SARS-CoV N protein aptamer

May 6, 2024 • Jiali Wang, Bo Fu

Description

In 2009, Ahn DG, Jeon IJ, Kim JD, et al. used the SELEX method to select the aptamer with high compatibility for the SARS-CoV nucleocapsid (N) protein. The aptamer antibody mixed immunoassay method they studied may be used for rapid and sensitive detection of SARS-CoV N protein, which has potential application value for improving the treatment and prognosis of SARS^[1].

SELEX

In 2009, Ahn DG, Jeon IJ, Kim JD, et al. screened an RNA aptamer pool with approximately 10¹⁴ random, 40-nt long aptamers by SELEX to isolate those binding to SARS-CoV N protein. After a total of nine rounds of SELEX process, including five rounds of preliminary screening and four rounds of screening under more stringent conditions (a 5-fold reduction in the amount of N protein). After nine rounds of screening, the cDNA of the selected RNA population was cloned, and 17 independent clones were randomly selected for sequencing. They further validated the binding specificity and affinity of the selected aptamers with N protein through electrophoretic mobility change analysis (EMSA) and surface plasmon resonance (SPR) analysis^[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. Aptamer 1 binds to SARS-CoV nucleocapsid (N) protein^[1].

5'-GGGAGAGCGGAAGCGUGCUGGGCCUGUCGUUCGCUGUCUUGCUACGUUACGUUACACGGUUGGCAUAACCCAGAGGUCGAUGG-3'

Ligand information

SELEX ligand

Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved domains. The N-terminal domain (NTD) (N1b), the C-terminal domain (CTD)(N2b) and the N3 region. The N1b and N2b domains from SARS CoV, infectious bronchitis virus (IBV), human CoV 229E and mouse hepatic virus (MHV) display similar topological organisations. N proteins form dimers, which are asymmetrically arranged into octamers via their N2b domains. Domains N1b and N2b are linked by another domain N2a that contains an SR-rich region in which phosphorylation of specific serine residues allows the N protein to associate with the RNA helicase DDX1 permitting template read-through, and enabling the transition from discontinuous transcription of subgenomic mRNAs (sgmRNAs) to continuous synthesis of longer sgmRNAs and genomic RNA (gRNA). It has been shown that N proteins interact with nonstructural protein 3 (NSP3) and thus are recruited to the replication-transcription complexes (RTCs).-----From Pfam

Name	Uniprot ID	Pfam	MW	Amino acids sequences	PDB	Gene ID
SARS-CoV nucleocapsid (N) protein	P59595	PF00937	13.913 kDa	NTASWFTALTQHGKEELRFPRGQGVPINTNSGPDDQIGYYRRATRRVRGGDGKMKELSPRWYFYYLGTGPEASLPYGANKEGIVWVATEGALNTPKDHIGTRNPNNNAATVLQLPQGTTLPKGFYA	2OFZ	AY278741

Some isolated sequences bind to the affinity of the protein.

Name	Sequence	Ligand	Affinity
apatamer 1	5'-GGGAGAGCGGAAGCGUGCUGGGCCUGUCGUUCGCUGUCUUGCUACGUUACGUUACACGGUUGGCAUAACCCAGAGGUCGAUGG-3'	SARS-CoV N protein	1.65 ± 0.41 nM (equilibrium dissociation constant) 0.81 nM (apparent dissociation constant)
apatamer 2	5'-GGGAGAGCGGAAGCGUGCUGGGCCUCAUUACACACAUCUCACGGGAGACAUAGCUGACGAUAUCCAUAACCCAGAGGUCGAUGG-3'	SARS-CoV N protein	3.35 nM (apparent dissociation constant)

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
5N4K-A	16.8	1.8	Nucleoprotein
8FD5-A	5.2	3.5	Nucleoprotein

References

[1] RNA aptamer-based sensitive detection of SARS coronavirus nucleocapsid protein.
Ahn, D. G., Jeon, I. J., Kim, J. D., Song, M. S., Han, S. R., Lee, S. W., Jung, H., & Oh, J. W.
The Analyst, 134(9), 1896–1901. (2009)