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Dopamine aptamer
Timeline
Development of direct competitive enzyme-linked aptamer assay for determination of dopamine in serum[2]
RNA aptamer-based electrochemical biosensor for selective and label-free analysis of dopamine[4]
Surface state of the dopamine RNA aptamer affects specific recognition and binding of dopamine by the aptamer-modified electrodes[5]
Electrochemical Label-Free Aptasensor for Specific Analysis of Dopamine in Serum in the Presence of Structurally Related Neurotransmitters[6]
Dopamine Binding and Analysis in Undiluted Human Serum and Blood by the RNA-Aptamer Electrode[7]
Description
In 1997, G P Tocchini-Valentini et al. screened dopa2/c.1 aptamer that specifically bind dopamine, revealed structural features of their binding sites, and found that ligand binding may cause RNA conformational changes. In 2011, Insook Rhee Paeng et al. development of a Direct Competitive Enzyme-Linked Aptamer Assay for the Determination of Dopamine Levels in Serum. In 2015, Elena E Ferapontova et al. investigated the specific analysis of dopamine by electrochemical aptasensor via electrostatic adsorption of RNA aptamers onto cystamine-modified electrodes, found that the aptamer surface density affects dopamine binding in a bell-shaped curve, and achieved robust monitoring in the range of 0.01-1 μM dopamine fluctuations through optimization of the conditions, which improved the sensitivity and specificity of dopamine detection in biological systems[1].SELEX
Tocchini-Valentini GP et al. successfully selected RNA aptamers specifically binding to dopamine using in vitro selection (SELEX) from an initial pool containing 3.4 × 1014 different RNA molecules. After nine rounds of affinity chromatography, the most abundant sequence, dopa2, was selected for primary study. The binding affinity (Kd) of dopa2 for dopamine was determined to be 2.8 µM using equilibrium dialysis and iso-concentration elution methods. Further secondary screening and structural analysis revealed a consensus structural motif among the aptamers, consisting of two stem-loop structures that form a stable framework through tertiary interactions. Finally, through mutational analysis and the design of small functional aptamers, the minimal active sequence and key nucleotides for constructing the dopamine-binding pocket were identified. The refined aptamer, dopa2/c.1, exhibited an improved binding affinity of 1.6 µM[1].
Detailed information are accessible on SELEX page.
Structure
The sequence and secondary prediction structure of the aptamer will be shown here, here we used ribodraw to complete the figure. The 2D structure of the figure is based on the article by ribodraw tool to draw[1].5'-GGGAAUUCCGCGUGUGCGCCGCGGAAGACGUUGGAAGGAUAGAUACCUACAACGGGGAAUAUAGAGGCCAGCACAUAGUGAGGCCCUCCUCCC-3'
Ligand information
SELEX ligand
Dopamine is catechol in which the hydrogen at position 4 is substituted by a 2-aminoethyl group. It has a role as a cardiotonic drug, a beta-adrenergic agonist, a dopaminergic agent, a sympathomimetic agent, a human metabolite, an Escherichia coli metabolite and a mouse metabolite. It is a conjugate base of a dopaminium(1+).-----From ChEBI| Name | Molecular Formula | MW | CAS | Solubility | PubChem | MedChemExpress |
|---|---|---|---|---|---|---|
| Dopamine | C8H11NO2 | 153.18 g/mol | 51-61-6 | 100 mg/mL (in DMSO) | 681 | DB00988 |
Similar compound
We used the PubChem database to screen compounds that were more similar to Dopamine, and selected the most similar compounds for display. For those without CAS numbers, we will supplement them with Pubchem CID.
| Named | CAS | Pubchem CID | Structure |
|---|---|---|---|
| Norepinephrine | 51-41-2 | 439260 |  |
| Dopamine Hydrochloride | 62-31-7 | 65340 |  |
| m-Tyramine | 588-05-6 | 11492 |  |
| dl-Norepinephrine | 138-65-8 | 951 |  |
| Deoxyepinephrine | 501-15-5 | 4382 |  |
| alpha-Methyldopamine | 555-64-6 | 17005 |  |
References
[1] In vitro selection of dopamine RNA ligands.Mannironi C, Di Nardo A, Fruscoloni P, Tocchini-Valentini GP
Biochemistry. 1997 Aug 12;36(32):9726-34. (1997)
[2] Development of direct competitive enzyme-linked aptamer assay for determination of dopamine in serum.
Park H, Paeng IR
Analytica chimica acta. 2011 Jan 24;685(1):65-73. (2011)
[3] Construction of ratiometric fluorescent sensors by ribonucleopeptides.
Annoni C, Nakata E, Tamura T, Liew FF, Nakano S, Gelmi ML, Morii T
Organic & biomolecular chemistry. 2012 Nov 28;10(44):8767-9. (2012)
[4] RNA aptamer-based electrochemical biosensor for selective and label-free analysis of dopamine.
Farjami E, Campos R, Nielsen JS, Gothelf KV, Kjems J, Ferapontova EE
Analytical chemistry. 2013 Jan 2;85(1):121-8. (2013)
[5] Surface state of the dopamine RNA aptamer affects specific recognition and binding of dopamine by the aptamer-modified electrodes.
Álvarez-Martos I, Campos R, Ferapontova EE
The Analyst. 2015 Jun 21;140(12):4089-96. (2015)
[6] Electrochemical Label-Free Aptasensor for Specific Analysis of Dopamine in Serum in the Presence of Structurally Related Neurotransmitters.
Álvarez-Martos I, Ferapontova EE
Analytical chemistry. 2016 Apr 5;88(7):3608-16. (2016)
[7] Dopamine Binding and Analysis in Undiluted Human Serum and Blood by the RNA-Aptamer Electrode.
Álvarez-Martos I, Møller A, Ferapontova EE
ACS chemical neuroscience. 2019 Mar 20;10(3):1706-1715. (2019)
[8] Engineering a Synthetic Dopamine-Responsive Riboswitch for In Vitro Biosensing.
Harbaugh SV, Silverman AD, Chushak YG, Zimlich K, Wolfe M, Thavarajah W, Jewett MC, Lucks JB, Chávez JL
ACS synthetic biology. 2022 Jul 15;11(7):2275-2283. (2022)