NFAT aptamer

•

横向排列的点击按钮

Timeline

2002

Soo-Jin Bae et.al present an in vitro selection of RNA aptamer to NFATc DNA binding domain (DBD)[2]

2004

Jung-Sun Cho et.al isolated two RNA aptamers to the NFAT DNA binding domain (DBD)[1]

2015

K A Malsagova et al. found that SOI-nanowires (NWs) were modified with aptamers against NFAT 1 used as molecular probes[3]

2021

Yan Yun et al. found that R1SR13, as the RNA aptamer of RCAN1 identified by SELEX and reduced neuronal apoptosis[4]

Description

 In 2004, Jung-Sun Cho and colleagues used an In vitro selection strategy to isolate high affinity RNA aptamers that bind to NFAT DNA binding domain. The aptamers have a specific and high affinity (apparent KD~10 to 100 nM) for the NFAT DBD[1].

SELEX

In 2004, Jung-Sun Cho and Young Ju Lee used existing research to design the method required for the in vitro genetic-selection. Starting from a RNA pool that had a sequence of 40 random nucleotide positions, aptamers that bind specifically to NFAT DBD were selected after 10 rounds of selection and amplification. The aptamer, RNA aptamer #1, can bind specifically to NFAT DBD were selected with high affinity[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'-GGGAGAGCGGAAGCGUGCUGGGCCGAUAUGAAGGAGUGGAGAGGGUGGCAGCAUGGUCCGGAUCCAUAACCCAGAGGUCGAUGGAUCCU-3'

 drawing


Ligand information

SELEX ligand

Antigenic stimulation of T lymphocytes initiates a complex series of intracellular signal transduction pathways that leads to the expression of a panel of immunoregulatory genes, whose function is critical to the initiation and coordination of the immune response. The multi-subunit nuclear factor of activated T cells (NFAT) transcription factor family plays a pivotal role in this process and is involved in the expression of a number of immunologically important genes.-----From Pfam

Name Uniprot ID Pfam MW Amino acids sequences PDB Gene ID
NFAT DBD(the NFAT DNA binding domain) Q12968 IPR008366 115.594 kDa MTTANCGAHDELDFKLVFGEDGAPAPPPPGSRPADLEPDDCASIYIFNVDPPPSTLTTPLCLPHHGLPSHSSVLSPSFQLQSHKNYEGTCEIPESKYSPLGGPKPFECPSIQITSISPNCHQELDAHEDDLQINDPEREFLERPSRDHLYLPLEPSYRESSLSPSPASSISSRSWFSDASSCESLSHIYDDVDSELNEAAARFTLGSPLTSPGGSPGGCPGEETWHQQYGLGHSLSPRQSPCHSPRSSVTDENWLSPRPASGPSSRPTSPCGKRRHSSAEVCYAGSLSPHHSPVPSPGHSPRGSVTEDTWLNASVHGGSGLGPAVFPFQYCVETDIPLKTRKTSEDQAAILPGKLELCSDDQGSLSPARETSIDDGLGSQYPLKKDSCGDQFLSVPSPFTWSKPKPGHTPIFRTSSLPPLDWPLPAHFGQCELKIEVQPKTHHRAHYETEGSRGAVKASTGGHPVVKLLGYNEKPINLQMFIGTADDRYLRPHAFYQVHRITGKTVATASQEIIIASTKVLEIPLLPENNMSASIDCAGILKLRNSDIELRKGETDIGRKNTRVRLVFRVHIPQPSGKVLSLQIASIPVECSQRSAQELPHIEKYSINSCSVNGGHEMVVTGSNFLPESKIIFLEKGQDGRPQWEVEGKIIREKCQGAHIVLEVPPYHNPAVTAAVQVHFYLCNGKRKKSQSQRFTYTPVLMKQEHREEIDLSSVPSLPVPHPAQTQRPSSDSGCSHDSVLSGQRSLICSIPQTYASMVTSSHLPQLQCRDESVSKEQHMIPSPIVHQPFQVTPTPPVGSSYQPMQTNVVYNGPTCLPINAASSQEFDSVLFQQDATLSGLVNLGCQPLSSIPFHSSNSGSTGHLLAHTPHSVHTLPHLQSMGYHCSNTGQRSLSSPVADQITGQPSSQLQPITYGPSHSGSATTASPAASHPLASSPLSGPPSPQLQPMPYQSPSSGTASSPSPATRMHSGQHSTQAQSTGQGGLSAPSSLICHSLCDPASFPPDGATVSIKPEPEDREPNFATIGLQDITLDDVNEIIGRDMSQISVSQGAGVSRQAPLPSPESLDLGRSDGL 8OW4 4775

The aptamer bind to the affinity of the protein.

Name Sequence Ligand Affinity
RNA aptamer #1 5'-GGGAGAGCGGAAGCGUGCUGGGCCGAUAUGAAGGAGUGGAGAGGGUGGCAGCAUGGUCCGGAUCCAUAACCCAGAGGUCGAUGGAUCCU-3' NFAT DBD 11.1 nM
RNA aptamer #1 5'-GGGAGAGCGGAAGCGUGCUGGGCCGAGGGAGGCGAUAUGAAGGUGUAGAGAGGCCUCCUGGACACAUAACCCAGAGGUCGAUGGAUCCCCCC-3' NFAT DBD 120 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
8OW4-B 43.7 0.0 Nuclear factor of activated T-cells, cytoplasmic
2O61-A 15.4 3.4 36-mer
1OY3-C 15.2 1.4 Transcription factor p65
2CXK-A 10.3 1.9 Calmodulin binding transcription
3HRP-A 10.2 2.3 Uncharacterized protein
3MLP-A 10.2 14.0 Transcription factor coe1
4JCL-A 9.8 5.1 Cyclomaltodextrin glucanotransfe
4N6R-B 9.5 2.9 Vosa
6STX-C 9.2 9.5 Kelch domain-containing protein
3KYA-A 8.7 2.2 Putative phosphatase


References

[1] In vitro selection of specific RNA aptamers for the NFAT DNA binding domain.
Cho JS, Lee YJ, Shin KS, Jeong S, Park J, Lee SW.
Mol Cells. 18(1):17-23. (2004)
[2] In vitro selection of specific RNA inhibitors of NFATc.
Bae SJ, Oum JH, Sharma S, Park J, Lee SW.
Biochem Biophys Res Commun. 298(4):486-92. (2002)
[3] [SOI-nanowire biosensor for the detection of D-NFAT 1 protein].
Malsagova KA, Ivanov YD, Pleshakova TO, Kozlov AF, Krohin NV, Kaysheva AL, Shumov ID, Popov VP, Naumova OV, Fomin BI, Nasimov DA.
Biomed Khim. 61(4):462-7. (2015)
[4] Regulator of calcineurin 1 is a novel RNA-binding protein to regulate neuronal apoptosis.
Yun Y, Zhang Y, Zhang C, Huang L, Tan S, Wang P, Vilariño-Gúell C, Song W, Sun X.
Mol Psychiatry. 26(4):1361-1375. (2021)