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Series GSE124865 Query DataSets for GSE124865
Status Public on Sep 30, 2019
Title ssDNA aptamers against amyloid-β peptide as biomarker and inhibtor [SELEX]
Organism Homo sapiens
Experiment type Other
Summary We report high-affinity ssDNA aptamers as biomarkers and antagonists of amyloid-β peptide. We generated three novel aptamer sequences from the pool of aptamers through the SELEX process, and evaluated their affinity and sensitivity using enzyme-linked immunosorbent assay (ELISA). (The forward primer: ATTAGTCAAGAGGTAGACGCACATA, reverse primer TTCTGGTCGTCGTGACTCCTAT) The ssDNA aptamers modeled into a three-dimensional structure; interaction and mechanism of action derived through molecular dynamics simulations (MD). MD simulations revealed the nature of binding and inhibition of aggregation by binding with amyloid-β peptide monomers, dimers, and other oligomers. The presence of high non-bonded interaction energy along with hydrogen bonds constitutes the complex structure of the aptamer-amyloid-β peptide. Furthermore, the changes in the secondary structure induced by aptamers may help remove the peptide through the blood-brain barrier. This study provided a framework for the application of aptamers against amyloid-β peptides as biomarkers and antagonists.
Overall design generationa and modeling of aptamers against amyloid-β peptide and its mechanism of action.
Please note that the raw data corresponding for the aptamers were submitted which is required for the study (rest of the readings/files are discarded) and since the resulting raw data contains only 4 lines with 23 or 64 bp reads, they are included as GEO sample supplementary files.
Contributor(s) Maroli N
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Submission date Jan 09, 2019
Last update date Jun 14, 2023
Contact name Nikhil Maroli
Phone 7200515138
Organization name DRDO BU CLS
Department Physics
Lab Computational Biology
Street address Bharathiar University
City Coimbatore
State/province TAMIL NADU
ZIP/Postal code 670691
Country India
Platforms (1)
GPL16288 AB 5500xl Genetic Analyzer (Homo sapiens)
Samples (3)
GSM3557554 Aptamer-1
GSM3557555 Aptamer-2
GSM3557556 Aptamer-3
BioProject PRJNA514043

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE124865_RAW.tar 140.0 Kb (http)(custom) TAR (of FASTQ, PDB, TXT)
Raw data provided as supplementary file
Processed data provided as supplementary file

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