Stephen D. Minchin.

in Nucleic Acids Research

October 2004; p ublished online October 2004 .

Journal Article. Subjects: Research Methods in Life Sciences; Proteins; Molecular Biology and Genetics. 10847 words.

The Escherichia coli cyclic AMP receptor protein (CRP) is a global regulator that controls transcription initiation from more than 100 promoters by binding to a specific DNA sequence within...

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Immunodetection of human topoisomerase I-DNA covalent complexes

Anand G. Patel, Karen S. Flatten, Kevin L. Peterson, Thomas G. Beito, Paula A. Schneider, Angela L. Perkins, Daniel A. Harki and Scott H. Kaufmann.

in Nucleic Acids Research

April 2016; p ublished online February 2016 .

Journal Article. Subjects: Research Methods in Life Sciences; Proteins; Molecular Biology and Genetics. 7150 words.

A number of established and investigational anticancer drugs slow the religation step of DNA topoisomerase I (topo I). These agents induce cytotoxicity by stabilizing topo I-DNA covalent...

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