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Computational docking simulations of a DNA-aptamer for argininamide and related ligands

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Abstract

The binding properties of sequence-specific nucleic acids (aptamers) to low-molecular-weight ligands, macromolecules and even cells attract substantial scientific interest. These ligand-DNA complexes found different applications for sensing, nanomedicine, and DNA nanotechnology. Structural information on the aptamer-ligand complexes is, however, scarce, even though it would open-up the possibilities to design novel features in the complexes. In the present study we apply molecular docking simulations to probe the features of an experimentally documented L-argininamide aptamer complex. The docking simulations were performed using AutoDock 4.0 and YASARA Structure software, a well-suited program for following intermolecular interactions and structures of biomolecules, including DNA. We explored the binding features of a DNA aptamer to L-argininamide and to a series of arginine derivatives or arginine-like ligands. We find that the best docking results are obtained after an energy-minimization of the parent ligand-aptamer complexes. The calculated binding energies of all mono-substituted guanidine-containing ligands show a good correlation with the experimentally determined binding constants. The results provide valuable guidelines for the application of docking simulations for the prediction of aptamer-ligand structures, and for the design of novel features of ligand-aptamer complexes.

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Notes

  1. It should be noted that upon retrieval of the structure, the C-terminal moiety of the LARM ligands was not the expected carboxamide, but an enol (i.e. Cα(OH)=CH2). This was first corrected into the carboxamide before the rest of the computations were performed.

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Acknowledgments

This research is supported by the Israel Science Foundation.

Conflict of Interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. The Center for Nanoscience and Nanotechnology, Institute of Chemistry, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel

    H. Bauke Albada, Eyal Golub & Itamar Willner

Authors
  1. H. Bauke Albada
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  2. Eyal Golub
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  3. Itamar Willner
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Corresponding author

Correspondence to Itamar Willner.

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Albada, H.B., Golub, E. & Willner, I. Computational docking simulations of a DNA-aptamer for argininamide and related ligands. J Comput Aided Mol Des 29, 643–654 (2015). https://doi.org/10.1007/s10822-015-9844-5

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