DIR2s-apt aptamer

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Timeline

2017

An RNA aptamer selected for binding to the fluorogenic cyanine dye dimethylindole red (DIR), also binds oxazole thiazole blue (OTB)[1]

2018

The crystal structures of both the apo and OTB-SO3 bound forms of DIR2s at 2.0 Å and 1.8 Å resolution respectively was solved[2]

Description

 In 2017, Xiaohong Tan and Tudor P.Constantin et al. screened out aptamer, which has affinity to both dimethylindole red and oxazole thiazole blue and could give two well-resolved emission colors. In 2018, Sandip A. Shelke and Yaming Shao et al. solved the overall structure of OTB-SO3-bound DIR2s aptamer-Fab complex by collecting Small Angle X-ray Scattering data of crystals[1,2].

SELEX

Biotinylated DIR was used as Positive target to facilitate the enrichment process. The RNA pool used for this selection contained ~1014 unique sequences and universal, stem-loop forming sequence flanked by randomized region. RNA pool was asymmetric, with the putative stem-loop shifted toward the 5'-end of the sequence. The aptamer from the asymmetric pool was abundantly represented after 14 rounds of selection. After sequence minimization and optimization, a 57 nucleotide anti-DIR RNA aptamer (DIR2s-Apt) which can bind and activate DIR fluorescence was obtained[1].
Detailed information are accessible on SELEX page.



Structure

2D representation

Here we used ribodraw to complete the figure, through the 3D structure information[1].

5'-GGAUGCGCCUUGAAAAGCCUGCUUCGGCAGCUGGUGAAUGACAGCUAUGGCGCAUCC-3'

 drawing

3D visualisation

In 2018, Sandip A. Shelke and Yaming Shao et al. solved the overall structure of OTB-SO3 fluorophore-bound DIR2s aptamer-Fab complex at 2.0 Å and DIR2s aptamer structures in the presence and absence of the OTB-SO3 fluorophore at 1.8 Å by collecting small angle X-ray scattering data of crystals. The PDB ID of the two structures are 6DB8 and 6DB9[2].
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: 6DB8 by NMR and collecting small angle X-ray scattering data of crystals. OTB-SO3 (shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with OTB-SO3 or other nucleotides surround small molecules.

drawing drawing


Ligand information

SELEX ligand

Binding affinity was determined by fluorescence titration in the buffer and calculated by the concentration correlation function between aptamer concentration and fluorescence intensity[1].

drawing

Structure ligand
PubChem CID Molecular Formula MW CAS Solubility Drugbank ID
54402972 C17H15N2OS+ 295.4 g/mol NA NA NA
drawing drawing

Similar compound

We screened the compounds with great similarity to OTB 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
ZINC2509998 3-methyl-2-[(3-methyl-1,3-benzothiazol-3-ium-2-yl)methylidene]-1,3-benzothiazole NA 17729 drawing
ZINC20070324 (2Z)-5-chloro-3-methyl-2-[(3-methyl-1,3-benzothiazol-3-ium-2-yl)methylidene]-1,3-benzothiazole NA 22332836 drawing
ZINC844804 2-[(Z)-2-methoxy-3-phenylprop-1-enyl]-3-methyl-1,3-benzothiazol-3-ium NA 1110831 drawing
ZINC107280752 3-methyl-N-(3-methyl-1,3-benzothiazol-3-ium-2-yl)-1,3-benzothiazol-2-imine NA 54298998 drawing
ZINC32105922 2-[(3-methyl-1,3-benzothiazol-3-ium-2-yl)methyl]-1,3-benzoxazole NA 12690696 drawing
ZINC272646 3-methyl-2-[2-(3-methyl-1,3-benzothiazol-3-ium-2-yl)ethyl]-1,3-benzothiazol-3-ium NA 779797 drawing
ZINC100399021 (E)-3-methyl-N-[(E)-(3-methyl-1,3-benzoxazol-2-ylidene)amino]-1,3-benzoxazol-2-imine NA 5816761 drawing
ZINC100141140 (2E)-3-methyl-2-(3-methyl-1,3-benzothiazol-2-ylidene)-1,3-benzothiazole NA 6432295 drawing
ZINC169438545 (2E)-2-(1,3-benzothiazol-2-ylmethylidene)-3-methyl-1,3-benzothiazole NA 154540469 drawing


References

[1] Fluoromodules consisting of a promiscuous RNA aptamer and red or blue fluorogenic cyanine dyes: Selection, characterization, and bioimaging.
Tan, X., Constantin, T. P., Sloane, K. L., Waggoner, A. S., Bruchez, M. P., & Armitage, B. A.
Journal of the American Chemical Society, 139(26), 9001–9009. (2017)
[2] Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif.
Shelke, S. A., Shao, Y., Laski, A., Koirala, D., Weissman, B. P., Fuller, J. R., Tan, X., Constantin, T. P., Waggoner, A. S., Bruchez, M. P., Armitage, B. A., & Piccirilli, J. A.
Nature communications, 9(1), 4542. (2018)