HSV-1 US11 aptamer

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Description

In 2005, Coen, D. M et al. used the SELEX method to select RNA aptamers that could specifically bind to the US11 protein of Herpes simplex virus-1 (HSV-1). These aptamers were selected from 80 base sequences with 30 random base regions. These findings contribute to a further understanding of the RNA binding characteristics of HSV-1 US11 protein and may provide clues for studying how viruses regulate gene expression in host cells[1].



SELEX

In 2005, Coen, D. M et al. conducted an in vitro selection of RNA aptamers binding to US11 from an RNA library comprising over 1014 80-nucleotide sequences, which varied in a 30-base randomised region. They carried out 12 rounds of automated selection for aptamers that bound MBP-US11. A total of 23 selected aptamers were cloned and sequenced, and a consensus emerged from these sequences: UUCGCAAUYCUGCAYUG (where Y denotes a pyrimidine base)[1].

Detailed information are accessible on SELEX page.



Structure

The 2D structure of the figures is based on the prediction results of the RNA fold website by ribodraw tool to draw. C17 aptamer binds to herpes simplex virus-1 (HSV-1) US11. C17 aptamer was named by Coen, D. M et al[1].

5'-GGGAAUGGAUCCACAUCUACGAAUUCGCAAUCCUGUAUUGAACUUCUCACUAAAACUUCACUGCAGACUUGACGAAGCUU-3'

drawing

Ligand information

SELEX ligand

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

Name Sequence Ligand Affinity
C17 5'-GGGAAUGGAUCCACAUCUACGAAUUCGCAAUCCUGUAUUGAACUUCUCACUAAAACUUCACUGCAGACUUGACGAAGCUU-3' US11 70 nM
C17 5'-GGGAAUGGAUCCACAUCUACGAAUUCGCAAUCCUGUAUUGAACUUCUCACUAAAACUUCACUGCAGACUUGACGAAGCUU-3' US11-RBD 220 ± 60 nM
Lyso 5'-GGGAAUGGAUCCACAUCUACGAAUUCAUCAGGGCUAAAGAGUGCAGAGUUACUUAGUUCACUGCAGACUUGACGAAGCUU-3' US12-RBD No binding detected
dsC17 5'-GGGAAUGGAUCCACAUCUACGAAUUCGCAAUCCUGUAUUGAACUUCUCACUAAAACUUCACUGCAGACUUGACGAAGCUU-3'
3'-CCCUUACCUAGGUGUAGAUGCUUAAGCGUUAGGACAUAACUUGAAGAGUGAUUUUGAAGUGACGUCUGAACUGCUUCGAA-5'		 US13-RBD 1400 ± 170 nM
dsLyso 5'-GGGAAUGGAUCCACAUCUACGAAUUCAUCAGGGCUAAAGAGUGCAGAGUUACUUAGUUCACUGCAGACUUGACGAAGCUU-3'
5'-CCCUUACCUAGGUGUAGAUGCUUAAGUAGUCCCGAUUUCUCACGUCUCAAUGAAUCAAGUGACGUCUGAACUGCUUCGAA-3'		 US14-RBD 1200 ± 200 nM

Structure ligand

Herpes simplex virus-1 (HSV-1) US11, is a relatively small (~23 kDa), highly basic phosphoprotein that is expressed late in infection but is present at early times post-infection as it enters the cell as a component of the virion.-----From Wiki

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
Herpes simplex virus-1 (HSV-1) US11 D0V0N2 NA 16.704 kDa
...... MSQTQPPAPVGPGDPDVYLKGVPSAGMHPRGVHAPRGHPRMISGPPQRGDNDQAAGQCGDSGLLRVGADTTISKPSEAVRPPTIPRTPRVPREPRVPRPPREPREPRVPRAPRDPRVPRDPRDPRQPREPRPPREPRTPRTPREPRTARGSV
NA AY832929.1


References

[1] Binding of herpes simplex virus-1 US11 to specific RNA sequences.
Bryant, K. F., Cox, J. C., Wang, H., Hogle, J. M., Ellington, A. D., & Coen, D. M.
Nucleic acids research, 33(19), 6090–6100. (2005)