Development of DNA Aptamers for Visualization of Glial Brain Tumors and Detection of Circulating Tumor Cells

Kichkailo A, Narodov A, Komarova M, Zamay T, Zamay G, Kolovskaya O, Erakhtin E, Glazyrin Y, Veprintsev D, Moryachkov R, Zabluda V, Shchugoreva I, Artyushenko P, Mironov V, Morozov D, Khorzhevskii V, Gorbushin A, Koshmanova A, Nikolaeva E, Grinev I, Voronkovskii I, Grek D, Belugin K, Volzhentsev A, Badmaev O, Luzan N, Lukyanenko K, Peters G, Lapin I, Kirichenko A, Konarev P, Morozov E, Mironov G, Gargaun A, Muharemagic D, Zamay S, Kochkina E, Dymova M, Smolyarova T, Sokolov A, Modestov A, Tokarev N, Shepelevich N, Ozerskaya A, Chanchikova N, Krat A, Zukov R, Bakhtina V, Shnyakin P, Shesternya P, Svetlichnyi V, Petrova M, Artyukhov I, Tomilin F, Berezovski M, Molecular Therapy - Nucleic Acids (2023) DOI

SASDRY7 – Gli-55 - ssDNA aptamer to glioma brain tumor cells

Gli-55 - ssDNA aptamer to glioma brain tumor cells
MWexperimental 19 kDa
MWexpected 19 kDa
VPorod 35 nm3
log I(s) 1.06×103 1.06×102 1.06×101 1.06×100
Gli-55 - ssDNA aptamer to glioma brain tumor cells small angle scattering data  s, nm-1
ln I(s)
Gli-55 - ssDNA aptamer to glioma brain tumor cells Guinier plot ln 1.06×103 Rg: 2.8 nm 0 (2.8 nm)-2 s2
(sRg)2I(s)/I(0)
Gli-55 - ssDNA aptamer to glioma brain tumor cells Kratky plot 1.104 0 √3 sRg
p(r)
Gli-55 - ssDNA aptamer to glioma brain tumor cells pair distance distribution function Rg: 2.9 nm 0 Dmax: 11.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Gli-55 - ssDNA aptamer to glioma brain tumor cells DAMMIF model
log I(s)
 s, nm-1
Gli-55 - ssDNA aptamer to glioma brain tumor cells GROMACS model
Synchrotron SAXS data from solutions of Gli-55 - ssDNA aptamer to glioma brain tumor cells in Dulbecco phosphate-buffered saline (DPBS), pH 7.4 were collected on the EMBL P12 beam line at PETRA III (DESY, Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). The s-axis was calibrated with silver behenate. In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 100.00 μl sample at 10 mg/ml was injected at a 0.40 ml/min flow rate onto a GE Superdex 75 Increase 10/300 column at 20.4°C. The eluent of the employed chromatography column was passed through a 1.7 mm quartz capillary held under vacuum. 3600 individual 1 s exposure X-ray data frames were measured from the continuously-flowing column eluate across one column volume. The two-dimensional SAXS intensities were reduced to I(s) vs s using the integrated analysis pipeline SASFLOW. The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering of an appropriate solvent-blank was subtracted.

To distinguish the oligomeric constituents in solution the joint technique of size-exclusion chromatography with SAXS (SEC-SAXS) was applied. To decompose the partially overlapping components in SEC-SAXS data the evolving factor analysis (EFA) was applied using the program EFAMIX.

Gli-55 - ssDNA aptamer to glioma brain tumor cells (Gli-55)
Mol. type   DNA
Organism   synthetic construct
Olig. state   Monomer
Mon. MW   18.6 kDa
Sequence   FASTA