Home
Database
Research
About us
Search
Tetracycline aptamer
Timeline
Tetracycline aptamers have been found to play a significant role in regulating gene expression at the level of yeast translation initiation[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 method addition of tetracycline induced the formation of the tetracycline aptamer, opening the terminator structure and allowing transcription[16]
A cassette exon was designed that could be either retained or skipped by addition of tetracycline via the insertion of the aptamer near the 3’ splice site of the cassette exon[17]
Developed a bioinformatics model that construct with 40-fold inhibition of GFP expression in the presence of tetracycline was discovered[19]
Used high-throughputapproach found tetracycline aptamer was also attached to the twister ribozyme[20]
Description
In 2001, Berens and colleagues utilised in vitro selection techniques to isolate aptamers with high-affinity binding sites for tetracycline. They identified that cb28 exhibited a notably high affinity. In 2003, Suess and team introduced a conditional gene expression system in Saccharomyces cerevisiae, which capitalises on direct RNA-metabolite interactions as a means of genetic regulation. Concurrently, Hanson and colleagues elucidated post-transcriptional gene regulation in yeast, predicated on direct RNA-ligand interactions. Advancing to 2008, Hong and associates unveiled the co-crystal structure of the aptamer at a resolution of 2.2 Å. In 2011, Wittmann and colleagues detailed the extensive application of the tetracycline aptamer in a diverse array of ribozyme designs[1,2,3,8,11].
SELEX
In 2001, Berens C and colleagues utilised an in vitro selection strategy to selex RNA aptamers with a high affinity for tetracycline. They constructed an RNA library consisting of a 113-nucleotide sequence that included a 74-nucleotide random region, employing tetracycline-agarose as an affinity column to filter RNA molecules capable of binding tetracycline, with tetracycline attached to the agarose via the cb28 site. By increasing the number of column washes (from 5 to 8, 12, and ultimately to 20 column volumes) and reducing the concentration of tetracycline in the affinity buffer to 10 mM from the ninth round onwards, they intensified the selective pressure. After 15 rounds of selection and amplification, the RNA pool that demonstrated high-affinity binding to tetracycline was able to interact specifically with the tetracycline affinity column and could be eluted with tetracycline. They amplified the eluted RNA through PCR and reverse transcription, subjected cb28 to phosphorylation treatment, utilised Pb2+-induced cutting of RNA to observe changes in RNA cleavage patterns in the presence of tetracycline, determined the binding sites of tetracycline on RNA using UV, and employed DMA modification to probe the RNA secondary structure[1].
Detailed information are accessible on SELEX page.
Structure
2D representation
In 2008, Xiao et al. elucidated the structure of the tetracycline aptamer using methods such as MAD, which primarily comprises three helices, P1, P2, and P3, along with loop L3 that links these helices in the secondary structure, as shown in the figure below. Here, we utilised RiboDraw software to complete this illustration, based on the 3D structural information[8].
5'-GAGGGAGAGGUGAAGAAUACGACCACCUAGGUACCAUUGCACUCCGGUACCUAAAACAUACCCUC-3'
3D visualisation
In 2008, Xiao and colleagues determined the tertiary structure of the tetracycline aptamer using X-ray crystallography at 2.2 Å resolution. This structure is characterised by a pseudoknot-like fold formed through tertiary interactions between an 11-nucleotide loop (L3) and the minor groove of an irregular helix, comprising three helices (P1, P2, and P3) that form an H-shaped architecture. The tetracycline binding site is located at the junction of two helical stacks, formed by the minor grooves of L3 and helices J1/2 and J2/3. 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)
|
|
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 magenta. Right: The hydrogen bonds of binding sites of the aptamer bound with tetracycline.
|
|
Ligand information
SELEX ligand
Xiao and colleagues employed several methods, including isocratic elution from tetracycline-agarose and RNA elution, to determine the dissociation constant of the tetracycline-aptamer complex both on the column and in solution. These approaches were utilised to thoroughly assess the affinity and stability of the tetracycline-aptamer interaction under various experimental conditions, thereby providing a robust evaluation of the binding affinity and dynamics between RNA molecules and tetracycline in diverse environments[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 reversibly binding 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.-----From Drugbank
PubChem CID: a unique identifier for substances in the PubChem database.
CAS number: a global registry number for chemical substances.
Drugbank: a comprehensive database with detailed information on drugs and drug targets.
| Name | PubChem CID | Molecular Formula | Molecular Weight | CAS | Solubility | Drugbank ID |
|---|---|---|---|---|---|---|
| Tetracycline | 54675776 | C22H24N2O8 | 444.4 g/mol | 60-54-8 | 700 mg/L(H2O, at 20 °C) | DB00759 |
 |
 |
Similar compound(s)
We screened compounds with a high degree of similarity to tetracycline using the ZINC database and presented some of the compounds' structural diagrams. For certain CAS numbers that were not available, we will augment them with PubChem CIDs.
ZINC ID: a compound identifier used by the ZINC database, one of the largest repositories for virtual screening of drug-like molecules.
PubChem CID: a unique identifier for substances in the PubChem database.
CAS number: a global registry number for chemical substances.
| ZINC ID | Name | 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)