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Preclinical Medicine x Proteins 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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Accurate <i>ab initio</i> prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes

Andrea Victora, Heiko M. Möller and Thomas E. Exner.

in Nucleic Acids Research

December 2014; p ublished online November 2014 .

Journal Article. Subjects: Molecular and Cell Biology; Proteins; Molecular Biology and Genetics. 7813 words.

NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very...

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Affinity selection of DNA-binding protein complexes using mRNA display

Seiji Tateyama, Kenichi Horisawa, Hideaki Takashima, Etsuko Miyamoto-Sato, Nobuhide Doi and Hiroshi Yanagawa.

in Nucleic Acids Research

February 2006; p ublished online February 2006 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics. 5778 words.

Comprehensive analysis of DNA–protein interactions is important for mapping transcriptional regulatory networks on a genome-wide level. Here we present a new application of mRNA display for null...

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Analysis of scanning force microscopy images of protein-induced DNA bending using simulations

Remus T. Dame, Joost van Mameren, Martijn S. Luijsterburg, Monika E. Mysiak, Ana Janićijević, Grzegorz Pazdzior, Peter C. van der Vliet, Claire Wyman and Gijs J.L. Wuite.

in Nucleic Acids Research

January 2005; p ublished online January 2005 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics. 4744 words.

Bending of DNA is a feature essential to the function of many DNA-binding proteins. Bending angles can be estimated with a variety of techniques, but most directly from images obtained...

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Assessing the translational landscape of myogenic differentiation by ribosome profiling

Eleonora de Klerk, Ivo F.A.C. Fokkema, Klaske A.M.H. Thiadens, Jelle J. Goeman, Magnus Palmblad, Johan T. den Dunnen, Marieke von Lindern and Peter A.C. ‘t Hoen.

in Nucleic Acids Research

May 2015; p ublished online April 2015 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics. 13318 words.

The formation of skeletal muscles is associated with drastic changes in protein requirements known to be safeguarded by tight control of gene transcription and mRNA processing. The...

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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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Binding dynamics of a monomeric SSB protein to DNA: a single-molecule multi-process approach

Michael J. Morten, Jose R. Peregrina, Maria Figueira-Gonzalez, Katrin Ackermann, Bela E. Bode, Malcolm F. White and J. Carlos Penedo.

in Nucleic Acids Research

December 2015; p ublished online November 2015 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics. 13821 words.

Single-stranded DNA binding proteins (SSBs) are ubiquitous across all organisms and are characterized by the presence of an OB (oligonucleotide/oligosaccharide/oligopeptide) binding motif...

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ChIP Display: novel method for identification of genomic targets of transcription factors

Artem Barski and Baruch Frenkel.

in Nucleic Acids Research

January 2004; p ublished online January 2004 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics. 5250 words.

Novel protein–DNA interactions in mammalian cells are traditionally discovered in the course of promoter studies. The genomic era presents opportunities for the reverse; namely, the...

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Combining SELEX with quantitative assays to rapidly obtain accurate models of protein–DNA interactions

Jiajian Liu and Gary D. Stormo.

in Nucleic Acids Research

October 2005; p ublished online October 2005 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics. 4775 words.

Models for the specificity of DNA-binding transcription factors are often based on small amounts of qualitative data and therefore have limited accuracy. In this study we demonstrate a...

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Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces

Vladimir Reinharz, Yann Ponty and Jérôme Waldispühl.

in Nucleic Acids Research

June 2016; p ublished online April 2016 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics. 6896 words.

Systematic structure probing experiments (e.g. SHAPE) of RNA mutants such as the mutate-and-map (MaM) protocol give us a direct access into the genetic robustness of ncRNA structures....

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