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210 results for “G-quadruplex”
G-quadruplex in the gene of the large subunit of plant RNA polymerase II: billion years old story
<p><strong>Supplementary material to the journal article</strong></p> <p>Consist of:</p> <p>Supplementary material S1: Analyzed <em>RPB1 </em>sequences in 40 plant species together with detailed characteristics and G-quadruplex prediction using four different computational approaches.</p> <p>Supplementary material S2: G4 locus is the most conserved within the <em>RPB1</em> gene (40 bp long potential G4 locus is the most conserved site in the whole ~ 6000 bp long <em>RPB1</em> gene. See the histogram below the alignment: the position of the G4 locus is depicted, together with the horizontal red dashed line indicating relative nucleotide conservation among aligned sequences of<em> RPB1</em>)</p> <p>Supplementary material S3: Multiple alignment of G4 locus of <em>RPB1</em> paralogs in <em>Arabidopsis thaliana </em>centered to G4 locus of <em>RPB1 </em></p> <p>Supplementary material S4: Modelled 3D structure of G4 from <em>Bathycoccus prasinos</em> in PDB format</p> <p>Supplementary material S5: Gel electrophoresis and ThT staining of the selected G4-forming sequences</p> <p>Supplementary material S6: All analyzed <em>RPB1</em> sequences in FASTA format</p> <p>Supplementary material S7: Aligned <em>RPB1</em> sequences in FASTA format</p> <p>Supplementary material S8: <em>RPB1</em> paralogs in <em>Arabidopsis thaliana</em></p> <p>Supplementary material S9: Spectral composition of light used in the UV experiment. Analysis of emitted light was performed by Ocean Optics (HR4000CG-UV-NIR, USA) device.</p> <p>Supplementary material S10: Difference CD spectra - comparison without and with previous UV treatment</p>
Phase I trial of CX-5461, a first-in-class G-quadruplex stabilizer in patients with advanced solid tumors enriched for DNA-repair deficiencies (CCTG IND.231) - Variant Calls
<p>Variant Calls from Phase I trial of CX-5461, a first-in-class G-quadruplex stabilizer in patients with advanced solid tumors enriched for DNA-repair deficiencies (CCTG IND.231)</p> <p>See publication for methodology.</p>
G-quadruplexes as pivotal components of cis-regulatory elements in the human genome
<p>This repository stores the scripts for analyzing the relationship between G-quadruplexes (G4s) and <em>cis</em>-regulatory elements (CREs), as well as the data generated directly from the manuscript.</p> <p>Manuscript: <a href="https://doi.org/10.1186/s12915-024-01971-5" target="_blank" rel="noopener">G-quadruplexes as pivotal components of <em>cis</em>-regulatory elements in the human genome</a></p> <p>G4Hunter_w25_s1.5_hg38.txt: All potential G-quadruplexes in the human genome predicted by the G4Hunter software. </p> <ul> <li>Genome assembly: hg38.</li> <li>G4Hunter software parameters were set as follows: score threshold 1.5, window size 25.</li> </ul> <p>G4_cCRE_annotation.txt: Annotation file indicating the presence of G4s in cCREs (candidate CREs; from <a title="SCREEN database" href="https://screen.encodeproject.org/" target="_blank" rel="noopener">SCREEN database</a>).</p> <p>scripts.zip: Source code used for data analysis in this project, based on the R language.</p>
Strand-switching mechanism of Pif1 helicase induced by its collision with a G-quadruplex embedded in dsDNA_data_NAR
<p>This document includes data corresponding to the paper entitled :"Strand-switching mechanism of Pif1 helicase induced by its collision with a G-quadruplex embedded in dsDNA" published in Nucleic Acid Research, 2022. The link to the zenodo depository of the homemade software to open the data is given in the readme.txt file as well as the way the data files are organized</p>
NMR titration experiments that study binding of a NIR emitting osmium polypyridyl probe to cMYC and hTel G-quadruplex DNA
<p>1D and 2D NMR spectra of cMYC and hTel G-quadruplex DNA and their complexes with Λ-<strong> </strong>and Δ<strong>-</strong>enantiomers of the osmium polypyridyl probe [Os(TAP)<sub>2</sub>(dppz)]<sup>2+</sup>. Spectra were recorded on a 600 MHz NMR spectrometer with 70 mM KCl, 20 or 25 mM K-phosphate buffer, pH 7, 298 K, in 90% H<sub>2</sub>O and 10% D<sub>2</sub>O at 25 °C.</p>
PARALLEL G-QUADRUPLEX FOLDS VIA MULTIPLE PATHS INVOLVING G-TRACT STACKING AND STRUCTURING FROM COIL ENSEMBLE
<p>Data from all-atom molecular dynamics simulations of DNA G-quadruplex and various G-hairpins: input files (Gromacs and Amber), stripped trajectory files (reactive trajectories and reference replicas for G4, and reactive trajectories, and reference replicas for selected hairpin simulations), metadynamics bias files, and the ΔG_fold calculation protocol.</p>
Altering translation allows E. coli to overcome G-quadruplex stabilizers
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Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation
<p>Please refer to the publication Shin et al. (2021): "Shin CR, Choi EH, Kim G. et al. (2021). Characterization of metapopulation of <em>Ellobium chinense</em> through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation. Scientific Reports 11: 12239.</p> <p><span>The land snail <i>Ellobium chinense</i> (Pulmonata, Ellobiida, Ellobiidae), which inhabits the salt marshes along the coastal areas of northwestern Pacific, is an endangered species on the IUCN Red List. Over recent decades, the population size of <i>E. chinense</i> has consistently decreased due to environmental interference caused by natural disasters and human activities. Here, we provide the first assessment of the genetic diversity and population genetic structures of northwestern Pacific <i>E. chinense </i>based on <i>COI</i> and 10 microsatellite markers. The analyses of 140 <i>COI </i>data from South Korea and Japan and 54 microsatellite data from South Korea revealed that <i>E. chinense</i> has high haplotype and low nucleotide diversity without showing any genetic structures that reflect geographical isolations. It strongly implies that the subfamily Ellobiinae may have first appeared around the Eocene Optimum immediately after the Paleocene–Eocene Thermal Maximum (PETM; ca. 55 mya) and the examined <i>E. chinense</i> populations in Northwestern Pacific may have been maintained in a metapopulation under the influence of the Kuroshio warm currents through the Late-Middle Pleistocene (0.350−0.126 mya) and Late Pleistocene (0.126−0.012 mya). We also found four phylogenetic groups, regardless of geographical distributions, which were easily distinguishable by four unidirectional and stepwise adenine-to-guanine transitions in <i>COI</i> (sites 207-282-354-420: A-A-A-A, A-A-G-A, G-A-G-A, and G-G-G-G). Additionally, the four <i>COI</i> hotspots were robustly connected with a high degree of covariance between them. We discuss the role of these covariate guanines which link to form four consecutive G-quadruplexes, and their possible beneficial effects under positive selection pressure. </span></p>
Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes
<p>Molecular dynamics trajectories associated with the paper "Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes", by Marcelo D. Polêto and Justin A. Lemkul</p>
Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation
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Dataset to manuscript "Trans-cis isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells" accepted for publication in Nucleic Acids Research
<p><strong>This folder contains all raw data underlying the results presented in a manuscript, accepted for publication in Nucleic Acids Research, and entitled:</strong></p> <p> </p> <p><strong><em>Trans</em></strong><strong>-<em>cis</em> isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells </strong></p> <p> </p> <p><strong>Authored by:</strong></p> <p>Akira Kitamura<sup>2,*</sup>, Johan Tornmalm<sup>1,*</sup>, Baris Demirbay<sup>1</sup>, Joachim Piguet<sup>1</sup>, Masataka Kinjo<sup>2</sup>, Jerker Widengren<sup>1+</sup></p> <p> </p> <p><sup>1</sup> Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm, Sweden</p> <p><sup>2</sup> Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan</p> <p><sup>* </sup>Contributed equally</p> <p><sup>+</sup> To whom correspondence should be addressed. Email: jwideng@kth.se. Tel: +46-8-7907813</p> <p> </p> <p><strong>The data files are grouped into the different techniques used to generate them, and refer to the figures/tables in the manuscript where the extracted results are presented. </strong></p> <p> </p> <p><strong>ABSTRACT</strong></p> <p>Guanine (G)-rich nucleic acids are prone to assemble into four-stranded structures, so-called G-quadruplexes. Abnormal GGGGCC repeat elongations, and in particular their folding states, are associated with amyotrophic lateral sclerosis and frontotemporal dementia. Due to methodological constraints however, most studies of G quadruplex structures are restricted to <em>in vitro</em> conditions. Evidence of how GGGGCC repeats form into G-quadruplexes <em>in vivo</em> is sparse. We devised a readout strategy, exploiting the sensitivity of <em>trans</em>-<em>cis</em> isomerization of cyanine dyes to local viscosity and sterical constraints. Thereby, folding states of cyanine-labeled RNA, and in particular G-quadruplexes, can be identified in a sensitive manner. The isomerization kinetics, monitored via fluorescence blinking generated upon transitions between a fluorescent <em>trans</em> isomer and a non-fluorescent <em>cis</em> isomer, was first characterized for RNA with GGGGCC repeats in aqueous solution using fluorescence correlation spectroscopy and transient state (TRAST) monitoring. With TRAST, monitoring the isomerization kinetics from how the average fluorescence intensity varies with laser excitation modulation characteristics, we could then detect folding states of fluorescently tagged RNA introduced into live cells.</p>
Basket-type G-Quadruplex with Two Tetrads in the Presence of TMAO and Urea: A Molecular Dynamics Study
<p>Molecular Dynamics simulation trajectories of basket-type DNA G-quadruplex (PDB: 2KF7). The structures have been simulated in the temperatures 300 K and 360 K in pure water, 1 M TMAO solution, 2 M urea solution and the mixture of 1 M TMAO and 2 M urea.</p> <p> </p>
Raw gels are presented in the paper rG4detector, a novel RNA G-quadruplex predictor, uncovers their impact on stress granule formation
<p>This pptx. file collects the all raw gels (EMSA and WB) related to Figure 4 and Fig.S8-9, 11 in the paper: "rG4detector, a novel RNA G-quadruplex predictor, uncovers their impact on stress granule formation", in Nucleic Acids Research journal.</p>
Carbazole derivatives binding to Bcl-2 promoter sequence G-quadruplex
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Ligand-induced unfolding mechanism of an RNA G-quadruplex
<p>These are the trajectories for unbiased simulations of PQS-18-1 and TMPyP4.</p>
Metal ions confinement defines the architecture of G-quartet, G-quadruplex fibrils and their assembly into nematic tactoids
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Global analyses of RNA G-quadruplexes
GEO Series GSE83617. Mus musculus; Parasynechococcus marenigrum WH 8102; Pseudomonas putida; Saccharomyces cerevisiae; Homo sapiens; Escherichia coli. 35 samples. Type: Other.
DNA G-Quadruplex Recognition In Vitro and in Live Cells by a Structure-Specific Nanobody
GEO Series GSE207567. Homo sapiens. 24 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 1]
GEO Series GSE133365. synthetic construct. 32 samples. Type: Other.
Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 2]
GEO Series GSE133366. synthetic construct. 12 samples. Type: Other.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.