Citrulline aptamer

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Timeline

1994

The first in vitro screening of L-citrulline RNA aptamers and their evolution into an L-arginine binder[1]

1995

Structural probing and damage selection of citrulline- and arginine-specific RNA aptamers identify base positions required for binding[2]

1996

Another RNA aptamers that bind L-arginine with sub-micromolar dissociation constants and high enantioselectivity[3]

1996

NMR structures of the citrulline aptamer complex and the arginine aptamer complex[4]

1996

A stable 38-mer L-oligonucleotide ligand that binds L-arginine and a short peptide containing the basic region of the HIV-1 Tat protein[5]

2005

The anti-l-arginine d-RNA aptamer creates a CSP based on the l-RNA aptamer, the mirror image of the d-RNA aptamer[6]

Description

In 1994, Famulok, M. employed in vitro selection techniques to isolate aptamers with high-affinity binding sites for L-Citrulline. Subsequently, following the selection for L-citrulline, one of the citrulline-binding sequences (Clone 16) was used to generate a mutated pool for further selection. The capability to shift binding specificity from L-citrulline to L-arginine was demonstrated. In 1996, Famulok, M. et al. elucidated the structure of the aptamer complexed with L-Citrulline and L-arginine using multidimensional nuclear magnetic resonance spectroscopy and molecular dynamics calculations[1,4].



SELEX

The SELEX began with an initial RNA pool consisting of approximately 1015 different RNA molecules.This pool was subjected to in vitro selection targeting specific binding to L-citrulline. RNA molecules that demonstrated affinity for L-citrulline were isolated using an epoxy-activated Sepharose 6B agarose column, to which L-citrulline was coupled. After seven cycles, the selected RNA pool was cloned and sequenced. Sequencing of 21 aptamers from this pool revealed 19 different sequences, with two sequences appearing twice, indicating a convergence towards certain sequence motifs that have higher affinity for L-citrulline. Following the selection for L-citrulline, one of the citrulline-binding sequences (Clone 16) was used to generate a mutated pool for further selection. The pool was mutated at a rate of 30% per base position to introduce diversity and potential for adaptation to new targets. This mutated pool was then used in subsequent selection cycles aimed at isolating RNA aptamers with binding specificity for L-arginine. After four cycles, 22 sequences derived from the L-arginine pool were analyzed. Of these, 11 sequences were found to potentially fold into a motif slightly different from the L-citrulline-binding motif but were highly specific to L-arginine[1].

Detailed information are accessible on SELEX page.



Structure

2D representation

Here we used ribodraw to complete the figure, through the 3D structure information. The L-citrulline aptamer aptamer was named by Famulok, M. in the article[1].

5'-CAGUGAGGAAGAGAAAGCUCGCUGGAUUGGCUG-3'

drawing

3D visualisation

The solution structures of the L-citrulline and L-arginine RNA aptamers complexed with their respective ligands were determined by Famulok, M. et al. through multidimensional NMR spectroscopy. The PDB ID of this structure is 1KOD[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)      

drawing PDBe Molstar