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Vitamin B12-aptamer
Timeline
Preliminary characterization of crystals of an in vitro evolved cyanocobalamin (vitamin B12) binding RNA[2]
The structure of the vitamin B12 RNA aptamer in complex with its ligand has been determined at 2.3 A resolution by X-ray crystallography[4]
Evanescent-field-coupled (EFC) waveguide-mode sensors can be used to detect interactions between RNA and a small ligand, cyanocobalamin(vitamin B12)[5]
Description
In 1994, Jack W. Szostak'J et al. employed in vitro selection techniques to isolate aptamers with high-affinity binding sites for Cyanocobalamin (vitamin B12). In 2000, Charles Wilson et al. have determined the structure of the vitamin B12 RNA complex with its ligand by X-ray crystallography at 2.3 Å resolution.In 2012, M S Thakur et al. Pioneering nano RNA aptamer wires for analyzing vitamin B12[1].SELEX
Jack W. Szostak isolated RNA chimeras specific for cyanocobalamin (vitamin B12) by in vitro screening using affinity chromatography. They first created a random sequence RNA library consisting of approximately 5*1014 molecules. After eight rounds of screening and enzyme amplification, the library contained two main RNA sequences, with the primary sequence comprising 60% of the library. To determine the binding affinity, the dissociation constants (Kd) for the interaction between cyanocobalamin and the RNA aptamers were measured using equilibrium dialysis. The primary aptamer sequence had a Kd of approximately 320 nM with cyanocobalamin, while a smaller synthesized aptamer showed a Kd of 88 nM. Several RNA aptamers were identified, noted for their strong specificity and affinity to cyanocobalamin[1].
Detailed information are accessible on SELEX page.
Structure
2D representation
Here we use ribodraw to complete the figure, through the 3D structure information[4].
5'-GGAACCGGUGCGCAUAACCACCUCAGUGCGAGCAA-3'
3D visualisation
Charles Wilson et al. determined the structure of the vitamin B12 RNA aptamer using X-ray crystallography. The structure was resolved at a high resolution of 2.3 Å.The vitamin B12 RNA aptamer is characterized by a unique tertiary structure that includes a water-filled channel through the core of an RNA triplex. This triplex structure is notably stabilized by water molecules which form bridging hydrogen bonds across planar base triples that lack significant direct base-base contacts. This structural arrangement is critical for the aptamer’s stability and specificity in binding vitamin B12. The PDB ID of this structure is 1ET4[4].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: 1ET4 by X-ray crystallography. Cyanocobalamin (vitamin B12) (shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with vitamin B12.
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Ligand information
SELEX ligand
Jack W. Szostak et al. used equilibrium dialysis to measure the dissociation constants (Kd) of the interaction between cyanocobalamin, cobinamide dicyanide, and a 35-nucleotide RNA aptamer. The dissociation constants were determined using a dialysis chamber setup, with the aptamer at a concentration of approximately 10 pM, and different concentrations of the ligands were tested to calculate the Kd values[1].
Structure ligand
Cyanocobalamin (commonly known as Vitamin B12) is a highly complex, essential vitamin, owing its name to the fact that it contains the mineral, cobalt. This vitamin is produced naturally by bacteria, and is necessary for DNA synthesis and cellular energy production. Vitamin B12 has many forms, including the cyano-, methyl-, deoxyadenosyl- and hydroxy-cobalamin forms. The cyano form, is the most widely used form in supplements and prescription drugs,. Several pharmaceutical forms of cyanocobalamin have been developed, including the tablet, injection, and nasal spray forms,,.-----From Drugbank
| PubChem CID | Molecular Formula | MW | CAS | Solubility | Drugbank ID |
|---|---|---|---|---|---|
| 5311498 | C63H88CoN14O14P | 1355.4 g/mol | 68-19-9 | Solubility in DMSO : 20.83 mg/mL | DB00115 |
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Similar compound
We used the PubChem database to screen compounds that were more similar to Cyanocobalamin (vitamin B12), 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 |
|---|---|---|---|
| Crystamine | NA | 118701720 |  |
| Hydroxocobalamin | 13422-51-0 | 44475014 |  |
| Bevidox | NA | 44176380 |  |
| cob(I)alamin | NA | 25195380 |  |
| Cobalin | NA | 54605677 |  |
| Cob(II)alamin | 13408-78-1 | 5460183 |  |
| Mecobalamin | 13422-55-4 | 6474318 |  |
| Methylcobalamin | 13422-55-4 | 123134034 |  |
References
[1] In vitro selection of RNA aptamers specific for cyanocobalamin.Lorsch JR, Szostak JW
Biochemistry. 1994 Feb 1;33(4):973-82. (1994)
[2] Preliminary characterization of crystals of an in vitro evolved cyanocobalamin (vitamin B12) binding RNA.
Sussman D, Greensides D, Reilly K, Wilson C
Acta crystallographica. Section D, Biological crystallography. 1999 Jan;55(Pt 1):326-8. (1999)
[3] The structural basis for molecular recognition by the vitamin B 12 RNA aptamer.
Sussman D, Nix JC, Wilson C
Nature structural biology. 2000 Jan;7(1):53-7. (2000)
[4] A water channel in the core of the vitamin B(12) RNA aptamer.
Sussman D, Wilson C
Structure. 2000 Jul 15;8(7):719-27. (2000)
[5] Influence of nanometric holes on the sensitivity of a waveguide-mode sensor: label-free nanosensor for the analysis of RNA aptamer-ligand interactions.
Gopinath SC, Awazu K, Fujimaki M, Sugimoto K, Ohki Y, Komatsubara T, Tominaga J, Gupta KC, Kumar PK
Analytical chemistry. 2008 Sep 1;80(17):6602-9. (2008)
[6] Nano RNA aptamer wire for analysis of vitamin B₁₂.
Selvakumar LS, Thakur MS
Analytical biochemistry. 2012 Aug 15;427(2):151-7. (2012)