Comparison of DNA analysis on biochips with brush polymer cells and cross-linked polymer cells

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Abstract

The regulation of substrate surface properties in biochip technology opens the possibility of optimizing platforms for efficient biomolecule recognition. The research is aimed at exploring the use of brush polymers to improve the sensitivity and speed of DNA analysis on biochips. Brush polymer cells for biochips were prepared by UV-initiated polymerization of monomers from the surface on polyethylene terephthalate substrates. Cross-linked hydrogel polymer cells for biochips were prepared on polybutylene terephthalate substrates by copolymerization of gel components with DNA probes. The probes in brush polymer cells were immobilized through activated carboxyl groups. A single-stranded DNA target with a length of 124 nucleotides corresponding to the 7th exon of the human ABO gene was used for hybridization analysis. Hybridization of the DNA target was studied on biochips with cells made of brush polymers and cross-linked polyacrylamide hydrogels. The results of hybridization analysis on biochips were evaluated by digital fluorescence microscopy. Higher intensity of fluorescence signals and higher ratio of signals of cells with perfect duplexes to those of cells with imperfect duplexes were observed in cells from brush polymers compared to cells from 3D cross-linked polymers. Achievement of hybridization signal up to 90% of saturation occurred in the same time in both cell types. The relevance of this work stems from the need for highly accurate and efficient diagnostic methods to analyze biomolecules with minimal time and reagent consumption. The development of biochips based on brush polymers will increase the accuracy and sensitivity of molecular studies, which is especially important for early diagnosis of diseases.

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About the authors

R. A. Miftakhov

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Author for correspondence.
Email: mr.miftahov20@yandex.ru
Russian Federation, ul. Vavilova 32/1, Moscow, 119991 Russia

G. F. Shtylev

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: mr.miftahov20@yandex.ru
Russian Federation, ul. Vavilova 32/1, Moscow, 119991 Russia

I. Yu. Shishkin

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: mr.miftahov20@yandex.ru
Russian Federation, ul. Vavilova 32/1, Moscow, 119991 Russia

V. Е. Shershov

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: mr.miftahov20@yandex.ru
Russian Federation, ul. Vavilova 32/1, Moscow, 119991 Russia

V. E. Kuznetsova

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: mr.miftahov20@yandex.ru
Russian Federation, ul. Vavilova 32/1, Moscow, 119991 Russia

S. A. Surzhikov

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: mr.miftahov20@yandex.ru
Russian Federation, ul. Vavilova 32/1, Moscow, 119991 Russia

V. A. Vasiliskov

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: mr.miftahov20@yandex.ru
Russian Federation, ul. Vavilova 32/1, Moscow, 119991 Russia

О. А. Zasedateleva

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: mr.miftahov20@yandex.ru
Russian Federation, ul. Vavilova 32/1, Moscow, 119991 Russia

А. Yu. Ikonnikova

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: mr.miftahov20@yandex.ru
Russian Federation, ul. Vavilova 32/1, Moscow, 119991 Russia

Т. V. Nasedkina

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: mr.miftahov20@yandex.ru
Russian Federation, ul. Vavilova 32/1, Moscow, 119991 Russia

A. V. Chudinov

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: mr.miftahov20@yandex.ru
Russian Federation, ul. Vavilova 32/1, Moscow, 119991 Russia

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Supplementary files

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2. Fig. 1. (a) – Schematic representation of DNA hybridization in a cell made of brush polymers; (b) – schematic representation of DNA hybridization in a cross-linked hydrogel cell.

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3. Fig. 2. (a) – Fluorescent images of cells from brush cells in the Cy3 channel after immobilization of oligonucleotides; (b) – histogram of the intensity of fluorescent signals after immobilization of oligonucleotides.

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4. Fig. 3. (a) – Fluorescent images in the Cy5 channel after hybridization on biochips with cells made of brush polymers; (b) – fluorescent images in the Cy5 channel after hybridization on biochips with cells made of cross-linked polymers; (c) – graph of the dependence of integral fluorescent signals on the hybridization time on biochips with cells made of brush polymers and cross-linked polymers; (d) – graph of the dependence of the discrimination ratio on the hybridization time on biochips with cells made of brush polymers and cross-linked polymers.

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