Theophylline aptamer

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Timeline

1994

Aptamers are isolated out for the first time[1]

1997

First demonstrated that the aptamer could be linked to stem II of a self-cleaving hammerhead ribozyme[2]

1997

Determination of RNA structural interactions in the theophylline ligand binding site using NMR techniques[3]

1999

First discovery of theophylline-reactive riboswitches for controlling gene expression in vivo[4]

2001

Created a binary RNA switch by linking the theophylline and FMN aptamers to the hammerhead[5]

2005

Demonstrated that the aptamer can be truncated to a 13-mer aptamer and still retain selective binding[6]

2005

Theophylline-controlled 'anti-switch' found to control green fluorescent protein expression in Saccharomyces cerevisiae[7]

2006

Young and Deiters added a second level of control by photocaging the theophylline ligand, resulting in a photochemical activation of the ribozyme by liberation of the caging group[8]

2007

Developed a computational model to generate functional theophylline ribozymes[9]

2009

A flow cytometry-based screen for identifying synthetic riboswitches that induce robust increases in gene expression in the presence of theophylline[10]

2013

Using a computational model, Penchovsky developed and tested a theophyllinehammerhead ribozyme fusion that was inactivated with a 30-fold dynamic range[11]

2013

Developed three OFF theophylline switches that are functional in vivo [12]

2015

The aptamers found to optimise ribose enlightenment[13]

2015

The better standardization of gene expression or cellular processes[14]

2015

Six new theophylline aptamers discovered using computerised screening[15]

2018

The aptamers can build logic gates in cells[16]

2018

New theophylline-reactive aptamers are screened from a synthetic library in Escherichia coli[17]

Description

 In 1994, Zimmermann et al. used SELEX to screen the solution structures of high-affinity RNA aptamers with theophylline. in1997 the interaction of RNA structures in the ligand-binding site was visualised using NMR techniques. in1998 it was found that U27 and G27 RNAs bound theophylline with low affinity (Kd values > 4 μM). the NMR spectra of U27 RNA showed the presence of an A7-U27 base pair in the free RNA that prevented the formation of a key base platform motif. NMR spectroscopy of U27 RNA revealed the presence of the A7-U27 base pair in free RNA, which prevented the formation of structural motifs in the critical base platform, and these interactions inhibited theophylline binding[3,4,7].

SELEX

Robert D. Jenison et al. used SELEX to screen for RNA molecules with affinity for theophylline, generated a pool of 1014 RNA molecules that contain a 40-nucleotide region of random sequence. The RNA pool was added to a Sepharose column to which 1-carboxypropyl theophylline was covalently cross-linked. Bound RNA was eluted by the addition of 0.1 M theophylline. The eluted RNA was converted to DNA and amplified by polymerase chain reaction (PCR) as described[1].
Detailed information are accessible on SELEX page.



Structure

2D representation

Here we use ribodraw to complete the figure, through the 3D structure information. TCT8-4 was the aptamer sequence mainly studied in SELEX article.[3].

5'-GGCAUACCAGCCGAAAGGCCCUUGGCAGCGUC-3'

 drawing

3D visualisation

Zimmermann et al, by using NMR and X-PLOR 3.113 calculations, demonstrated the solution structure of the high-affinity RNA theophylline complex, with the C27 nucleotide being the key residue that recognizes theophylline and distinguishes it from caffeine, which has a PDB ID of 1EHT[3].
Additional available structures that have been solved and detailed information are accessible on Structures page.

(Clicking the "Settings/Controls info" to turn Spin off)      
drawing PDBe Molstar




Binding pocket

Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 1EHT by NMR. Theophylline (shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with theophylline.

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Ligand information

SELEX ligand

Zimmermann et al. The binding properties of specific RNAs obtained from the theophylline SELEX experiments were determined by using SELEX, PCR, counter-SELEX. by equilibrium filtration analyses using Equilibrium filtration analysis was performed on theophylline, a 38-nucleotide truncated version of TCT8-4 RNA and theophylline, TCT8-4 RNA (mTCT8-4) to determine the minimum requirement for high-affinity binding to theophylline. Minimum requirement for high affinity binding to theophylline. This RNA interacts with theophylline with a Kd of 0.1uM, confirming that all structural determinants required for theophylline binding are contained in this truncated RNA[3].

drawing

Structure ligand

A methylxanthine derivative from tea with diuretic, smooth muscle relaxant, bronchial dilation, cardiac and central nervous system stimulant activities. Mechanistically, theophylline acts as a phosphodiesterase inhibitor, adenosine receptor blocker, and histone deacetylase activator. Theophylline is marketed under several brand names such as Uniphyl and Theochron, and it is indicated mainly for asthma, bronchospasm, and COPD.-----From DrugBank
PubChem CID Molecular Formula MW CAS Solubility Drugbank ID
2153 C7H8N4O2 180.16 g/mol 58-55-9 7360mg/L (at 25 °C) DB00277
drawing drawing

Similar compound

We screened the compounds with great similarity totheophylline 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
ZINC18043251 Theophylline 58-55-9 2153 drawing
ZINC13517144 1-Methylxanthine 6136-37-4 80220 drawing
ZINC4685854 3-Methylxanthine 1076-22-8 70639 drawing
ZINC100018165 8-Chlorotheophylline 85-18-7 10661 drawing
ZINC100005670 8-Bromotheophylline 10381-75-6 11808 drawing
ZINC1084 caffeine 21399 2519 drawing
ZINC8616085 3-Methylguanine 2958-98-7 76292 drawing
ZINC100043983 1,3-Dimethyluric acid 944-73-0 70346 drawing
ZINC403604 Isocaffeine 519-32-4 1326 drawing


References

[1] High-resolution molecular discrimination by RNA.
Jenison, R. D., Gill, S. C., Pardi, A., & Polisky, B.
Science (New York, N.Y.), 263(5152), 1425–1429. (1994)
[2] Rational design of allosteric ribozymes.
Tang, J., & Breaker, R. R.
Chemistry & biology, 4(6), 453–459. (1997)
[3] Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA.
Zimmermann, G. R., Jenison, R. D., Wick, C. L., Simorre, J. P., & Pardi, A.
Nature structural biology, 4(8), 644–649. (1997)
[4] A semiconserved residue inhibits complex formation by stabilizing interactions in the free state of a theophylline-binding RNA.
Zimmermann, G. R., Shields, T. P., Jenison, R. D., Wick, C. L., & Pardi, A.
Biochemistry, 37(25), 9186–919. (1998)
[5] Engineering precision RNA molecular switches.
Soukup, G. A., & Breaker, R. R.
Proceedings of the National Academy of Sciences of the United States of America, 96(7), 3584–3589. (1999)
[6] Design of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization.
Soukup, G. A., & Breaker, R. R.
Structure (London, England : 1993), 7(7), 783–791. (1999)
[7] Molecular interactions and metal binding in the theophylline-binding core of an RNA aptamer.
Zimmermann, G. R., Wick, C. L., Shields, T. P., Jenison, R. D., & Pardi, A.
RNA (New York, N.Y.), 6(5), 659–667. (2000)
[8] Cooperative binding of effectors by an allosteric ribozyme.
Jose, A. M., Soukup, G. A., & Breaker, R. R.
Nucleic acids research, 29(7), 1631–1637. (2001)
[9] Unnatural base pairs mediate the site-specific incorporation of an unnatural hydrophobic component into RNA transcripts.
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[10] A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo.
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[11] Unusually short RNA sequences: design of a 13-mer RNA that selectively binds and recognizes theophylline.
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[12] Programmable ligand-controlled riboregulators of eukaryotic gene expression.
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[13] Photochemical hammerhead ribozyme activation.
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[14] Computational selection of nucleic acid biosensors via a slip structure model.
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[16] A flow cytometry-based screen for synthetic riboswitches.
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[17] Design principles for ligand-sensing, conformation-switching ribozymes.
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[18] Kinetic analysis of aptazyme-regulated gene expression in a cell-free translation system: modeling of ligand-dependent and -independent expression.
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[20] Theophylline-dependent riboswitch as a novel genetic tool for strict regulation of protein expression in Cyanobacterium Synechococcus elongatus PCC 7942.
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[22] Thermodynamic and kinetic folding of riboswitches.
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[23] Engineering dynamic cell cycle control with synthetic small molecule-responsive RNA devices.
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[24] Searching the Sequence Space for Potent Aptamers Using SELEX in Silico.
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[25] Ynthesizing artificial devices that redirect cellular information at will.
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