2024
Gabrusenok, P. V.; Ramazanov, R. R.; Kasyanenko, N. A.; Lantushenko, A. O.; Sokolov, P. A.
pH-dependent binding of ATP aptamer to the target and competition strands: Fluorescent melting curve fitting study Journal Article
In: Biochimica et Biophysica Acta — General Subjects, vol. 1868, no. 11, pp. 130689, 2024, ISSN: 18728006.
@article{Gabrusenok2024,
title = {pH-dependent binding of ATP aptamer to the target and competition strands: Fluorescent melting curve fitting study},
author = {P. V. Gabrusenok and R. R. Ramazanov and N. A. Kasyanenko and A. O. Lantushenko and P. A. Sokolov},
url = {https://doi.org/10.1016/j.bbagen.2024.130689},
doi = {10.1016/j.bbagen.2024.130689},
issn = {18728006},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Biochimica et Biophysica Acta - General Subjects},
volume = {1868},
number = {11},
pages = {130689},
publisher = {Elsevier B.V.},
abstract = {The pH varies in different tissues and organelles and also changes during some diseases. In this regard, the application of molecular switches that use a competition-based aptamer switch design in biological systems requires studying the thermodynamics of such systems at different pH values. In this work, we studied the binding of the classical ATP aptamer to ATP and competition strands under different pH and ionic conditions using fluorescent melting curve analysis. We have developed an original approach to processing source data from a PCR thermal cycler. It is based on constructing a thermodynamic model of the melting profile and the subsequent fit of experimental curves within this model. We have shown that this approach enables us to narrow the temperature region under study to the width of the melting region without a significant loss in the quality of the result. This impressively expands the application area of this approach compared to frequently used techniques that require mandatory measurement of the signal outside the melting region. The results obtained by the method showed that the thermodynamic parameters of the ATP aptamer and its duplexes with competition strands change depending on pH. Therefore, molecular switches that use a competition strand to the ATP aptamer may have a pH-dependent sensitivity that has not been previously considered. This should be taken into account for future rational design of similar systems.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The pH varies in different tissues and organelles and also changes during some diseases. In this regard, the application of molecular switches that use a competition-based aptamer switch design in biological systems requires studying the thermodynamics of such systems at different pH values. In this work, we studied the binding of the classical ATP aptamer to ATP and competition strands under different pH and ionic conditions using fluorescent melting curve analysis. We have developed an original approach to processing source data from a PCR thermal cycler. It is based on constructing a thermodynamic model of the melting profile and the subsequent fit of experimental curves within this model. We have shown that this approach enables us to narrow the temperature region under study to the width of the melting region without a significant loss in the quality of the result. This impressively expands the application area of this approach compared to frequently used techniques that require mandatory measurement of the signal outside the melting region. The results obtained by the method showed that the thermodynamic parameters of the ATP aptamer and its duplexes with competition strands change depending on pH. Therefore, molecular switches that use a competition strand to the ATP aptamer may have a pH-dependent sensitivity that has not been previously considered. This should be taken into account for future rational design of similar systems.
2023
Gabrusenok, P. V.; Ramasanoff, R. R.; Buchelnikov, A. S.; Sokolov, P. A.
Influence of pH on the Conformation of a Modified Aptamer to Nucleolin Protein Journal Article
In: Biophysics (Russian Federation), vol. 68, no. 2, pp. 176–181, 2023, ISSN: 15556654.
@article{Gabrusenok2023,
title = {Influence of pH on the Conformation of a Modified Aptamer to Nucleolin Protein},
author = {P. V. Gabrusenok and R. R. Ramasanoff and A. S. Buchelnikov and P. A. Sokolov},
doi = {10.1134/S0006350923020057},
issn = {15556654},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Biophysics (Russian Federation)},
volume = {68},
number = {2},
pages = {176–181},
abstract = {Abstract: The search for agents for targeted delivery of anticancer drugs remains a crucial challenge for medicine. In this context, DNA aptamers targeting cancer cell-specific proteins have medical use. At the same time, additional fine-tuning of aptamer properties to diminish their affinity for potential target cells outside tumor tissues makes the aptamers promising tools in clinical applications due to reduced immunogenicity and fewer side effects. One of the approaches is to employ the deregulation of acidity in cancer cells and tissues. In this work, the AS1411 aptamer to nucleolin was modified by adding a nucleotide sequence to its binding site to create a pH-sensitive linker. UV melting and fluorescence methods were employed to demonstrate that the conformation of the new aptamer depends on pH of the medium.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract: The search for agents for targeted delivery of anticancer drugs remains a crucial challenge for medicine. In this context, DNA aptamers targeting cancer cell-specific proteins have medical use. At the same time, additional fine-tuning of aptamer properties to diminish their affinity for potential target cells outside tumor tissues makes the aptamers promising tools in clinical applications due to reduced immunogenicity and fewer side effects. One of the approaches is to employ the deregulation of acidity in cancer cells and tissues. In this work, the AS1411 aptamer to nucleolin was modified by adding a nucleotide sequence to its binding site to create a pH-sensitive linker. UV melting and fluorescence methods were employed to demonstrate that the conformation of the new aptamer depends on pH of the medium.
Kasyanenko, Nina; Baryshev, Andrei; Artamonova, Daria; Sokolov, Petr
Packaging of DNA Integrated with Metal Nanoparticles in Solution Journal Article
In: Entropy, vol. 25, no. 7, pp. 1052, 2023, ISSN: 10994300.
@article{Kasyanenko2023,
title = {Packaging of DNA Integrated with Metal Nanoparticles in Solution},
author = {Nina Kasyanenko and Andrei Baryshev and Daria Artamonova and Petr Sokolov},
doi = {10.3390/e25071052},
issn = {10994300},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Entropy},
volume = {25},
number = {7},
pages = {1052},
abstract = {The transformation of high-molecular DNA from a random swollen coil in a solution to a discrete nanosized particle with the ordered packaging of a rigid and highly charged double-stranded molecule is one of the amazing phenomena of polymer physics. DNA condensation is a well-known phenomenon in biological systems, yet its molecular mechanism is not clear. Understanding the processes occurring in vivo is necessary for the usage of DNA in the fabrication of new biologically significant nanostructures. Entropy plays a very important role in DNA condensation. DNA conjugates with metal nanoparticles are useful in various fields of nanotechnology. In particular, they can serve as a basis for creating multicomponent nanoplatforms for theranostics. DNA must be in a compact state in such constructions. In this paper, we tested the methods of DNA integration with silver, gold and palladium nanoparticles and analyzed the properties of DNA conjugates with metal nanoparticles using the methods of atomic force microscopy, spectroscopy, viscometry and dynamic light scattering. DNA size, stability and rigidity (persistence length), as well as plasmon resonance peaks in the absorption spectra of systems were studied. The methods for DNA condensation with metal nanoparticles were analyzed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The transformation of high-molecular DNA from a random swollen coil in a solution to a discrete nanosized particle with the ordered packaging of a rigid and highly charged double-stranded molecule is one of the amazing phenomena of polymer physics. DNA condensation is a well-known phenomenon in biological systems, yet its molecular mechanism is not clear. Understanding the processes occurring in vivo is necessary for the usage of DNA in the fabrication of new biologically significant nanostructures. Entropy plays a very important role in DNA condensation. DNA conjugates with metal nanoparticles are useful in various fields of nanotechnology. In particular, they can serve as a basis for creating multicomponent nanoplatforms for theranostics. DNA must be in a compact state in such constructions. In this paper, we tested the methods of DNA integration with silver, gold and palladium nanoparticles and analyzed the properties of DNA conjugates with metal nanoparticles using the methods of atomic force microscopy, spectroscopy, viscometry and dynamic light scattering. DNA size, stability and rigidity (persistence length), as well as plasmon resonance peaks in the absorption spectra of systems were studied. The methods for DNA condensation with metal nanoparticles were analyzed.
2022
Sokolov, P. A.; Ramazanov, R. R.
Probing the conjugation of gold NPs using single-stranded DNA comprising two polyadenine adhesive tails Journal Article
In: Journal of Adhesion, 2022, ISSN: 15455823.
@article{Sokolov2022b,
title = {Probing the conjugation of gold NPs using single-stranded DNA comprising two polyadenine adhesive tails},
author = {P. A. Sokolov and R. R. Ramazanov},
url = {https://www.tandfonline.com/doi/full/10.1080/00218464.2022.2047942},
doi = {10.1080/00218464.2022.2047942},
issn = {15455823},
year = {2022},
date = {2022-03-01},
urldate = {2022-03-01},
journal = {Journal of Adhesion},
publisher = {Taylor & Francis},
abstract = {The spatial arrangement of nanoobjects by using DNA is a promising nano-design technology. Polyadenine adhesive tails are increasingly used to anchor functional oligonucleotides on the surface of gold nanoparticles at low pH. Further hybridization of such functional oligonucleotides allows nanoparticles to be organized within the desired design. In this work, we studied the effect of temperature, ionic strength, and strand design on the adsorption rate of polyadenines on the surface of gold nanoparticles at different pH. We found that there are temperature and ionic strength ranges in which the adsorption rate increases and vice versa. There are also significant differences in the effects of monovalent sodium and divalent magnesium ions. We have shown that dual-tail DNA strand design allows for increased surface density, which is significantly higher than that obtained with the standard one-tail strand design.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The spatial arrangement of nanoobjects by using DNA is a promising nano-design technology. Polyadenine adhesive tails are increasingly used to anchor functional oligonucleotides on the surface of gold nanoparticles at low pH. Further hybridization of such functional oligonucleotides allows nanoparticles to be organized within the desired design. In this work, we studied the effect of temperature, ionic strength, and strand design on the adsorption rate of polyadenines on the surface of gold nanoparticles at different pH. We found that there are temperature and ionic strength ranges in which the adsorption rate increases and vice versa. There are also significant differences in the effects of monovalent sodium and divalent magnesium ions. We have shown that dual-tail DNA strand design allows for increased surface density, which is significantly higher than that obtained with the standard one-tail strand design.
Sokolov, Petr A; Ramasanoff, Ruslan R; Gabrusenok, Pavel V; Baryshev, Andrey V; Kasyanenko, Nina A
Hybridization-Driven Adsorption of Polyadenine DNA onto Gold Nanoparticles Journal Article
In: Langmuir, 2022.
@article{Sokolov2022,
title = {Hybridization-Driven Adsorption of Polyadenine DNA onto Gold Nanoparticles},
author = {Petr A Sokolov and Ruslan R Ramasanoff and Pavel V Gabrusenok and Andrey V Baryshev and Nina A Kasyanenko},
doi = {10.1021/acs.langmuir.2c02668},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Langmuir},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ramasanoff, Ruslan R.; Sokolov, Petr A.
The binding model of adenosine-specific DNA aptamer: Umbrella sampling study Journal Article
In: Journal of Molecular Graphics and Modelling, pp. 108338, 2022, ISSN: 10933263.
@article{Ramasanoff2022,
title = {The binding model of adenosine-specific DNA aptamer: Umbrella sampling study},
author = {Ruslan R. Ramasanoff and Petr A. Sokolov},
url = {https://doi.org/10.1016/j.jmgm.2022.108338},
doi = {10.1016/j.jmgm.2022.108338},
issn = {10933263},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Journal of Molecular Graphics and Modelling},
pages = {108338},
abstract = {Please cite this article as: R.R. Ramasanoff, P.A. Sokolov, The binding model of adenosine-specific DNA aptamer: Umbrella sampling study, Journal of Molecular Graphics and Modelling (2022), doi: https://doi.org/10.1016/j.jmgm.2022.108338. This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Please cite this article as: R.R. Ramasanoff, P.A. Sokolov, The binding model of adenosine-specific DNA aptamer: Umbrella sampling study, Journal of Molecular Graphics and Modelling (2022), doi: https://doi.org/10.1016/j.jmgm.2022.108338. This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
2021
Ramazanov, R. R.; Sokolov, P. A.
Molecular dynamics study of complexes of a DNA aptamer with AMP and GMP Journal Article
In: Computer Research and Modeling, vol. 13, no. 6, pp. 1191–1203, 2021, ISSN: 20776853.
@article{Ramazanov2021,
title = {Molecular dynamics study of complexes of a DNA aptamer with AMP and GMP},
author = {R. R. Ramazanov and P. A. Sokolov},
doi = {10.20537/2076-7633-2021-13-6-1191-1203},
issn = {20776853},
year = {2021},
date = {2021-01-01},
journal = {Computer Research and Modeling},
volume = {13},
number = {6},
pages = {1191–1203},
abstract = {This study is devoted to a comparative study of the conformational stability of the DNA aptamer to adenosine derivatives in a free state and in a complex with AMP and HMP molecules by use of molecular dynamics. It was shown that, in the free state, the structure of the inner loop of the DNA aptamer hairpin, due to the special packing of guanines, closes the cavity of the binding site from external ligands, and the condition for the specific selection of adenosine derivatives in comparison with guanine arises. New stabilization factors of the AMP and aptamer complex have been revealed — hydrogen bonds between the O3' of the ribose atom of the ligands with the oxygen of the nearest phosphate group. It was also shown that guanines, which form hydrogen bonds with AMP within the binding site, are additionally stabilized by hydrogen bonds with phosphate groups opposing along the chain. The proposed scheme is in qualitative agreement with the experimental data, according to which the aptamer in solution acquires a hairpin conformation with the formation of a binding site, while the formed site exhibits high specificity when interacting only with adenosine derivatives.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
This study is devoted to a comparative study of the conformational stability of the DNA aptamer to adenosine derivatives in a free state and in a complex with AMP and HMP molecules by use of molecular dynamics. It was shown that, in the free state, the structure of the inner loop of the DNA aptamer hairpin, due to the special packing of guanines, closes the cavity of the binding site from external ligands, and the condition for the specific selection of adenosine derivatives in comparison with guanine arises. New stabilization factors of the AMP and aptamer complex have been revealed — hydrogen bonds between the O3′ of the ribose atom of the ligands with the oxygen of the nearest phosphate group. It was also shown that guanines, which form hydrogen bonds with AMP within the binding site, are additionally stabilized by hydrogen bonds with phosphate groups opposing along the chain. The proposed scheme is in qualitative agreement with the experimental data, according to which the aptamer in solution acquires a hairpin conformation with the formation of a binding site, while the formed site exhibits high specificity when interacting only with adenosine derivatives.
2020
Popova, M. A.; Rolich, V. I.; Ramazanov, R. R.; Kasyanenko, N. A.; Sokolov, P. A.
C-Ag+-C based repetitive DNA sequence Journal Article
In: Journal of Physics: Conference Series, vol. 1679, no. 2, pp. 22049, 2020, ISSN: 17426596.
@article{Popova2020,
title = {C-Ag+-C based repetitive DNA sequence},
author = {M. A. Popova and V. I. Rolich and R. R. Ramazanov and N. A. Kasyanenko and P. A. Sokolov},
doi = {10.1088/1742-6596/1679/2/022049},
issn = {17426596},
year = {2020},
date = {2020-01-01},
journal = {Journal of Physics: Conference Series},
volume = {1679},
number = {2},
pages = {22049},
publisher = {IOP Publishing},
abstract = {DNA is a convenient and well-studied tool for nanostructures fabrication. Metal-mediated hybridization of DNA strands opens up new possibilities for nanobiotechnology. In this work, we studied the possibility of long DNA formation from short ones by gluing them through the formation of C-Ag+-C complexes. Such long formations were investigated using static light scattering and atomic force microscopy. It was found that the duplexes can efficiently be linked in the presence of silver ions if the length of the cytosine sequence exceeds 6 nucleobases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
DNA is a convenient and well-studied tool for nanostructures fabrication. Metal-mediated hybridization of DNA strands opens up new possibilities for nanobiotechnology. In this work, we studied the possibility of long DNA formation from short ones by gluing them through the formation of C-Ag+-C complexes. Such long formations were investigated using static light scattering and atomic force microscopy. It was found that the duplexes can efficiently be linked in the presence of silver ions if the length of the cytosine sequence exceeds 6 nucleobases.
Sokolov, Petr A.; Ramazanov, Ruslan R.; Rolich, Valeriy I.; Popova, Maria A.; Shalygin, Vyacheslav E.; Kasyanenko, Nina A.
Stabilization of DNA by sodium and magnesium ions during the synthesis of DNA-bridged gold nanoparticles Journal Article
In: Nanotechnology, vol. 32, no. 4, pp. 045604, 2020, ISSN: к.
@article{Sokolov2020,
title = {Stabilization of DNA by sodium and magnesium ions during the synthesis of DNA-bridged gold nanoparticles},
author = {Petr A. Sokolov and Ruslan R. Ramazanov and Valeriy I. Rolich and Maria A. Popova and Vyacheslav E. Shalygin and Nina A. Kasyanenko},
url = {https://doi.org/10.1088/1361-6528/abc037},
doi = {10.1088/1361-6528/abc037},
issn = {к},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {Nanotechnology},
volume = {32},
number = {4},
pages = {045604},
publisher = {IOP Publishing Ltd},
abstract = {Nanostructures synthesized using DNA-conjugated gold nanoparticles have a wide range of applications in the field of biosensorics. The stability of the DNA duplex plays a critical role as it determines the final geometry of these nanostructures. The main way to control DNA stability is to maintain a high ionic strength of the buffer solution; at the same time, high salt concentrations lead to an aggregation of nanoparticles. In this study, by means of the instrumentality of DNA-bridged seeds using tris(hydroxymethyl)aminomethane as a soft reducing agent the dumbbell-like gold nanoparticles up to 35 nm were synthesized with a high concentration of sodium ions of up to 100 mM and magnesium ions up to 1 mM. We also examined at the atomic level the details of the effect of the gold nanoparticle surface, as well as Na+ and Mg2+ ions, on the stability of nucleotide pairs located in close proximity to the grafting site.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nanostructures synthesized using DNA-conjugated gold nanoparticles have a wide range of applications in the field of biosensorics. The stability of the DNA duplex plays a critical role as it determines the final geometry of these nanostructures. The main way to control DNA stability is to maintain a high ionic strength of the buffer solution; at the same time, high salt concentrations lead to an aggregation of nanoparticles. In this study, by means of the instrumentality of DNA-bridged seeds using tris(hydroxymethyl)aminomethane as a soft reducing agent the dumbbell-like gold nanoparticles up to 35 nm were synthesized with a high concentration of sodium ions of up to 100 mM and magnesium ions up to 1 mM. We also examined at the atomic level the details of the effect of the gold nanoparticle surface, as well as Na+ and Mg2+ ions, on the stability of nucleotide pairs located in close proximity to the grafting site.