Next Article in Journal
Antileishmanial Compounds Isolated from Psidium Guajava L. Using a Metabolomic Approach
Next Article in Special Issue
Aptamers Chemistry: Chemical Modifications and Conjugation Strategies
Previous Article in Journal
Adsorption and Desorption Performance and Mechanism of Tetracycline Hydrochloride by Activated Carbon-Based Adsorbents Derived from Sugar Cane Bagasse Activated with ZnCl2
Previous Article in Special Issue
Anything You Can Do, I Can Do Better: Can Aptamers Replace Antibodies in Clinical Diagnostic Applications?
Open AccessArticle

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

1
Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Ames, IA 50011, USA
2
Aptalogic Inc., Ames, IA 50014, USA
3
Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
4
Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Laura Cerchia
Molecules 2019, 24(24), 4535; https://doi.org/10.3390/molecules24244535
Received: 31 October 2019 / Revised: 30 November 2019 / Accepted: 5 December 2019 / Published: 11 December 2019
(This article belongs to the Special Issue Aptamers: Successes, Limitations and Future Directions)
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. View Full-Text
Keywords: neomycin-B RNA aptamer; aminoglycoside; 2-aminopurine (2AP), molecular dynamics; isothermal titration calorimetry neomycin-B RNA aptamer; aminoglycoside; 2-aminopurine (2AP), molecular dynamics; isothermal titration calorimetry
Show Figures

Figure 1

MDPI and ACS Style

Ilgu, M.; Yan, S.; Khounlo, R.M.; Lamm, M.H.; Nilsen-Hamilton, M. Common Secondary and Tertiary Structural Features of Aptamer–Ligand Interaction Shared by RNA Aptamers with Different Primary Sequences. Molecules 2019, 24, 4535.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Search more from Scilit
 
Search
Back to TopTop