TY - JOUR
T1 - Designed assembly and disassembly of DNA in supramolecular structure: From ion regulated nuclear formation and machine learning recognition to running DNA cascade
AU - Aliev, Timur A.
AU - Timralieva, Alexandra A.
AU - Kurakina, Tatiana A.
AU - Katsuba, Konstantin E.
AU - Egorycheva, Yulia A.
AU - Dubovichenko, Mikhail V.
AU - Kutyrev, Maxim A.
AU - Shilovskikh, Vladimir V.
AU - Orekhov, Nikita
AU - Kondratyuk, Nikolay
AU - Semenov, Sergey N.
AU - Kolpashchikov, Dmitry M.
AU - Skorb, Ekaterina V.
N1 - The work was carried out with the support of the Ministry of Science and Higher Education of the Russian Federation (agreement № 075-15-2021-1349). The Priority 2030 Federal Academic Leadership Program is acknowledged for infrastructural support. The SEM and EDX studies have been performed in the Centre for Geo-Environmental Research and Modelling of St. Petersburg State University. Support from the Basic Research Program of the National Research University Higher School of Economics is gratefully acknowledged for the part of work on the molecular dynamics models development and the following simulations. The calculations were performed using the resources of HPC facilities at HSE University.[45]
PY - 2022/11
Y1 - 2022/11
N2 - Abstract In this paper, we introduce a novel encapsulation system for DNA oligonucleotides. Supramolecular assembly of melamine cyanurate encapsulates DNA at pH 7 and start to release it at pH less than 6.5. We study the assembly and disassembly in time in specially designed reaction-diffusion system. Magnesium ions allow spatial separation of DNA with the highest DNA concentration in the core of melamine cyanurate capsule. Molecular dynamics (MD) simulation shows that DNA acts as a nucleation centre for melamine cyanurate. Dataset of fluorescent images analysed by machine learning algorithms indicates correlation between structure of melamine cyanurate capsules for DNA trapping and concentration of magnesium ions. The concentration of magnesium ions can be recognized with 96% accuracy proving that all environmental conditions are extremely important during the self-assembly and should be considered for laboratory and industrial applications of the suggested approach. Moreover, the encapsulated DNA can undergo a cascade reaction consisting of hybridization with complementary strand and its cleavage at a designated site. This reactivity opens a fresh avenue for various applications in biosensing, diagnostics, DNA compartmentalization, and even gives new hints for the origin-of-life questions.
AB - Abstract In this paper, we introduce a novel encapsulation system for DNA oligonucleotides. Supramolecular assembly of melamine cyanurate encapsulates DNA at pH 7 and start to release it at pH less than 6.5. We study the assembly and disassembly in time in specially designed reaction-diffusion system. Magnesium ions allow spatial separation of DNA with the highest DNA concentration in the core of melamine cyanurate capsule. Molecular dynamics (MD) simulation shows that DNA acts as a nucleation centre for melamine cyanurate. Dataset of fluorescent images analysed by machine learning algorithms indicates correlation between structure of melamine cyanurate capsules for DNA trapping and concentration of magnesium ions. The concentration of magnesium ions can be recognized with 96% accuracy proving that all environmental conditions are extremely important during the self-assembly and should be considered for laboratory and industrial applications of the suggested approach. Moreover, the encapsulated DNA can undergo a cascade reaction consisting of hybridization with complementary strand and its cleavage at a designated site. This reactivity opens a fresh avenue for various applications in biosensing, diagnostics, DNA compartmentalization, and even gives new hints for the origin-of-life questions.
U2 - 10.1002/nano.202200092
DO - 10.1002/nano.202200092
M3 - مقالة
SN - 2688-4011
VL - 3
SP - 1526
EP - 1536
JO - Nano Select
JF - Nano Select
IS - 11
ER -