Thermal Energy Electrons and OH-Radicals Induce Strand Breaks in DNA in an Aqueous Environment: Some Salts Offer Protection Against Strand Breaks

Nayek, Upendra; Unnikrishnan, V. K.; Salam, Abdul Ajees Abdul; Chidangil, Santhosh; Mathur, D.

doi:10.1021/acs.jpca.0c00009

Cited by 3 publications

(3 citation statements)

References 31 publications

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“…Accordingly, the efficacy of the salt concentration towards DNA degradation was assessed in this study. The concentration of the salt varied within the range of 0.5-10 % as per previous literature reports on degradation (Nayek et al, 2020). The entire set of experimentations was carried out at three different time intervals of 24, 48, and 72 hours.…”

Section: Resultsmentioning

confidence: 99%

An optimization-based study of the impact of different parameters on dna degradation

Bashar

Bardhan²,

Paul³

2022

IJERR

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Human remains exposed to various conditions throughout time are frequently utilized for DNA analysis of tissue or bone for identification reasons. The deterioration and loss of DNA in particular environmental settings have previously created a dilemma for investigators. The post-mortem interval (PMI) or time since death is sometimes the most sought-after piece of information in a medical death investigation. Based on the discovery that DNA degradation has a disproportionate effect on the analysis of bigger genetic loci in particular studies, it was postulated that DNA degradation as a result of autolysis or putrefaction might be useful as a possible rate-of-change indicator of PMI. As a sample, goat liver tissue was used. It was incubated in three testing factors, namely pH, salt content, and sugar concentration, and was compared to a control sample that had not been incubated in any of these parameters. The samples were incubated for 24, 48, and 72 hours. An appropriate Lysis Buffer was used to isolate the DNA. Following the isolation of the DNA, quantitative analysis was performed in a UV-Visible Spectrophotometer (for both the control and incubated samples), followed by Agarose Gel Electrophoresis. It was discovered that the data provided by these studies, taken as a whole, show that we can give information relevant for calculating the post-mortem interval, mostly within the first 72 hours following death. Later, it was decided to use Response Surface Methodology (RSM) to optimize the parameters we had picked, with the BBD design model being the favoured choice. This was done with the help of software named, Design-Expert v11. A Fit Summary that showed a linear model fit for the data. ANOVA was used to generate an equation that may be used to quantify the amount of DNA present in a tissue sample that has been exposed to a specific value of pH, salt concentration, and sugar concentration. Finally, a 3-D response surface curve was produced, two factors at a time, to highlight the variance in DNA loss when those two parameters are taken into account.

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Section: Resultsmentioning

confidence: 99%

An optimization-based study of the impact of different parameters on dna degradation

Bashar

Bardhan²,

Paul³

2022

IJERR

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“…The formation of radicals in nucleic acids has been recognized as a major cause of chemical damage, resulting in nucleobase loss and strand breaks. − Among the major chemical DNA damage processes, electron attachment to DNA oligonucleotides , initiates nucleobase loss and generates deoxyribose radicals that can undergo further reactions. − Attack by hydroxyl radical and other reactive oxygen species can result in hydrogen abstraction, forming deoxyribose radicals that are prone to further reactions. , The formation of nucleotide sugar radicals by photoexcitation of ionized guanosine has been studied in solution and frozen glasses using electron paramagnetic resonance spectroscopy (EPR) . However, the mechanism and energetics of the radical formation have not been addressed except for simplified models. − Interstrand hydrogen atom abstraction has been reported to cause double-strand cleavage in DNA .…”

Section: Introductionmentioning

confidence: 99%

“…initiator chain by CID-MS3 ,29 according to Scheme 1 (Figure1b), finally produced the 5′-O-acetyl radical ion 2 +• at m/z 309 that was again selected by mass and further investigated by CID-MS4 and photodissociation. CID resulted in a ribose ring cleavage that was associated with the loss of a C 6 H 9 O 4 radical, forming the major m/z 164 (C 6 H 6 N 5 O + ) fragment ion (Figure 1c).…”

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confidence: 99%

Competitive Radical Migrations and Ribose Ring Cleavage in Adenosine and 2′-Deoxyadenosine Cation Radicals

Zima,

Marek,

Tureček

2024

J. Phys. Chem. A

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We report a combined experimental and computational study of adenosine cation radicals that were protonated at adenine and furnished with a radical handle in the form of an acetoxyl radical, • CH 2 COO, that was attached to ribose 5′-O. Radicals were generated by collision-induced dissociation (CID) and characterized by tandem mass spectrometry and UV−vis photodissociation action spectroscopy. The acetoxyl radical was used to probe the kinetics of intramolecular hydrogen transfer from the ribose ring positions that were specifically labeled with deuterium at C1′, C2′, C3′, C4′, C5′, and in the exchangeable hydroxyl groups. Hydrogen transfer was found to chiefly involve 3′-H with minor contributions by 5′-H and 2′-H, while 4′-H was nonreactive. The hydrogen transfer rates were affected by deuterium isotope effects. Hydrogen transfer triggered ribose ring cleavage by consecutive dissociations of the C4′−O and C1′− C2′ bonds, resulting in expulsion of a C 6 H 9 O 4 radical and forming a 9-formyladenine ion. Rice-Ramsperger-Kassel-Marcus (RRKM) and transition-state theory (TST) calculations of unimolecular constants were carried out using the effective CCSD(T)/6-311+ +G(3d,2p) and M06-2X/aug-cc-pVTZ potential energy surfaces for major isomerizations and dissociations. The kinetic analysis showed that hydrogen transfer to the acetoxyl radical was the rate-determining step, whereas the following ring-opening reactions in ribose radicals were fast. Using DFT-computed energies, a comparison was made between the thermochemistry of radical reactions in adenosine and 2′-deoxyadenosine cation radicals. The 2′-deoxyribose ring showed lower TS energies for both the ratedetermining 3′-H transfer and ring cleavage reactions.

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Potential Agricultural and Biomedical Applications of Cold Atmospheric Plasma-Activated Liquids With Self-Organized Patterns Formed at the Interface

Chen

et al. 2020

IEEE Trans. Plasma Sci.

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Thermal Energy Electrons and OH-Radicals Induce Strand Breaks in DNA in an Aqueous Environment: Some Salts Offer Protection Against Strand Breaks

Cited by 3 publications

References 31 publications

An optimization-based study of the impact of different parameters on dna degradation

An optimization-based study of the impact of different parameters on dna degradation

Competitive Radical Migrations and Ribose Ring Cleavage in Adenosine and 2′-Deoxyadenosine Cation Radicals

Potential Agricultural and Biomedical Applications of Cold Atmospheric Plasma-Activated Liquids With Self-Organized Patterns Formed at the Interface

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