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Clone 31 aptamer
Timeline
Starting from a RNA pool that has a 120 base random sequence core, aptamers that bind specifically to the Tat protein were selected by repeating 11 rounds of selection and amplification[1]
Rika Yamamoto et al. used an in vitro selection method and isolated a novel aptamer RNATat, a 37-mer RNA oligomer, that binds efficiently to the Tat protein of HIV-1[2]
Junji Kawakami et al. used Zn2+ for in vitro selecting to isolate novel RNA molecules that bind to the HIV-1 Tat protein, known as zinc-dependent aptamers[3]
Akimasa Matsugami et al. determined the structure of an aptamer complexed with two argininamide molecules, two adjacent U:A:U base triples were formed[4]
Yudai Yamaoki et al. proposed an RNA aptamer that acquires binding capacity against HIV-1 Tat protein via G-quadruplex formation in response to potassium ions[5]
Mustafa Oguzhan Caglayan et al. reported the HIV-Tat protein detection performance of antiTat aptamers both for the spectroscopic ellipsometry (SE) and for the surface plasmon resonance enhanced total internal reflection ellipsometry (SPReTIRE) for the first time[6]
Description
In 2000, Junji Kawakami and colleagues isolated RNA aptamers that bind specifically to the HIV-1 Tat protein. It was worth mentioning that they used Zn2+ to participate in in vitro selecting and obtained a series of zinc-dependent aptamers[3].SELEX
In 2000, Junji Kawakam and colleagues prepared an RNA library having a 30 nucleotide random region and applied to an in vitro RNA aptamer selection with Zn2+. After 12 rounds of selecting, many unique sequences were revealed from a library selected with Zn2+ and the RNA with most abundant sequence (clone 31) bound to Tat tightly only when Zn2+ existed[3].
Detailed information are accessible on SELEX page.
Structure
Clone 31 was the aptamer sequence mainly studied in the article, which had a high affinity with HIV-1 Tat protein. The 2D structure of the figures is based on the article by ribodraw tool to draw. These are two different prediction results in the article[3].5'-GGGAGAAUUCCGACCAGAAGCUUUGGUUAUCAUGUUUAUGCGUACGGGCGCCCAUAUGUGCGUCUACAUGGAUCCUCA-3'
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Ligand information
SELEX ligand
The retroviral Tat protein binds to the TAR RNA. This activates transcriptional initiation and elongation from the LTR promoter. Binding is mediated by an arginine rich region.-----From Pfam| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| HIV-1 Tat protein | P04608 | PF00539 | 9.8 kDa | MEPVDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKALGISYGRKKRRQRRRAHQNSQTHQASLSKQPTSQPRGDPTGPKE | 6CYT | 155871 |
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| clone 31 | GGGAGAAUUCCGACCAGAAGCUUUGGUUAUCAUGUUUAUGCGUACGGGCGCCCAUAUGUGCGUCUACAUGGAUCCUCA | HIV-1 Tat protein | 0.31 μM |
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 |
|---|---|---|---|
| 3MI9-C | 9.7 | 0.0 | Cell division protein kinase 9 |
| 3MIA-C | 8.9 | 0.2 | Cell division protein kinase 9 |
| 4OR5-C | 8.6 | 0.4 | Cyclin-dependent kinase 9 |
| 4OGR-D | 8.6 | 0.5 | Cyclin-dependent kinase 9 |
| 4OR5-H | 8.6 | 0.3 | Cyclin-dependent kinase 9 |
| 4OGR-H | 8.6 | 0.8 | Cyclin-dependent kinase 9 |
| 4OGR-M | 8.5 | 0.5 | Cyclin-dependent kinase 9 |
| 6CYT-D | 8.4 | 0.5 | Cyclin-dependent kinase 9 |
| 5L1Z-D | 8.1 | 0.9 | Cyclin-dependent kinase 9 |
| 6GS9 | 0.303 | 1.36 | NMR structure of aurein 2.5 in SDS micelles |
References
[1] In vitro selection of RNA aptamers that can bind specifically to Tat protein of HIV-1.Yamamoto, R., Toyoda, S., Viljanen, P., Machida, K., Nishikawa, S., Murakami, K., Taira, K., & Kumar, P. K.
Nucleic acids symposium series, (34), 145–146. (1995)
[2] A novel RNA motif that binds efficiently and specifically to the Ttat protein of HIV and inhibits the trans-activation by Tat of transcription in vitro and in vivo.
Yamamoto, R., Katahira, M., Nishikawa, S., Baba, T., Taira, K., & Kumar, P. K.
Genes to cells : devoted to molecular & cellular mechanisms, 5(5), 371–388. (2000)
[3] In vitro selection of aptamers that act with Zn2+.
Kawakami, J., Imanaka, H., Yokota, Y., & Sugimoto, N.
Journal of inorganic biochemistry, 82(1-4), 197–206. (2000)
[4] Structural basis of the highly efficient trapping of the HIV Tat protein by an RNA aptamer.
Matsugami, A., Kobayashi, S., Ouhashi, K., Uesugi, S., Yamamoto, R., Taira, K., Nishikawa, S., Kumar, P. K., & Katahira, M.
Structure (London, England : 1993), 11(5), 533–545. (2003)
[5] Development of an RNA aptamer that acquires binding capacity against HIV-1 Tat protein via G-quadruplex formation in response to potassium ions.
Yamaoki, Y., Nagata, T., Mashima, T., & Katahira, M.
Chemical communications (Cambridge, England), 53(52), 7056–7059. (2017)
[6] Spectrophotometric ellipsometry based Tat-protein RNA-aptasensor for HIV-1 diagnosis.
Caglayan, M. O., & Üstündağ, Z.
Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy, 227, 117748. (2020)
[7] Complex Formation of an RNA Aptamer with a Part of HIV-1 Tat through Induction of Base Triples in Living Human Cells Proven by In-Cell NMR.
Eladl, O., Yamaoki, Y., Kondo, K., Nagata, T., & Katahira, M.
International journal of molecular sciences, 24(10), 9069. (2023)