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HSV-1 US11-aptamer
Description
In 2005, Bryant KF, Cox JC 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, Bryant KF, Cox JC et al. performed in vitro selection of RNA aptamers that bind US11 from a RNA library consisting of > 1014 80 base sequences which differ in a 30 base randomized region. They performed 12 rounds of automated selection for aptamers that bound MBP-US11. A total of 23 selected aptamers were cloned and sequenced, and from this pool there emerged a consensus (UUCGCAAUYCUGCAYUG, where Y is a pyrimidine base) within the selected sequences[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[1].5'-GGGAAUGGAUCCACAUCUACGAAUUCGCAAUCCUGUAUUGAACUUCUCACUAAAACUUCACUGCAGACUUGACGAAGCUU-3'
Ligand information
SELEX 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 Binding of herpes simplex virus-1 US11 to specific RNA sequences.
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Herpes simplex virus-1 (HSV-1) US11 | D0V0N2 | NA | 16.704 kDa | MSQTQPPAPVGPGDPDVYLKGVPSAGMHPRGVHAPRGHPRMISGPPQRGDNDQAAGQCGDSGLLRVGADTTISKPSEAVRPPTIPRTPRVPREPRVPRPPREPREPRVPRAPRDPRVPRDPRDPRQPREPRPPREPRTPRTPREPRTARGSV | NA | AY832929.1 |
Some isolated sequences bind to the affinity of the protein.
| 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 |
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)