Open AccessDesigned assembly and disassembly of DNA in supramolecular structure: From ion regulated nuclear formation and machine learning recognition to running DNA cascade
Author(s) -
Aliev Timur A.,
Timralieva Alexandra A.,
Kurakina Tatiana A.,
Katsuba Konstantin E.,
Egorycheva Yulia A.,
Dubovichenko Mikhail V.,
Kutyrev Maxim A.,
Shilovskikh Vladimir V.,
Orekhov Nikita,
Kondratyuk Nikolay,
Semenov Sergey N.,
Kolpashchikov Dmitry M.,
Skorb Ekaterina V.
Publication year - 2022
Publication title -
nano select
Language(s) - English
Resource type - Journals
ISSN - 2688-4011
DOI - 10.1002/nano.202200092
Subject(s) - supramolecular chemistry , dna , melamine , biosensor , chemistry , nanotechnology , cascade , ion , molecular machine , combinatorial chemistry , oligonucleotide , materials science , biophysics , biochemistry , chromatography , molecule , organic chemistry , biology
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.