The Possibility of Blocking the Process of DNA Base Pairs Opening by Hydrogen Peroxide

Zdorevskyi, Oleksii; Волков, С. Н.

doi:10.15407/ujpe64.6.500

Cited by 5 publications

(2 citation statements)

References 33 publications

(44 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Recently, defects in DNA glycosylases have been linked with colorectal cancer. , Furthermore, by selectively hindering the repair pathway, it is possible to obtain improved antibiotics . For instance, hydrogen peroxide used in ion beam therapy for the treatment of cancer has been shown to stabilize base-pairs, making it difficult for enzymes to flip out the base during nucleotide excision repair (NER) and mismatch repair (MMR) . Hence, inhibiting the DNA repair machinery can kill cancer cells and may thus provide a route to treatment. − …”

Section: Introductionmentioning

confidence: 99%

“…21 For instance, hydrogen peroxide used in ion beam therapy for the treatment of cancer has been shown to stabilize base-pairs, making it difficult for enzymes to flip out the base during nucleotide excision repair (NER) and mismatch repair (MMR). 22 Hence, inhibiting the DNA repair machinery can kill cancer cells and may thus provide a route to treatment. 23 In 1925, Johnson and Coghill reported "The discovery of 5-Methyl-cytosine in tuberculinic acid, the nucleic acid of the tubercle bacillus".…”

Section: ■ Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Energy Landscapes for Base-Flipping in a Model DNA Duplex

2022

View full text Add to dashboard Cite

We explore the process of base-flipping for four central bases, adenine, guanine, cytosine, and thymine, in a deoxyribonucleic acid (DNA) duplex using the energy landscape perspective. NMR imino-proton exchange and fluorescence correlation spectroscopy studies have been used in previous experiments to obtain lifetimes for bases in paired and extrahelical states. However, the difference of almost 4 orders of magnitude in the base-flipping rates obtained by the two methods implies that they are exploring different pathways and possibly different open states. Our results support the previous suggestion that minor groove opening may be favored by distortions in the DNA backbone and reveal links between sequence effects and the direction of opening, i.e., whether the base flips toward the major or the minor groove side. In particular, base flipping along the minor groove pathway was found to align toward the 5′ side of the backbone. We find that bases align toward the 3′ side of the backbone when flipping along the major groove pathway. However, in some cases for cytosine and thymine, the base flipping along the major groove pathway also aligns toward the 5′ side. The sequence effect may be caused by the polar interactions between the flipping-base and its neighboring bases on either of the strands. For guanine flipping toward the minor groove side, we find that the equilibrium constant for opening is large compared to flipping via the major groove. We find that the estimated rates of base opening, and hence the lifetimes of the closed state, obtained for thymine flipping through small and large angles along the major groove differ by 6 orders of magnitude, whereas for thymine flipping through small angles along the minor groove and large angles along the major groove, the rates differ by 3 orders of magnitude.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Energy Landscapes for Base-Flipping in a Model DNA Duplex

2022

View full text Add to dashboard Cite

show abstract

Molecular dynamics study of the competitive binding of hydrogen peroxide and water molecules with DNA phosphate groups

2021

View full text Add to dashboard Cite

On possible role of hydrogen peroxide molecules in ion beam therapy of cancer cells

Волков

2021

Low Temperature Physics

View full text Add to dashboard Cite

The possible role of molecular products of cell radiolysis, in particular, hydrogen peroxide molecules, in blocking DNA activity in cancer cells during irradiation with heavy ions is investigated. It is supposed that hydrogen peroxide molecules can form long-lived molecular complexes with DNA atomic groups and, thus, prevent the realization of genetic information in the biological cells. Using the quantum-mechanical approach based on density functional method and implicitly taking into account the aqueous medium, the competitive interactions of water and hydrogen peroxide molecules with DNA nucleic bases have been analyzed. Estimates of the characteristic lifetimes of complexes of water molecules and hydrogen peroxide with atomic groups of DNA allow showing the possibility to block the genetic activity of DNA by hydrogen peroxide in biological cells after their irradiation with ion beams. The effect of DNA blocking in cancer cells could be enhanced by a decrease in the cell temperature.

show abstract

The Possibility of Blocking the Process of DNA Base Pairs Opening by Hydrogen Peroxide

Cited by 5 publications

References 33 publications

Energy Landscapes for Base-Flipping in a Model DNA Duplex

Energy Landscapes for Base-Flipping in a Model DNA Duplex

Molecular dynamics study of the competitive binding of hydrogen peroxide and water molecules with DNA phosphate groups

On possible role of hydrogen peroxide molecules in ion beam therapy of cancer cells

Contact Info

Product

Resources

About