Designed assembly and disassembly of DNA in supramolecular structure: From ion regulated nuclear formation and machine learning recognition to running DNA cascade

Timur A. Aliev, Alexandra A. Timralieva, Tatiana A. Kurakina, Konstantin E. Katsuba, Yulia A. Egorycheva, Mikhail V. Dubovichenko, Maxim A. Kutyrev, Vladimir V. Shilovskikh, Nikita Orekhov, Nikolay Kondratyuk, Sergey N. Semenov, Dmitry M. Kolpashchikov, Ekaterina V. Skorb

Research output: Contribution to journalArticlepeer-review

Abstract

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.
Original languageEnglish
Pages (from-to)1526-1536
Number of pages11
JournalNano Select
Volume3
Issue number11
Early online date20 Sep 2022
DOIs
StatePublished - Nov 2022

Fingerprint

Dive into the research topics of 'Designed assembly and disassembly of DNA in supramolecular structure: From ion regulated nuclear formation and machine learning recognition to running DNA cascade'. Together they form a unique fingerprint.

Cite this