The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

Morozov, Dmitry; Mironov, Vladimir; Moryachkov, Roman V.; Shchugoreva, Irina A.; Artyushenko, Polina V.; Zamay, Galina S.; Kolovskaya, Olga S.; Zamay, Tatiana N.; Krat, Alexey V.; Molodenskiy, Dmitry S.; Zabluda, Vladimir N.; Veprintsev, Dmitry V.; Sokolov, Alexey E.; Zukov, Ruslan A.; Berezovski, Maxim V.; Tomilin, Felix N.; Fedorov, Dmitri G.; Alexeev, Yuri; Kichkailo, Anna S.

doi:10.1016/j.omtn.2021.07.015

Title: The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

Journal Article · 28 July 2021 · Molecular Therapy - Nucleic Acids

DOI: https://doi.org/10.1016/j.omtn.2021.07.015 · OSTI ID:1830225

Morozov, Dmitry ^[1]; Mironov, Vladimir ^[2]; Moryachkov, Roman V. ^[3]; Shchugoreva, Irina A. ^[4]; Artyushenko, Polina V. ^[4]; Zamay, Galina S. ^[5]; Kolovskaya, Olga S. ^[5]; Zamay, Tatiana N. ^[6]; Krat, Alexey V. ^[6]; Molodenskiy, Dmitry S. ^[7]; Zabluda, Vladimir N. ^[8]; Veprintsev, Dmitry V. ^[6]; Sokolov, Alexey E. ^[3]; Zukov, Ruslan A. ^[6]; Berezovski, Maxim V. ^[9]; Tomilin, Felix N. ^[10]; Fedorov, Dmitri G. ^[11]; Alexeev, Yuri ^[12]; Kichkailo, Anna S. ^[5]

University of Jyväskylä (Finland). Nanoscience Center
Lomonosov Moscow State University (Russia)
Kirensky Institute of Physics, Krasnoyarsk (Russia). Laboratory of Physics of Magnetic Phenomena; Russian Academy of Sciences (RAS) Krasnoyarsk Science Center (Russia). Laboratory for Digital Controlled Drugs and Theranostics
Russian Academy of Sciences (RAS) Krasnoyarsk Science Center (Russia). Laboratory for Digital Controlled Drugs and Theranostics; Krasnoyarsk State Medical University (Russia); Siberian Federal University, Krasnoyarsk (Russia)
Russian Academy of Sciences (RAS) Krasnoyarsk Science Center (Russia). Laboratory for Digital Controlled Drugs and Theranostics; Krasnoyarsk State Medical University (Russia)
Krasnoyarsk State Medical University (Russia)
Hamburg Outstation (Germany). European Molecular Biology Laboratory
Kirensky Institute of Physics, Krasnoyarsk (Russia). Laboratory of Physics of Magnetic Phenomena
Univ. of Ottawa, ON (Canada)
Kirensky Institute of Physics, Krasnoyarsk (Russia). Laboratory of Physics of Magnetic Phenomena; Siberian Federal University, Krasnoyarsk (Russia)
National Inst. of Advanced Industrial Science and Technology (AIST), Tsukuba (Japan). Research Center for Computational Design of Advanced Functional Materials
Argonne National Lab. (ANL), Lemont, IL (United States)

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.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: Bundesministerium für Bildung und Forschung (BMBF); Japan Society for the Promotion of Science (JSPS) - KAKENHI; Russian Federation - Ministry of Education and Science; USDOE

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1830225

Journal Information:: Molecular Therapy - Nucleic Acids, Journal Name: Molecular Therapy - Nucleic Acids Vol. 25; ISSN 2162-2531

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
SAXS
aptamer
fragment molecular orbital
lung adenocarcinoma
molecular dynamics
molecular simulations
oligonucleotide
small-angle X-ray scattering
spatial structure
tertiary structure

Title: The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

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References (79)

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