Structure and Interaction Based Design of Anti‐SARS‐CoV‐2 Aptamers

Mironov V, Shchugoreva I, Artyushenko P, Morozov D, Borbone N, Oliviero G, Zamay T, Moryachkov R, Kolovskaya O, Lukyanenko K, Song Y, Merkuleva I, Zabluda V, Peters G, Koroleva L, Veprintsev D, Glazyrin Y, Volosnikova E, Belenkaya S, Esina T, Isaeva A, Nesmeyanova V, Shanshin D, Berlina A, Komova N, Svetlichnyi V, Silnikov V, Shcherbakov D, Zamay G, Zamay S, Smolyarova T, Tikhonova E, Chen K, Jeng U, Condorelli G, de Franciscis V, Groenhof G, Yang C, Moskovsky A, Fedorov D, Tomilin F, Tan W, Alexeev Y, Berezovski M, Kichkailo A, Chemistry – A European Journal (2022) DOI

SASDMU7 – Apt31 - ssDNA aptamer specific to the receptor-binding domain of SARS-CoV-2

ssDNA aptamer Apt31 specific to the receptor-binding domain of SARS-CoV-2
MWexperimental 11 kDa
MWexpected 10 kDa
VPorod 12 nm3
log I(s) 4.91×10-3 4.91×10-4 4.91×10-5 4.91×10-6
ssDNA aptamer Apt31 specific to the receptor-binding domain of SARS-CoV-2 small angle scattering data  s, nm-1
ln I(s)
ssDNA aptamer Apt31 specific to the receptor-binding domain of SARS-CoV-2 Guinier plot ln 4.92×10-3 Rg: 1.9 nm 0 (1.9 nm)-2 s2
(sRg)2I(s)/I(0)
ssDNA aptamer Apt31 specific to the receptor-binding domain of SARS-CoV-2 Kratky plot 1.104 0 √3 sRg
p(r)
ssDNA aptamer Apt31 specific to the receptor-binding domain of SARS-CoV-2 pair distance distribution function Rg: 1.9 nm 0 Dmax: 6.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
ssDNA aptamer Apt31 specific to the receptor-binding domain of SARS-CoV-2 GROMACS model
log I(s)
 s, nm-1
ssDNA aptamer Apt31 specific to the receptor-binding domain of SARS-CoV-2 DAMMIN model
Synchrotron SAXS data from solutions of Apt31 - ssDNA aptamer specific to the receptor-binding domain of SARS-CoV-2 in Tris-HCl, pH 7.4 were collected on the 13A beam line at the Taiwan Photon Source, NSRRC storage ring (Hsinchu, Taiwan) using a Eiger X 9M detector at a sample-detector distance of 1.2 m and at a wavelength of λ = 0.0827 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A sample at 13.4 mg/ml was injected onto a column at 22°C. 136 successive 2 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

To reconstruct the spatial structure of the Apt31 aptamer, the size-exclusion-chromatography (SEC) SAXS measurements were performed at the TPS 13A BioSAXS beamline at NSRRC, Taiwan. The sample was prepared in Tris buffer solution and exposed by X-rays of 15 keV at 22°C with an online HPLC system. The initial concentration was 13.4 mg/ml, HPLC column provided a high dilution of the sample during the measurements. The X-Ray beam size at the sample position was 320x260 μm². Sample to detector distance was 1210.06 mm. Total 128 data frames were recorded by the detector Eiger X 9M, each 2s exposure time per frame. All of the frames recorded with a constant Rg value over the HPLC (high-performance liquid chromatography) sample flow were radially averaged into the one-dimensional SAXS curve, two of them were merged into the resulted SAXS curve.

ssDNA aptamer Apt31 specific to the receptor-binding domain of SARS-CoV-2 (Apt31)
Mol. type   DNA
Organism   Artificially synthesized
Olig. state   Monomer
Mon. MW   9.5 kDa
Sequence   FASTA