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Tetracycline aptamer
Timeline
Tetracycline aptamers have been found to play an important role in regulating gene expression at the yeast translation initiation level[2]
Tetracycline aptamers can reduce gene expression up to 50-fold when analysed in a yeast cell-free system in vivo[3]
A rapid and simple method to improve the use of the aptamer system has been established by developing[9]
The tetracycline aptamer control of translation initiation was demonstrated in the methanogenic archaeon Methanosarcina acetivorans[11]
Demonstrated by predicting the secondary structure methodAddition of tetracycline induced the formation of the tetracycline aptamer, opening the terminator structure and allowing transcription [16]
Developed a bioinformatics model that construct with 40-fold inhibition of GFP expression in the presence of tetracycline was discovered[19]
Use high-throughputapproach found tetracycline aptamer was also attached to the twister ribozyme[20]
Description
In 2001, Berens et al.employed in vitro selection techniques to isolate aptamers with high-affinity binding sites forTetracycline，They were found that cb28 has a high affinity. In 2003, Suess et al. present a conditional gene expression system in Saccharomyces cerevisiae which exploits direct RNA-metabolite interactions as a mechanism of genetic control. In 2003, Hanson et al. described post-transcriptional gene regulation in yeast based on direct RNA-ligand interaction. In 2008, Hong et al. discovered the cocrystal structure of the aptamer at a resolution of 2.2 A. In 2011, wittmann et al. described the tetracycline aptamer has been used in a wide variety of ribozyme designs[1,2,3,8,11].SELEX
RNA pool selection was performed using 74 random nucleotide sequences in vitro, after which tetracycline was conjugated to an epoxy-activated sepharose column under alkaline conditions and exposed to 5′-radiolabeled RNA eluted from 100 μM tetracycline for 15 rounds, and the sequences were found to be significantly enriched. And from the 13th and 14th rounds of cloning sequencing, the highest affinity of CB28 was found[1].
Detailed information are accessible on SELEX page.
Structure
2D representation
Here we use ribodraw to complete the figure, through the 3D structure information[8].
5'-GAGGGAGAGGUGAAGAAUACGACCACCUAGGUACCAUUGCACUCCGGUACCUAAAACAUACCCUC-3'
3D visualisation
The 2.2 A˚ resolution cocrystal structure of the aptamer reveals a pseudoknot-like fold formed by tertiary interactions between an 11 nucleotide loop and the minor groove of an irregular helix. The PDB ID of this structure is 3EGZ[8].Additional available structures that have been solved and detailed information are accessible on Structures page.
(Clicking the "Settings/Controls info" to turn Spin off)
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Binding pocket
Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 3EGZ by X-ray. Tetracycline(shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with tetracycline.
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Ligand information
SELEX ligand
The target molecule tetracycline was coupled to an epoxy-activated sepharose column under alkaline conditions and brought into contact with the 5’-radiolabeled RNA. The column was then washed several times, with the number of column wash steps increasing every few rounds to increase stringency. Elution was initially performed with 100 µM tetracycline, which was reduced to 10 µM after round 8 to further increase stringency. A significant enrichment of sequences eluted specifically with tetracycline was observed after 15 rounds. 44 candidates from rounds 13 and 14 were cloned and sequenced. This led to the discovery of sequence cb28, which binds to tetracycline with high affinity and was used to generate a truncated 60 nt minimer version of the aptamer[8].
Structure ligand
Tetracycline is a broad spectrum polyketide antibiotic produced by the Streptomyces genus of Actinobacteria. It exerts a bacteriostatic effect on bacteria by binding reversible to the bacterial 30S ribosomal subunit and blocking incoming aminoacyl tRNA from binding to the ribosome acceptor site. It also binds to some extent to the bacterial 50S ribosomal subunit and may alter the cytoplasmic membrane causing intracellular components to leak from bacterial cells. The FDA withdrew its approval for the use of all liquid oral drug products formulated for pediatric use containing tetracycline in a concentration greater than 25 mg/ml.2 Other formulations of tetracycline continue to be used.-----From drugBank
| Name | PubChem CID | Molecular Formula | MW | CAS | Solubility | Drugbank ID |
|---|---|---|---|---|---|---|
| Tetracycline | 54675776 | C22H24N2O8 | 444.4 g/mol | 60-54-8 | 700 mg/L(H2O, at 20℃) | DB00759 |
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Similar compound
We screened the compounds with great similarity to tetracycline by using the ZINC database and showed some of the compounds' structure diagrams. For some CAS numbers not available,we will supplement them with Pubchem CID.
| Zinc_id | Named | CAS | Pubchem CID | Structure |
|---|---|---|---|---|
| ZINC100303073 | Tetracycline ,(S) | 65517-29-5 | 54685515 |  |
| ZINC100303062 | (4S,4aR,5aR,6S,12aR)-4-(dimethylamino)-1,6,10,11,12a-pentahydroxy-6-methyl-3,12-dioxo-4,4a,5,5a-tetrahydrotetracene-2-carboxamide | NA | 54741712 |  |
| ZINC100303069 | Tetracycline zwitterion | NA | 51580080 |  |
| ZINC100303060 | (4S,4aR,5aS,6S,12aR)-4-(dimethylamino)-1,6,10,11,12a-pentahydroxy-6-methyl-3,12-dioxo-4,4a,5,5a-tetrahydrotetracene-2-carboxamide | NA | 54685767 |  |
| ZINC199039904 | (4S,4aS,5aS,6R,12aR)-4-(dimethylamino)-1,6,10,11,12a-pentahydroxy-6-methyl-3,12-dioxo-4,4a,5,5a-tetrahydrotetracene-2-carboxamide | NA | 54676644 |  |
| ZINC199362416 | (4S,4aS,5aR,6R,12aS)-4-(dimethylamino)-1,6,10,11,12a-pentahydroxy-6-methyl-3,12-dioxo-4,4a,5,5a-tetrahydrotetracene-2-carboxamide | NA | 124349182 |  |
| ZINC198562314 | (4S,4aR,5aR,6R,12aS)-4-(dimethylamino)-1,6,10,11,12a-pentahydroxy-6-methyl-3,12-dioxo-4,4a,5,5a-tetrahydrotetracene-2-carboxamide | NA | 99866033 |  |
| ZINC199057634 | (4S,4aS,5aS,6R,12aS)-4-(dimethylamino)-1,6,10,11,12a-pentahydroxy-6-methyl-3,12-dioxo-4,4a,5,5a-tetrahydrotetracene-2-carboxamide | NA | 54677780 |  |
| ZINC198562282 | (4S,4aR,5aS,6R,12aS)-4-(dimethylamino)-1,6,10,11,12a-pentahydroxy-6-methyl-3,12-dioxo-4,4a,5,5a-tetrahydrotetracene-2-carboxamide | NA | 54717006 |  |
| ZINC198633879 | Epitetracycline | NA | 54682506 |  |
| ZINC100026355 | Oxytetracycline | NA | 54675779 |  |
| ZINC199082002 | (4R,4aR,5aR,6R,12aS)-4-(dimethylamino)-1,6,10,11,12a-pentahydroxy-6-methyl-3,12-dioxo-4,4a,5,5a-tetrahydrotetracene-2-carboxamide | NA | 122172551 |  |
References
[1] A tetracycline-binding RNA aptamer.Berens, C., Thain, A. & Schroeder, R.
Bioorganic & medicinal chemistry, 9(10), 2549–2556 (2001)
[2] Conditional gene expression by controlling translation with tetracycline-binding aptamers.
Suess, B., Hanson, S., Berens, C., Fink, B., Schroeder, R., & Hillen, W
Nucleic acids research, 31(7), 1853-1858 (2003)
[3] Tetracycline-aptamer-mediated translational regulation in yeast.
Hanson, S., Berthelot, K., Fink, B., McCarthy, J. E. G. & Suess, B.
Molecular microbiology, 49(6), 1627–1637 (2003)
[4] Molecular analysis of a synthetic tetracycline-binding riboswitch.
Hanson, S., Bauer, G., Fink, B. & Suess, B
RNA (New York, N.Y.), 11(4), 503–511 (2005)
[5] Programmable ligand-controlled riboregulators of eukaryotic gene expression.
Bayer, T. S. & Smolke, C. D.
Nature biotechnology, 23(3), 337–343. (2005)
[6] Thermodynamic characterization of an engineered tetracyline-binding riboswitch.
Müller, M., Weigand, J., Weichenrieder, O. & Suess, B
Nucleic acids research, 34(9), 2607–2617 (2006)
[7] Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast.
Weigand, J. E. & Suess, B
Nucleic acids research, 35(12), 4179–4185 (2007)
[8] Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch.
Xiao, H., Edwards, T. E. & Ferré-D'Amaré, A. R.
Chemistry & biology, 15(10), 1125–1137 (2008)
[9] A fast and efficient translational control system for conditional expression of yeast genes.
Xiao, H., Edwards, T. E. & Ferré-D'Amaré, A. R.
Nucleic acids research, 37(18), e1205 (2009)
[10] Selection of tetracycline inducible self-cleaving ribozymes as synthetic devices for gene regulation in yeast.
Wittmann, A. & Suess, B
Molecular bioSystems, 7(8), 2419–2427 (2011)
[11] Development of β -lactamase as a tool for monitoring conditional gene expression by a tetracycline-riboswitch in Methanosarcina acetivorans.
Demolli, S., Geist, M. M., Weigand, J. E., Matschiavelli, N., Suess, B., & Rother, M
Archaea (Vancouver, B.C.), 2014, 725610 (2014)
[12] Tetracycline determines the conformation of its aptamer at physiological magnesium concentrations.
Reuss, A. J., Vogel, M., Weigand, J. E., Suess, B. & Wachtveitl, J
Biophysical journal, 107(12), 2962–2971 (2014)
[13] Conditional control of mammalian gene expression by tetracycline-dependent hammerhead ribozymes.
Beilstein, K., Wittmann, A., Grez, M., & Suess, B
ACS synthetic biology, 4(5), 526–534 (2015)
[14] Rational design of aptazyme riboswitches for efficient control of gene expression in mammalian cells.
Zhong, G., Wang, H., Bailey, C. C., Gao, G., & Farzan
eLife, 5, e18858 (2016)
[15] Directing cellular information flow via CRISPR signal conductors.
Liu, Y., Zhan, Y., Chen, Z., He, A., Li, J., Wu, H., Liu, L., Zhuang, C., Lin, J., Guo, X., Zhang, Q., Huang, W., & Cai, Z
Nature methods, 13(11), 938–944 (2016)
[16] Applicability of a computational design approach for synthetic riboswitches.
Domin, G., Findeiß, S., Wachsmuth, M., Will, S., Stadler, P. F., & Mörl, M
Nucleic acids research, 45(7), 4108–4119 (2017)
[17] A small, portable RNA device for the control of exon skipping in mammalian cells.
Vogel, M., Weigand, J. E., Kluge, B., Grez, M., & Suess, B
Nucleic acids research, 46(8), e48 (2018)
[18] Influence of Mg2+ on the conformational flexibility of a tetracycline aptamer.
Hetzke, T., Vogel, M., Gophane, D. B., Weigand, J. E., Suess, B., Sigurdsson, S. T., & Prisner, T. F
RNA (New York, N.Y.), 25(1), 158–167 (2019)
[19] Tuning the Performance of Synthetic Riboswitches using Machine Learning.
Groher, A. C., Jager, S., Schneider, C., Groher, F., Hamacher, K., & Suess, B
ACS synthetic biology, 8(1), 34–44 (2019)
[20] High-throughput identification of synthetic riboswitches by barcode-free amplicon-sequencing in human cells.
Strobel, B., Spöring, M., Klein, H., Blazevic, D., Rust, W., Sayols, S., Hartig, J. S., & Kreuz, S
Nature communications, 11(1), 714 (2020)
[21] Tapping the potential of synthetic riboswitches: reviewing the versatility of the tetracycline aptamer.
Kelvin, D. & Suess, B
RNA biology, 20(1), 457–468 (2023)
[22] Control of mammalian gene expression by modulation of polyA signal cleavage at 5' UTR.
Luo, L., Jea, J. D., Wang, Y., Chao, P. W., & Yen, L
Nature biotechnology, 10.1038/s41587-023-01989-0 (2024)