Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity.

Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods.

Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.

[maxbutton id=”4″ url=”https://doi.org/10.1016/j.omtn.2021.07.015″ text=”Read more” linktitle=”Molecular Therapy – Nucleic Acids: The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer” ]


Dmitry Morozov, Vladimir Mironov, Roman V. Moryachkov, Irina A. Shchugoreva, Polina V. Artyushenko, Galina S. Zamay, Olga S. Kolovskaya, Tatiana N. Zamay, Alexey V. Krat, Dmitry S. Molodenskiy, Vladimir N. Zabluda, Dmitry V. Veprintsev, Alexey E. Sokolov, Ruslan A. Zukov, Maxim V. Berezovski, Felix N. Tomilin, Dmitri G. Fedorov, Yuri Alexeev, Anna S. Kichkail (2022):
The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer.
Molecular Therapy – Nucleic Acids 25

About the author

Stian works in School of Computer Science, at the University of Manchester in Carole Goble‘s eScience Lab as a technical software architect and researcher. In addition to BioExcel, Stian’s involvements include Open PHACTS (pharmacological data warehouse), Common Workflow Language (CWL), Apache Taverna (scientific workflow system), Linked Data and identifiers, research objects (open science) and digital preservation, myExperiment (sharing scientific workflows), provenance (where did things come from and who did it) and annotations (who said what). orcid.org/0000-0001-9842-9718