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United States Department of Agriculture

Agricultural Research Service

Research Project: THE MAIZE GENETICS AND GENOMICS DATABASE Title: A systematic approach to evolve aptamers with new specificities

Authors
item Ilgu, Muslum -
item Yennamalli, Ragothaman -
item Kleckler, Megan -
item Sen, Taner
item Lamm, Monica -
item Nilsen-Hamilton, Marit -

Submitted to: Journal of Physical Chemistry
Publication Type: Abstract Only
Publication Acceptance Date: April 4, 2012
Publication Date: May 29, 2012
Citation: Ilgu, M., Yennamalli, R.M., Kleckler, M.M., Sen, T.Z., Lamm, M.H., Nilsen-Hamilton, M. 2012. A systematic approach to evolve aptamers with new specificities. Journal of Physical Chemistry. Paper No. 23.

Technical Abstract: Aptamers are single-stranded nucleic acids with high affinities and specificities for the targets against which they are selected. Both features, along with an ability to be integrated into a large variety of sensors, make possible a wide-range of aptamer applications. However, changing aptamer specificity and/or affinity generally requires additional rounds of in vitro selection. To eliminate this secondary selection, we are exploring a novel systematic approach in which we combined wet-lab experiments with molecular docking and molecular dynamics (MD) simulations to “evolve” aptamers with altered properties. The initial studies were performed with the neomycin aptamer and 11 aminoglycoside ligands. With the exception of one ligand (ribostamycin), the energy scores obtained using docking analysis were in good agreement with experimental values obtained by isothermal titration calorimetry (ITC). Parallel, molecular dynamics (MD) simulations of the neomycin aptamer without its ligand using GROMACS showed a mobile structure consistent with the ability of this aptamer to interact with a wide range of ligands. From molecular docking and MD simulations, we identified the neomycin aptamer residues that might contribute to its ligand selectivity and designed a series of new aptamers accordingly. Through this systematic approach, we have obtained a variety of aminoglycoside aptamers with different selectivities and specificities. We believe that this approach can be applied to develop other aptamers of desired specificity and affinity.

Last Modified: 11/26/2014