Aptamer Details

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S-1 (ID# 9460)

* The secondary structure may not be accurate because of MFOLD limitations on chemistries other than RNA/DNA.

Aptamer Chemistry: 2'-F-RNA

Target: RNA Helicase Protein DHX9

Antigen/Target Category: Protein

Affinity (Kd): 14 µM (reported value)

Binding Conditions/Buffer: radioactive filter-binding assay was performed. Briefly, for aptamer 32P labeling, in vitro transcribed RNA was purified by chromatography, then end-labeled with [γ-32P] ATP using T4 polynucleotide kinase followed by G-50 column purification. Binding assays were performed by incubating 32P-labeled RNA (3 pmol) with the protein at the indicated concentrations in binding buffer.

Binding Temp: 67.5 ºC°C

Refolding Protocol: To generate biotinylated aptamers, RNA 3′-end desthiobiotinylation kit (Pierce Biotechnology, Rockford, IL) that relies on the ability of T4 RNA ligase to attach a single desthiobiotinylated cytidine diphosphate to the 3′ end of the RNA strand was used. Briefly, 30 µl of RNA ligation mixture containing nonlabeled RNA or 50 pmol control RNA, 1 nmol biotinylated cytidine diphosphate, T4 RNA buffer 1X and ligase 40U, and PEG 30%, was incubated at 4 °C for overnight, then the RNA was recovered by extraction with chloroform:isoamyl alcohol and precipitation with 10 µl of 5mol/l NaCl, 1µl glycogen and 300 µl ice-cold 100% ethanol

Sequence ():

Length: 40

Molecular Weight: 12240.9 g/mole

Extinction Coefficient: 387700 L/(mole·cm)

Note: Information on this aptamer oligo was obtained from the literature and hasn't been validated by Aptagen.

Reference:

Mi J, Ray P, Liu J, Kuan CT, Xu J, Hsu D, Sullenger BA, White RR, Clary BM. In Vivo Selection Against Human Colorectal Cancer Xenografts Identifies an Aptamer That Targets RNA Helicase Protein DHX9. Mol Ther Nucleic Acids. 2016 Apr 26;5(4):e315. doi: 10.1038/mtna.2016.27. PMID: 27115840; PMCID: PMC5014527.

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