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C52 aptamer
Timeline
Aptamers were found to be functionally equivalent to the RBE when the assay system was saturated with Rev and better than the wild-type element when Rev was limiting[1]
Using the SELEX method, Wei Xu and colleagues obtained a series of anti-peptide aptamers that can recognize amino acid sequences[2]
HIV-1 17-mer rev peptide and RNA aptamer complex formation involves adaptive binding with the alpha-helical arginine-rich basic rev peptide targeting a widened RNA major groove centred about adjacent G.A and reversed A.A mismatches[3]
Specific inhibition of viral p24 production following co-transfection of the anti-HIV Rev-binding aptamer and HIV proviral DNAs was observed[4]
More than half of the residues have increased flexibility in the Rev-RNA aptamer complex that has a higher affinity. This further suggests that the retention of conformational flexibility may be important in high-affinity ARM-RNA recognition[5]
Description
In 1996, Wei Xu and colleagues used the SELEX method to isolate the anti-peptide aptamers with high affinity for the HIV-1 Rev protein. Several of the selected RNAs could bind the free peptide more tightly than a natural RNA ligand, the Rev-binding element[2].SELEX
In 1996, Wei Xu and colleagues used existing research to design the method required for the SELEX process. The RNA recognition domain of HIV-1 Rev is an ARM that spans residues 34-50. A 17-mer peptide (sRev) corresponding to this domain was used as a target for in vitro selection experiments. A RNA pool containing 71 random sequence positions was incubated with an affinity resin containing sRev[2].
Detailed information are accessible on SELEX page.
Structure
C52 was the aptamer sequence mainly studied in the article, which had a high affinity with HIV-1 Rev protein. The 2D structure of the figures is based on the prediction results of the RNA fold website by ribodraw tool to draw[2].5'-GGGAGAUACCAGCUUAUUCAAUUGCUUGGUACCGAGCUCGGAUCCACGUAGUAACGGGCCGCCAGUGUCUGGAAUUCGGGUCGUUCUUGAGAUAGUAAGUGCAAUCU-3'
Ligand information
SELEX ligand
REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally to relieve negative repression of GAG and ENV production. It is a phosphoprotein whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus. REV accumulates in the nucleoli.-----From Pfam| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| HIV-1 Rev protein | P04616 | PF00424 | 3.22 kDa | GAMATRQARRNRRRRWRERQRAAAAR(residue 34-50) | 2M1A | AAA44200.1 |
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| C52 | GGGAGAUACCAGCUUAUUCAAUUGCUUGGUACCGAGCUCGGAUCCACGUAGUAACGGGCCGCCAGUGUCUGGAAUUCGGGUCGUUCUUGAGAUAGUAAGUGCAAUCU | HIV-1 Rev protein | 19-36 nM |
| C17 | GGGAGAUACCAGCUUAUUCAAUUGUAUUCUCCGUGGUUUAAUCAGAGUAGAGGAGCUGACUCCUUUGGUUGGACUACGUGGAGGUGCUCUUAGAUAGUAAGUGCAAUCU | HIV-1 Rev protein | 19-36 nM |
| C8 | GGGAGAUACCAGCUUAUUCAAUUGAGCCAGUAAGUGACCCGUACUAAUACUGUUGAGUAGUAUGUAGAGGAGUGGUGAUCCUCCAAACUGCUGAGAUAGUAAGUGCAAUCU | HIV-1 Rev protein | 19-36 nM |
Similar compound
We used the RCSB PDB website's similar structure search to find the top 10 structures similar to HIV-1 Rev protein (residues 34-50), and calculated TM-socre values and RMSD values using the TM-align website.
| PDB | TM-socre | RMSD | Description |
|---|---|---|---|
| 2LD2 | 0.358 | 0.89 | Solution structure of the N-terminal domain of huntingtin (htt17) in presence of DPC micelles |
| 1DNG | 0.442 | 1.68 | NMR structure of a model hydrophilic amphipathic helical acidic peptide |
| 3N95-E | 0.034 | 1.7 | Crystal structure of human CRFR2 alpha extracellular domain in complex with Urocortin 2 |
| 1OMQ | 0.366 | 1.1 | Structure of penetratin in bicellar solution |
| 7LSO | 0.44 | 0.67 | L-Phenylseptin |
| 2RLG | 0.34 | 0.79 | NMR structure of the antimicrobial peptide RP-1 bound to SDS micelles |
| 3N93-E | 0.03 | 1.62 | Crystal structure of human CRFR2 alpha extracellular domain in complex with Urocortin 3 |
| 7LSP | 0.465 | 0.56 | D-Phenylseptin - The second residue of PHE of the peptide is a D-amino acid |
| 1O53 | 0.371 | 0.49 | Solution structure of the N-terminal membrane anchor of E. coli enzyme IIA(Glucose) |
| 6GS9 | 0.303 | 1.36 | NMR structure of aurein 2.5 in SDS micelles |
References
[1] RNA aptamers selected to bind human immunodeficiency virus type 1 Rev in vitro are Rev responsive in vivo.Symensma, T. L., Giver, L., Zapp, M., Takle, G. B., & Ellington, A. D.
Journal of virology, 70(1), 179–187. (1996)
[2] Anti-peptide aptamers recognize amino acid sequence and bind a protein epitope.
Xu, W., & Ellington, A. D.
Proceedings of the National Academy of Sciences of the United States of America, 93(15), 7475–7480. (1996)
[3] Deep penetration of an alpha-helix into a widened RNA major groove in the HIV-1 rev peptide-RNA aptamer complex.
Ye, X., Gorin, A., Ellington, A. D., & Patel, D. J.
Nature structural biology, 3(12), 1026–1033. (1996)
[4] Receptor ligand-facilitated cationic liposome delivery of anti-HIV-1 Rev-binding aptamer and ribozyme DNAs.
Konopka, K., Düzgüneş, N., Rossi, J., & Lee, N. S.
Journal of drug targeting, 5(4), 247–259. (1998)
[5] Retention of conformational flexibility in HIV-1 Rev-RNA complexes.
Wilkinson, T. A., Zhu, L., Hu, W., & Chen, Y.
Biochemistry, 43(51), 16153–16160. (2004)
[6] Structure of an RNA Aptamer that Can Inhibit HIV-1 by Blocking Rev-Cognate RNA (RRE) Binding and Rev-Rev Association.
Dearborn, A. D., Eren, E., Watts, N. R., Palmer, I. W., Kaufman, J. D., Steven, A. C., & Wingfield, P. T.
Structure (London, England : 1993), 26(9), 1187–1195.e4. (2018)