Basic fibroblast growth factor aptamer

•



Description

Ellington, A. D. et al. reported aptamers with affinity for bFGF in their article published in 1998. The ps11-20 aptamer was named by Ellington, A. D. et al. in the article[1].



SELEX

In their work published in 1998, Ellington, A. D. et al. used SELEX to isolate RNA aptamer sequences with affinity for bFGF from a nucleic acid library containing about 5×1012 sequences after 11 rounds of selection process. Human recombinant bFGF was purified from yeast expressing artificial bFGF cDNA[1].

Detailed information are accessible on SELEX page.



Structure

The 2D structure of the figure is based on the prediction results of the RNA fold website by ribodraw tool to draw. The figure shows the secondary structure prediction of the original aptamer sequence. This aptamer contains three stem loops of different lengths. The two stem loops closer to the 3' end are connected by a long junction[1].

5'-GGGAAUGGAUCCACAUCUACGAAUUCAAUCCCAAUGGCUUGAACUGCCAACGAACGUUCACUGCAGACUUGACGAAGCUU-3'

drawing


Ligand information

SELEX ligand

Growth factor actives in angiogenesis, and endothelial cell growth, stimulating their proliferation and migration and also has effects on the permeability of blood vessels. Growth factor may functions in angiogenesis of the venous and lymphatic vascular systems during embryogenesis, and also in the maintenance of differentiated lymphatic endothelium in adults. Growth factor binds and activates KDR/VEGFR2 and FLT4/VEGFR3 receptors. It acts as a ligand for FGFR1, FGFR2, FGFR3 and FGFR4, and as an integrin ligand which is required for FGF2 signaling.-----From Uniprot

UniProt ID: uniquely identifies protein sequences in the UniProt database, a resource for protein information.

Pfam: a widely recognised database of protein families and domains.

GenBank: maintained by NCBI(National Center for Biotechnology Information), is a database of nucleotide sequences from various organisms, vital for genetic and molecular biology research.

Mass: an intrinsic property of a body.

Name Uniprot ID Pfam Mass Protein sequence PDB ID GenBank
bFGF (basic fibroblast growth factor) P09038 PF00167 30.77 kDa
...... MVGVGGGDVEDVTPRPGGCQISGRGARGCNGIPGAAAWEAALPRRRPRRHPSVNPRSRAAGSPRTRGRRTEERPSGSRLGDRGRGRALPGGRLGGRGRGRAPERVGGRGRGRGTAAPRAAPAARGSRPGPAGTMAAGSITTLPALPEDGGSGAFPPGHFKDPKRLYCKNGGFFLRIHPDGRVDGVREKSDPHIKLQLQAEERGVVSIKGVCANRYLAMKEDGRLLASKCVTDECFFFERLESNNYNTYRSRKYTSWYVALKRTGQYKLGSKTGPGQKAILFLPMSAKS
1BAS 2247

Some isolated sequences bind to the affinity of the protein[1].

Name Sequence Ligand Affinity
ps11-20 aptamer 5'-GGGAAUGGAUCCACAUCUACGAAUUCAAUCCCAAUGGCUUGAACUGCCAACGAACGUUCACUGCAGACUUGACGAAGCUU-3' bFGF 1.8 ± 0.8 nM
drawing

Similar compound(s)

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.

Dail server website: a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB).

Z-score: 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) is used to measure the degree to which atoms deviate from the alignment position.

PDB: PDB ID+ chain name.

PDB Z-socre RMSD (Å) Description
1BAS-A 30.6 0 Original chain
1G82-A 23.7 1.1 Fibroblast growth factor 9
3A07-B 18.2 1.5 Actinohivin
1UPS-A 17.6 1.9 Glcnac-alpha-1,4-gal-releasing endo-beta-
2VSE-A 17.3 1.7 Mosquitocidal toxin
6LF2-B 17.1 1.8 Sevil
8BAD-B 16.8 1.8 Binary toxin a-like protein
1W3A-A 16.7 1.9 Hemolytic lectin lsla
6IFB-B 16.6 1.8 Lectin
4PC4-C 16.4 2.0 30k lipoprotein
2IHO-A 16.4 1.9 Lectin


References

[1] In vitro selection of phosphorothiolated aptamers.
Jhaveri, S., Olwin, B., & Ellington, A. D.
Bioorganic & medicinal chemistry letters, 8(17), 2285–2290. (1998)