Bovine factor IX aptamer

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Description

 In 2006, Gopinath, S. C., & Mizuno, H. selected an RNA aptamer by SELEX against bovine factor IX using an RNA pool containing 74-nucleotides randomized region. Selected RNA aptamer (Clone 5) could discriminate bovine factor IX effectively from human factor IX[1].

SELEX

In 2006, Gopinath, S. C., & Mizuno, H. selected an anti–bovine factor IX RNA aptamer with the starting RNA repertoire with randomized region over a 74-nucleotide. For each selection, the RNA pool and bovine factor IX were mixed and allowed to incubate for about 10 min, and then the bound oligonucleotide (Bovine factor IX–RNA complexes) are separated from the unbound oligonucleotides, either by filtration or xenoplate. Bound RNAs were recovered with hot 7 M urea and subsequently amplified by reverse transcription followed by PCR, and then the PCR products were transcribedin vitro. After five rounds of selection and amplification, about 54% of the RNA pool was bound to bovine IX[1].
Detailed information are accessible on SELEX page.



Structure

The 2D structure of the figure is based on the article by ribodraw tool to draw[1].

5'-GGGAGCUCAGCCUUCACUGCCUACGCGGGCGUUUACGUAACGGCUUAUGGGGAGCUGAGCGCUUGACCGUGGUAGUGCUAAGCAGUAAACGAGGGCACCACGGUCGGAUCCAC-3'

 drawing


Ligand information

SELEX ligand

Factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca2+ ions, phospholipids, and factor VIIIa.-----from InterPro
Name Uniprot ID Pfam MW Amino acids sequences PDB Gene ID
Bovine factor IX P00741 IPR006369 5.64 kDa YNSGKLEEFVRGNLERECKEEKCSFEEAREVFENTEKTTEFWKQYV 1J34 2158
Some isolated sequences bind to the affinity of the protein.
Name Sequence Ligand Affinity
Clone 5 5'-GGGAGCUCAGCCUUCACUGCCUACGCGGGCGUUUACGUAACGGCUUAUGGGGAGCUGAGCGCUUGACCGUGGUAGUGCUAAGCAGUAAACGAGGGCACCACGGUCGGAUCCAC-3' Bovine factor IX 10 nM
drawing

Similar compound

We used the Dail server website to compare the structural similarities of ligand proteins, and chose the top 10 in terms of similarity for presentation. The Dali server is a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB). Z-score is a standard score that is converted from an original score. The list of neighbours is sorted by Z-score. Similarities with a Z-score lower than 2 are spurious. RMSD(Root Mean Square Deviation) value is used to measure the degree to which atoms deviate from the alignment position.
PDB Z-socre RMSD Description
1IOD-G 8.9 0.8 Coagulation factor x binding protein
1NL1-A 8.1 0.8 Prothrombin
1PFX-L 7.2 1.6 Factor ixa


References

[1] An RNA aptamer that discriminates bovine factor IX from human factor IX.
Gopinath, S. C., Balasundaresan, D., Akitomi, J., & Mizuno, H.
Journal of biochemistry, 140(5), 667–676. (2006)