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73 results for “Aptamer”
Supplements for "Understanding the interaction between a human transferrin receptor aptamer-short double stranded RNA conjugate and its cell membrane target by in silico methods"
<p>Supplements for "Understanding the interaction between a human transferrin receptor aptamer-short double stranded RNA conjugate and its cell membrane target by in silico methods". </p> <p>This supplement includes the following files:</p> <p> </p> <p>1. Structures of the most stable Protein-Aptamer complexes predicted from HADDOCK</p> <p>Haddock_Cluster1.pdb <br> Haddock_Cluster2.pdb <br> Haddock_Cluster3.pdb </p> <p>2. Structure of the most stable conformation aligned with Protein-transferring complex PDB</p> <p>cluster1_aligned.pdb <br> transferrin_aligned.pdb </p> <p>3. MM-GBSA decomposition analysis of the three replicas for Protein-Aptamer</p> <p>aptamer_new_rep01_Decomp.dat <br> aptamer_new_rep02_Decomp.dat <br> aptamer_new_rep03_Decomp.dat </p> <p>4. MM-GBSA decomposition analysis of the three replicas for Protein-Aptamer-Conjugate<br> conjugate_new_rep01_Decomp.dat <br> conjugate_new_rep02_Decomp.dat <br> conjugate_new_rep03_Decomp.dat <br> </p> <p><br> <br> </p>
Functionalization of PEDOT:PSS for aptamer-based sensing of IL6 using organic electrochemical transistors
<div>Explanation of included data for following publication:</div> <div>-------------------------------------------------------------------------------------</div> <div> </div> <div>Functionalization of PEDOT:PSS for aptamer-based sensing of IL6 using organic electrochemical transistors</div> <div> <div>DOI: 10.1038/s44328-024-00007-w</div> </div> <div> </div> <div>Bernhard Burtscher (1), Chiara Diacci (1), Anatolii Makhinia (1,2), Marios Savvakis (1), Erik O Gabrielsson (1), Lothar Veith (3), Xianjie Liu (1), Xenofon Strakosas (1), Daniel T Simon (1)</div> <div> </div> <div>1. Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, 60174 Norrköping, Sweden</div> <div>2. RISE Research Institutes of Sweden, Digital Systems, Smart, Hardware, Printed, Bio- and Organic Electronics, 60221 Norrköping, Sweden</div> <div>3. Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany</div> <div> </div> <div>-------------------------------------------------------------------------------------</div> <div>The data is structured according to the first figure they appear in the manuscript.</div> <div> </div> <div>Figure 2:</div> <div>a) Transfer curves data as .txt at various stages of the functionalization process with information of</div> <div>(Time / s; Gate Voltage / V; Drain Voltage / V; Drain Current / A; Gate Current / A; VR (measured voltage at the reference electrode) / V)</div> <div>1) PEDOT:PSS</div> <div>2) 4-ABA + PEDOT:PSS</div> <div>3) Aptamer + 4-ABA + PEDOT:PSS</div> <div> </div> <div>b) Measurement data of constant sensing experiments of either IL6 (6 meas.), BSA (3 meas.) or a control without aptamers (4ABA-ETA_Control_IL6-measurement) with explanation of when analyte was changed to which concentration.</div> <div> </div> <div>c) Data of constant measurement of fully functionalized OECT in bovine plasma after incubation over night in bovine plasma and information regarding time and concentration of changes</div> <div> </div> <div> </div> <div>Figure 3: Raw image files of fluorescent test of AL4083 PEDOT:PSS formulation with PLL-FITC as .nd2 files:</div> <div>- 0.25% Gops with PLL-FITC (name: AL4083-Gops025_sample5_PLLFITC_FITC)</div> <div>- 0.25% Gops without PLL-FITC (name: AL4083-Gops025_sample3_4ABA_noPLLFITC_FITC_5s)</div> <div>- 1% Gops and 1% PSS with PLL-FITC (name: AL4083-Gops1_PSS1_sample4_PLLFITC_FITC)</div> <div>- 1% Gops and 1% PSS without PLL-FITC (name: AL4083-Gops1_PSS1_sample3_4ABA_noPLLFITC_FITC_5s)</div> <div> </div> <div> </div> <div>Figure 4: Frequency dependent OECT measurements of IL6 with PBS and different concentration of IL6. Each folder contains the nominal applied voltage (as .csv file) and the measurement voltage (in V) from the DAQ (as .tdms file in the ao1 column for each frequency). Data can then be processed with Python to fit the sine wave for each frequency to observe changes in the amplitude and phase.</div> <div> </div> <div>Figure 5: Data taken from Figure 2b and Figure 4</div>
Unravelling the Dependence of Aptamer–Target Binding Orientation and Strength on Nucleotide Modification Size, Position, and Number: A Computational Case Study of TBA
<p>Data deposition for "Unravelling the Dependence of Aptamer–Target Binding Orientation and Strength on Nucleotide Modification Size, Position, and Number: A Computational Case Study of TBA" published in Nucleic Acids Research. Data includes custom paramaterized nucleobase residues for use in AMBER molecular dyanmics simulations. Initial structures and setup code along with starting structures for generation of simulations in AMBER (pmemd.cuda). A in-house "MD-Generator" script to create nessessary files with our select simulation settings. Lastly, also included are CPPTRAJ analysis commands and scripts with visualizion scripts for use in Pymol 2.5 and above. </p>
UTexas Aptamer Dataset
<p>The deposited dataset is a snapshot of the data in the active and growing UTexas Aptamer Database, <a href="https://sites.utexas.edu/aptamerdatabase/">https://sites.utexas.edu/aptamerdatabase/</a>. This dataset is a collection of aptamer data that has been extracted from the literature every year since the inception of aptamer selections and includes multiple aptamer sequences from a given paper (as opposed to just sequences with the tightest binding). In all, the collection includes 1,415 aptamer sequences from 489 papers published over the last few decades (1990-2022). Since our dataset includes multiple sequences that emerged from a given selection experiment, it of necessity includes sequences that may not have been individually tested for binding activity, similar to the inclusion of all rRNA sequences in a metagenomic analysis of an environmental sample. By taking this metagenomic approach, we provide informaticians with a much wider range of sequences for subsequent analysis while still providing tools to find high-affinity aptamers for future use.</p> <p>For each aptamer sequence, the dataset includes information about the aptamer publication (i.e., year of publication, DOI, full citation, and corresponding author(s)), the aptamer target, as well as the following information about the specific aptamer: nucleic acid composition, name assigned in the original publication, sequence, GC percentage, sequence length, binding affinity (K<sub>d</sub>), binding/selection buffer, application as quoted in the referenced paper (e.g., drug delivery, biosensor, etc.), original nucleic acid pool used in the aptamer selection, post-selection modifications (if any), additional information, and our internally assigned serial number. We used simple Excel formulas for each aptamer record to calculate the GC content and length of each aptamer sequence.</p> <p> </p> <p>1.1.0 Version:</p> <ul> <li>Added 25+ aptamer sequences.</li> <li>Added the "Parent sequence serial number" data field/column.</li> <li>Fixed "Application as quoted in the referenced paper" data formatting/alignment error.</li> </ul>
RNA Ensembles From Solvent Accessibility Data: Application to the SAM-I Riboswitch Aptamer Domain
<p>SASA-derived ensembles of the -SAM and +SAM states of the SAM-responsive riboswitch.</p>
Raw data of high-dimensional aptamer selection generated by ProSELEX
<p>This is the raw selection dataset generated by ProSELEX pipeline (https://www.nature.com/articles/s41557-023-01207-z). The target of selection is human myeloperoxidase (MPO). See https://github.com/dwangnu/AptaZ for instructions.</p>
Project ADHERE: Clinical Proof-of-Concept of a Tenofovir (TFV) Aptamer-Based Biosensor
ClinicalTrials.gov study NCT04870671. IPD Sharing: NO. Countries: 1. Publications: 3.
A Safety and Efficacy Study of E10030 (Anti-PDGF Pegylated Aptamer) Plus Lucentis for Neovascular Age-Related Macular Degeneration
ClinicalTrials.gov study NCT01089517. IPD Sharing: Not stated. Countries: 1. Publications: 1.
A Study to Establish the Safety and Tolerability of Zimura™ (Anti-C5 Aptamer) in Combination With Anti-VEGF Therapy in Subjects With Idiopathic Polypoidal Choroidal Vasculopathy (IPCV)
ClinicalTrials.gov study NCT02397954. IPD Sharing: NO. Countries: 1. Publications: 1.
Data for "Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection"
<p>Once decompressed, the file contains a folder which contains:</p> <ul> <li>The files "s100_Nth.fasta" (where "N" is 5, 6, 7 or 8), which are the output of the SELEX experiment described in the paper with DOI: <a href="https://doi.org/10.1002/cbic.201900265">10.1002/cbic.201900265</a>. They are standard fasta files, and the descriptor of each sequence is of the form "seqX-Y", where "X" is an increasing label, and "Y" is the number of times "seqX" has been obtained (number of counts of "seqX").</li> <li>The file "Aptamer_Exp_Results.csv", which contains the sequences tested experimentally for the paper "Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection" (preprint available at https://doi.org/10.1101/2022.03.12.484094), with the following experimental results for each sequence: (i) whether the sequence was able to bind thrombin ('B' for binders, 'NB' for non-binders); (ii) the thrombin exosite used for binding ('I' for exosite I, 'II' for exosite II, 'n/a' for sequences not tested).</li> </ul> <p>Examples of usage of the data are available at https://github.com/adigioacchino/RBMsForAptamers.</p>
Dataset for Dual-Site Recognition in Classic DNA Aptamer
<p>This is a simulation dataset for molecular dynamics studying the dual-site recognition mechanism of a classical DNA aptamer. All data were generated using the simulation engine Gromacs 2021.4 with the Colvars module patched and accelerated with GPU (NVIDIA 3070). In the uploaded compressed file, the "mdp" folder contains the mdp files used during the simulation, as well as the topology files and force field parameters, mainly generated through the CHARMM-GUI program. "1AMP22" represents Site 1/AMP, "1AMP9" represents Site 2/AMP, and "2AMP" represents Sites 1, 2/2AMP models. The suffix "eq" indicates equilibrium simulations, "d" indicates 1-dimensional enhanced sampling simulations using distance as a collective variable, "dphi" indicates 2-dimensional enhanced sampling simulations using distance and flip angle as collective variables, and "co" indicates enhanced sampling simulations with both AMP ligands recognizing simultaneously.</p>
Direct electrochemical reduction of graphene oxide thin film for aptamer-based selective and highly sensitive detection of matrix metalloproteinase 2
<p>Simple and low-cost biosensing solutions are suitable for point-of-care applications aiming to overcome the gap between scientific concepts and technological production. To compete with sensitivity and <a title="Learn more about selectivity from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/earth-and-planetary-sciences/selectivity">selectivity</a> of golden standards, such as <a title="Learn more about liquid chromatography from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/materials-science/liquid-chromatography">liquid chromatography</a>, the functionalization of biosensors is continuously optimized to enhance the signal and improve their performance, often leading to complex chemical assay development. In this research, the efforts are made on optimizing the methodology for <a title="Learn more about electrochemical reduction from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/materials-science/electrochemical-reaction">electrochemical reduction</a> of <a title="Learn more about graphene oxide from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/chemistry/graphene-oxide">graphene oxide</a> to produce thin film-modified gold electrodes. Under the employed specific conditions, 20 cycles of <a title="Learn more about cyclic voltammetry from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/cyclic-voltammetry">cyclic voltammetry</a> (CV) are shown to be optimal for superior electrical activation of <a title="Learn more about graphene oxide from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/materials-science/graphene-oxide">graphene oxide</a> into electrochemically <a title="Learn more about reduced graphene oxide from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/materials-science/reduced-graphene-oxide">reduced graphene oxide</a> (ERGO). This platform is further used to develop a <a title="Learn more about matrix metalloproteinase 2 from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/mmp2">matrix metalloproteinase 2</a> (MMP-2) biosensor, where specific anti-MMP2 <a title="Learn more about aptamers from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/aptamer">aptamers</a> are utilized as a biorecognition element. MMP-2 is a protein which is typically overexpressed in tumor tissues, with important roles in tumor invasion, metastasis as well as in tumor <a title="Learn more about angiogenesis from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/earth-and-planetary-sciences/angiogenesis">angiogenesis</a>. Based on impedimetric measurements, we were able to detect as low as 3.32 pg mL<sup>−1</sup> of MMP-2 in PBS with a dynamic range of 10 pg mL<sup>−1</sup> – 10 ng mL<sup>−1</sup>. Further experiments with real blood samples revealed a promising potential of the developed sensor for direct measurement of MMP-2 in complex media. High specificity of detection is demonstrated – even to the closely related <a title="Learn more about enzyme from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/enzyme">enzyme</a> MMP-9. Finally, the potential of reuse was demonstrated by signal restoration after experimental detection of MMP-2.</p>
One-Step Photochemical Immobilization of Aptamer on Graphene for Label-Free Detection of NT-proBNP
<p>A novel photochemical technological route for one-step functionalization of a graphene surface with an azide-modified DNA aptamer for biomarkers is developed. The methodology is demonstrated for the functionalization of a DNA aptamer for an N-terminal B-type natriuretic peptide (NT-proBNP) heart failure biomarker on the surface of a graphene channel within a system based on a liquid-gated graphene field effect transistor (GFET). The limit of detection (LOD) of the aptamer-functionalized sensor is 0.01 pg/mL with short response time (75 s) for clinically relevant concentrations of the cardiac biomarker, which could be of relevance for point-of-care (POC) applications. The novel methodology could be applicable for the development of different graphene-based biosensors for fast, stable, real-time, and highly sensitive detection of disease markers.</p>
The raw images of Laser Confocal Microscopy experiments in the manuscript: Inert Pepper aptamer-mediated endogenous mRNA recognition and imaging in living cells
<p>The <strong>original imaging data</strong> folder contains the raw images of Laser confocal microscopy experiments in the manuscript: Inert Pepper aptamer-mediated endogenous mRNA recognition and imaging in living cells. <a href="https://doi.org/10.1093/nar/gkac368">https://doi.org/10.1093/nar/gkac368</a> </p>
In silico study on a binding mechanism of ssDNA aptamers targeting glycosidic bond-containing small molecules
<p>Files with the 5 ssDNA and their complexes with glycosidic bond-containing small molecules after docking, used in the MD simulations, along with MD simulation trajectories, are included as compressed files (.zip). </p><p>Glycosidic bond-containing small molecules docking performed using AutoDock Vina, and MD simulations based on amber software and DNA.bsc1 force fields.</p>
Dataset to Carbon nanotube field-effect transistor for resolving single-molecule aptamer-ligand binding kinetics
<p>Raw data of single molecular field effect transistor data from recordings of aptamer serotonin interactions.</p>
Dataset for: Molecular Dynamics study of the Recognition of the Nucleic Acid Aptamer to ATP
<p>Files with the initial aptamer structures (wt and three mutant forms) and their complexes with ATP after docking, used in the MD simulations, along with MD simulation trajectories and meta-eABF simulations, are included as tarballs (.tar.gz). </p> <p>Mutant structures were generated using PyMol, ATP docking performed using AutoDock Vina, and MD simulations based on NAMD software and Charmm36 and CGenFF force fields. </p> <p> </p>
Selective Modulation of the Protease Activated Protein C Using Exosite Inhibiting Aptamers
<p>Activated protein C (APC) is a serine protease with anticoagulant and cytoprotective activities. Nonanticoagulant APC mutants show beneficial effects as cytoprotective agents. To study, if such biased APC signaling can be achieved by APC-binding ligands, the aptamer technology has been used. A G-quadruplex-containing aptamer, G-NB3, has been selected that binds to the basic exosite of APC with a K<sub>D</sub> of 0.2 nM and shows no binding to APC-related serine proteases or the zymogen protein C. G-NB3 inhibits the inactivation of activated cofactors V and VIII with IC<sub>50</sub> values of 11.6 and 13.1 nM, respectively, without inhibiting the cytoprotective and anti-inflammatory functions of APC as tested using a staurosporine-induced apoptosis assay and a vascular barrier protection assay. In addition, G-NB3 prolongs the plasma half-life of APC through inhibition of APC-serine protease inhibitor complex formation. These physicochemical and functional characteristics qualify G-NB3 as a promising therapeutic agent usable to enhance the cytoprotective functions of APC without increasing the risk of APC-related hemorrhage.</p>
Probing TDP-43 Condensation using an In Silico Designed Aptamer
<p>Aptamer super-resolution and SAVE imaging data for Figure 4 and Figure 5 in publication. </p>
Molecular dynamic trajectories for PLGF and VEGF complexed with custom designed aptamers
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