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

被引：5

作者：

Aliev, Timur A. ^{[1
]}

Timralieva, Alexandra A. ^{[1
]}

Kurakina, Tatiana A. ^{[1
]}

Katsuba, Konstantin E. ^{[1
]}

Egorycheva, Yulia A. ^{[1
]}

Dubovichenko, Mikhail V. ^{[1
]}

Kutyrev, Maxim A. ^{[1
]}

Shilovskikh, Vladimir V. ^{[1
]}

Orekhov, Nikita ^{[2
,3
,4
]}

Kondratyuk, Nikolay ^{[2
,3
,5
]}

Semenov, Sergey N. ^{[6
]}

Kolpashchikov, Dmitry M. ^{[1
,7
,8
]}

Skorb, Ekaterina V. ^{[1
]}

机构：

[1] ITMO Univ, St Petersburg, Russia

[2] Moscow Inst Phys & Technol, Moscow, Russia

[3] Russian Acad Sci, Joint Inst High Temp, Moscow, Russia

[4] Bauman Moscow State Tech Univ, Moscow, Russia

[5] Natl Res Univ Higher Sch Econ, Moscow, Russia

[6] Weizmann Inst Sci, Dept Mol Chem & Mat Sci, Rehovot, Israel

[7] Univ Cent Florida, Dept Chem, Orlando, FL USA

[8] Univ Cent Florida, Burnett Sch Biomed Sci, Orlando, FL USA

来源：

NANO SELECT | 2022年 / 3卷 / 11期

关键词：

DNA cascade; encapsulation; machine learning; nucleation; self-assembly; supramolecular structure; PLASMID DNA; ENCAPSULATION; PROTECTION; STABILITY;

D O I：

10.1002/nano.202200092

中图分类号：

TB3 [工程材料学];

学科分类号：

0805 ; 080502 ;

摘要：

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.

引用

页码：1526 / 1536

页数：11

共 45 条

[21] Cut and Paste for Cancer Treatment: A DNA Nanodevice that Cuts Out an RNA Marker Sequence to Activate a Therapeutic Function [J].