Binding of native DNA to MoS$_{2}$ nanoflakes: the role of defects and edge atoms of MoS$_{2}$ nanostructures in their biofunctionalization
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| Autores principales: | , , , , , , , , , |
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| Formato: | Preprint |
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2025
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| _version_ | 1866915265741062144 |
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| author | Glamazda, Alexander Usenko, Evgeniya Svidzerska, Anastasiia Valeev, Vladimir Voloshin, Igor Laguta, Anna Petrushenko, Sergey Stepanian, Stepan Adamowicz, Ludwik Karachevtsev, Victor |
| author_facet | Glamazda, Alexander Usenko, Evgeniya Svidzerska, Anastasiia Valeev, Vladimir Voloshin, Igor Laguta, Anna Petrushenko, Sergey Stepanian, Stepan Adamowicz, Ludwik Karachevtsev, Victor |
| contents | In this work, the binding of native DNA to MoS$_{2}$ nanoflakes (FLs) was studied by using UV-visible absorption spectroscopy, thermal denaturation method, transmission electron microscopy (TEM), temperature-dependent dynamic light scattering (DLS), and the DFT computational-chemistry method. Analysis of the experimental data: TEM images and thermal denaturation measurements showed the binding of the biopolymer with MoS$_{2}$ FLs. An increase in the melting temperature of DNA and a decrease in the hyperchromic coefficient at binding with MoS$_{2}$ FLs indicates the formation of the DNA:MoS$_{2}$ FL nanoassemblies due primarily to the covalent interaction of the oxygen atoms of the phosphate groups of DNA with the MoS$_{2}$ FLs. Possible complexes of a nucleotide fragment (ribose-phosphate group) with MoS$_{2}$ nanolayer are considered and calculated employing the DFT method. Different structures of these complexes are optimized and the interaction energies between components are determined. Special attention in calculations is focused on the binding of this nucleotide fragment with Mo atoms located at the edge of the MoS$_{2}$ nanolayer and with point structural defects of the MoS$_{2}$ surface containing the S vacancy. Based on this calculation and experimental observation, a mechanism of binding of native DNA to MoS$_{2}$ FLs has been proposed, in which their conjugation begins with point contacts of DNA phosphate groups with Mo atoms (at the edge or/and in defects) through the formation of a strong coordination bond. The results indicate the critical role of defects and edge atoms of MoS$_{2}$ FLs in their biofunctionalization. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2504_20562 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Binding of native DNA to MoS$_{2}$ nanoflakes: the role of defects and edge atoms of MoS$_{2}$ nanostructures in their biofunctionalization Glamazda, Alexander Usenko, Evgeniya Svidzerska, Anastasiia Valeev, Vladimir Voloshin, Igor Laguta, Anna Petrushenko, Sergey Stepanian, Stepan Adamowicz, Ludwik Karachevtsev, Victor Biological Physics In this work, the binding of native DNA to MoS$_{2}$ nanoflakes (FLs) was studied by using UV-visible absorption spectroscopy, thermal denaturation method, transmission electron microscopy (TEM), temperature-dependent dynamic light scattering (DLS), and the DFT computational-chemistry method. Analysis of the experimental data: TEM images and thermal denaturation measurements showed the binding of the biopolymer with MoS$_{2}$ FLs. An increase in the melting temperature of DNA and a decrease in the hyperchromic coefficient at binding with MoS$_{2}$ FLs indicates the formation of the DNA:MoS$_{2}$ FL nanoassemblies due primarily to the covalent interaction of the oxygen atoms of the phosphate groups of DNA with the MoS$_{2}$ FLs. Possible complexes of a nucleotide fragment (ribose-phosphate group) with MoS$_{2}$ nanolayer are considered and calculated employing the DFT method. Different structures of these complexes are optimized and the interaction energies between components are determined. Special attention in calculations is focused on the binding of this nucleotide fragment with Mo atoms located at the edge of the MoS$_{2}$ nanolayer and with point structural defects of the MoS$_{2}$ surface containing the S vacancy. Based on this calculation and experimental observation, a mechanism of binding of native DNA to MoS$_{2}$ FLs has been proposed, in which their conjugation begins with point contacts of DNA phosphate groups with Mo atoms (at the edge or/and in defects) through the formation of a strong coordination bond. The results indicate the critical role of defects and edge atoms of MoS$_{2}$ FLs in their biofunctionalization. |
| title | Binding of native DNA to MoS$_{2}$ nanoflakes: the role of defects and edge atoms of MoS$_{2}$ nanostructures in their biofunctionalization |
| topic | Biological Physics |
| url | https://arxiv.org/abs/2504.20562 |