Common Secondary and Tertiary Structural Features of Aptamer–Ligand Interaction Shared by RNA Aptamers with Different Primary Sequences

Date
2019-12-11
Authors
Ilgu, Muslum
Yan, Shuting
Khounlo, Ryan
Lamm, Monica
Nilsen-Hamilton, Marit
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Abstract

Aptamer selection can yield many oligonucleotides with different sequences and affinities for the target molecule. Here, we have combined computational and experimental approaches to understand if aptamers with different sequences but the same molecular target share structural and dynamical features. NEO1A, with a known NMR-solved structure, displays a flexible loop that interacts differently with individual aminoglycosides, its ligand affinities and specificities are responsive to ionic strength, and it possesses an adenosine in the loop that is critical for high-affinity ligand binding. NEO2A was obtained from the same selection and, although they are only 43% identical in overall sequence, NEO1A and NEO2A share similar loop sequences. Experimental analysis by 1D NMR and 2-aminopurine reporters combined with molecular dynamics modeling revealed similar structural and dynamical characteristics in both aptamers. These results are consistent with the hypothesis that the target ligand drives aptamer structure and also selects relevant dynamical characteristics for high-affinity aptamer-ligand interaction. Furthermore, they suggest that it might be possible to “migrate” structural and dynamical features between aptamer group members with different primary sequences but with the same target ligand.

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This article is published as Ilgu, Muslum, Shuting Yan, Ryan M. Khounlo, Monica H. Lamm, and Marit Nilsen-Hamilton. "Common Secondary and Tertiary Structural Features of Aptamer–Ligand Interaction Shared by RNA Aptamers with Different Primary Sequences." Molecules 24, no. 24 (2019): 4535. DOI: 10.3390/molecules24244535. Posted with permission.

Keywords
neomycin-B RNA aptamer, aminoglycoside, 2-aminopurine (2AP), molecular dynamics, isothermal titration calorimetry
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