Behavior of Ethidium Bromide-Hoechst 33258-DNA and Ethidium Bromide-Methylene Blue-DNA Triple Systems by means of UV Melting

Vardevanyan, P. O.; Antonyan, Ara P.; Parsadanyan, Marine A.; Shahinyan, Mariam A.; Melkonyan, Gayane A.

doi:10.1155/2015/586231

Cited by 7 publications

(11 citation statements)

References 24 publications

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“…Such invariant values are changes of melting temperature and melting interval width invoked by DNA binding to low-molecular compounds (ligands) [6,[8][9][10][11]. From the point of view of the effect on DNA double-helix stability, ligands that are able to form complexes with polymers may be divided into stabilizers and destabilizers.…”

Section: Main Body 21 Theorymentioning

confidence: 99%

“Tie Calorimetry” as a Tool for Determination of Thermodynamic Parameters of Macromolecules

Karapetyan¹,

Vardevanyan²

2018

Calorimetry - Design, Theory and Applications in Porous Solids

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Determination of free energy of double helix formation from two single-stranded polynucleotides and estimation of energetics of different low-molecular compounds binding to nucleic acids provide valuable tools for understanding of mechanisms that govern noncovalent binding of ligands to their receptor targets. In order to completely understand the molecular forces that drive and stabilize double helix formation and its complexes with ligands, thermodynamic studies are needed to complement the structural data. Structural characterization of a number of DNA-ligand complexes by X-ray and high-resolution NMR method provides key insight relating to the properties of complex formation, but structural data alone, even when coupled with the most sophisticated current computational methods, cannot fully define the driving forces for binding interactions (or interactions) or even accurately predict their binding affinities. Thermodynamics provides quantitative data of use in elucidating these driving forces and for evaluating and understanding at a deeper level the effects of substituent changes on binding affinity.

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Section: Main Body 21 Theorymentioning

confidence: 99%

“Tie Calorimetry” as a Tool for Determination of Thermodynamic Parameters of Macromolecules

Karapetyan¹,

Vardevanyan²

2018

Calorimetry - Design, Theory and Applications in Porous Solids

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“…Structural state of biomacromolecules plays a prominent role as well as at their interaction with different biologically active compounds [7][8][9][10][11][12][13][14][15][16]. Among various ligands the compounds can be important that showing specificity to NA are able to interact with proteins as well.…”

Section: Introductionmentioning

confidence: 99%

“…MB possesses anti-malaria action and is widely used as a photosensibilizing agent for photodynamic inactivation of RNA-viruses, including HIV, virus hepatitis B and virus hepatitis C in plasma, intracellular viruses B-CoV and SARS-CoV2. Though, the fact is considered more important that MB also shows therapeutic properties toward the rest viruses from coronavirus family [10][11][12][13][14]16].…”

Section: Introductionmentioning

confidence: 99%

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Study of Structural Transitions of Complexes of Different Ligands With Dna and Bsa

Vardevanyan¹,

Petrosyan²

2022

Proc. YSU B: Chem. Biol. Sci.

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Structural transitions of DNA and bovine serum albumin (BSA) and their complexes with methylene blue (MB) and Hoechst 33258 (H33258) by UV-denaturation method have been studied. The obtained results revel that MB stabilizes both protein dimensional structure and DNA double-stranded structure, while H33258 stabilizes double-stranded structure of DNA and destabilizes protein structure. It was also revealed that the stabilizing effect of MB on native structure of DNA is more pronounced at relatively low ligand concentrations, than on protein.

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“…В подавляющем большинстве случаев, среда, в которой проводятся измерения с использованием ДНК-биосенсоров, содержит лиганды, которые могут адсорбироваться как на одноцепочные ДНК-мишени, так и на дуплексы ДНК, что может привести к изменению выходного сигнала ДНК-биосенсора. Следует отметить, что проблеме взаимодействия различных лигандов с ДНК посвящено множество теоретических и экспериментальных работ [6][7][8][9][10]. В данной работе рассмотрено влияние адсорбции лигандов на дуплексы ДНК на выходной сигнал ДНКбиосенсора.…”

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Influence of adsorption of ligands on output signal of DNA-biosensor

2019

Biophysical Bulletin

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Background: The important advantage of the application of DNA-biosensors as compared to traditional molecular-biological methods is connected to the miniaturization of the studied samples and analyzers, which significantly decreases the analysis value as well as the time of its realization. Though, the miniaturization inevitably results in both decreasing the DNA-biosensor output signal value and increasing the noise signal level. That is why the studies devoted to the influence of different factors, particularly ligands on the output signal value and noise level of DNA-biosensors become actual tasks. Objectives: To theoretically calculate the dependence of DNA-biosensor output signal on the concentration of ligands in the solution. To study the characteristic peculiarities of DNA-biosensor output signal. Theory: The model, in the frame of which the theoretical calculations were carried out, is described here. There is an underlayer, on which the single-stranded molecules of DNA-targets are immobilized. The underlayer borders on the solution, where there are both single-stranded DNA molecules complementary to DNA-targets and ligands able to be adsorbed on DNA duplexes. The value of output signal DNA-biosensor is proportional to the number of DNA duplexes. Adsorption of ligands on DNA duplexes results in changing the output signal of DNA-biosensor. It is accepted that the adsorbed ligand enhances DNA-biosensor output signal. Taking into account that the formation and decomposition of the complex of ligands with DNA duplex occur in a random way, the number of bound ligands to DNA duplexes will change randomly as well, which will inevitably result in DNA-biosensor output signal fluctuations. Results: It has been shown that along with increasing the concentration of ligands in the solution the output signal of DNA-biosensors rises monotonously and the relaxation time of the output signal decreases. It was also shown that the output signal dispersion of DNA-biosensor increases at first with the concentration increase of ligands in the solution, then passing through the maximum decreases and tends to zero at the further concentration enhancement of ligands in the solution. Conclusions: The obtained data can be applied practically in the preparation of micro DNA-biosensors and analysis of the measurement results.

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Behavior of Ethidium Bromide-Hoechst 33258-DNA and Ethidium Bromide-Methylene Blue-DNA Triple Systems by means of UV Melting

Cited by 7 publications

References 24 publications

“Tie Calorimetry” as a Tool for Determination of Thermodynamic Parameters of Macromolecules

“Tie Calorimetry” as a Tool for Determination of Thermodynamic Parameters of Macromolecules

Study of Structural Transitions of Complexes of Different Ligands With Dna and Bsa

Influence of adsorption of ligands on output signal of DNA-biosensor

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