Nucleotide Excision Repair in the Three Domains of Life

Farnell, David

doi:10.5206/wurjhns.2010-11.1

Cited by 4 publications

(3 citation statements)

References 32 publications

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“…Repair systems are striking for their poor representation of universal components, which contrasts with the case of translation machinery (Farnell 2011 ). The repair machinery shows considerable variability, in terms of the genes that are present or absent, even in closely related bacteria.…”

Section: Dna Repair Machinerymentioning

confidence: 99%

A History of Genomic Structures: The Big Picture

Carels

2015

Plant Biology and Biotechnology

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Section: Dna Repair Machinerymentioning

confidence: 99%

A History of Genomic Structures: The Big Picture

Carels

2015

Plant Biology and Biotechnology

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“…Due to the abundance of sugar and base lesions which are removed from the genome by BER, this protective system has become the most active and common, which is present in the nucleus and mitochondria [ 7 ]. The protein deficit/defect involved in this repair process causes changes in genetic information (i.e., mutation), which can lead to cancers or an acceleration in the aging process [ 8 ]. Activation of the BER enzyme cascade is triggered when a DNA lesion is recognized by mono- or bifunctional glycosylase [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

The Influence of Clustered DNA Damage Containing Iz/Oz and OXOdG on the Charge Transfer through the Double Helix: A Theoretical Study

Karwowski

2024

Molecules

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The genome—the source of life and platform of evolution—is continuously exposed to harmful factors, both extra- and intra-cellular. Their activity causes different types of DNA damage, with approximately 80 different types of lesions having been identified so far. In this paper, the influence of a clustered DNA damage site containing imidazolone (Iz) or oxazolone (Oz) and 7,8-dihydro-8-oxo-2′-deoxyguanosine (OXOdG) on the charge transfer through the double helix as well as their electronic properties were investigated. To this end, the structures of oligo-Iz, d[A1Iz2A3OXOG4A5]*d[T5C4T3C2T1], and oligo-Oz, d[A1Oz2A3OXOG4A5]*d[T5C4T3C2T1], were optimized at the M06-2X/6-D95**//M06-2X/sto-3G level of theory in the aqueous phase using the ONIOM methodology; all the discussed energies were obtained at the M06-2X/6-31++G** level of theory. The non-equilibrated and equilibrated solvent–solute interactions were taken into consideration. The following results were found: (A) In all the discussed cases, OXOdG showed a higher predisposition to radical cation formation, and B) the excess electron migration toward Iz and Oz was preferred. However, in the case of oligo-Oz, the electron transfer from Oz2 to complementary C4 was noted during vertical to adiabatic anion relaxation, while for oligo-Iz, it was settled exclusively on the Iz2 moiety. The above was reflected in the charge transfer rate constant, vertical/adiabatic ionization potential, and electron affinity energy values, as well as the charge and spin distribution. It can be postulated that imidazolone moiety formation within the CDL ds-oligo structure and its conversion to oxazolone can significantly influence the charge migration process, depending on the C2 carbon hybridization sp2 or sp3. The above can confuse the single DNA damage recognition and removal processes, cause an increase in mutagenesis, and harm the effectiveness of anticancer therapy.

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“…However, if the repair systems are defective, an unrepaired lesion can result in mutation, carcinogenesis, aging, neurodegenerative disorders, etc. [ 21 ]. On the other hand, if cdG is not removed from the genome, as in the case of xeroderma pigmentosum (a defect in NER), it can influence the repair process of a second lesion, e.g., OXO dG [ 22 , 23 , 24 , 25 ].…”

Section: Introductionmentioning

confidence: 99%

The Influence of 5′,8-Cyclo-2′-Deoxyguanosine on ds-DNA Charge Transfer Depends on Its Diastereomeric Form: A Theoretical Study

Karwowski

2023

Antioxidants

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The genetic information stored in the nucleobase sequence is continuously exposed to harmful extra- and intra-cellular factors, which can lead to different types of DNA damage, with more than 70 lesion types identified so far. In this article, the influence of a multi-damage site containing (5′R/S) 5′,8-cyclo-2′-deoxyguanosine (cdG) and 7,8-dihydro-8-oxo-2′-deoxyguanosine (OXOdG) on charge transfer through ds-DNA was taken into consideration. The spatial geometries of oligo-RcdG: d[A1(5′R)cG2A3OXOG4A5]*d[T5C4T3C2T1] and oligo-ScdG: d[A1(5′S)cG2A3OXOG4A5]*d[T5C4T3C2T1] were optimized at the M06-2X/6-D95**//M06-2X/sto-3G level of theory in the aqueous phase using ONIOM methodology. For all the electronic property energies under discussion, the M06-2X/6-31++G** level of theory was used. Additionally, the non-equilibrated and equilibrated solvent-solute interactions were into consideration. The obtained results confirm the predisposition of OXOdG to radical cation formation regardless of the presence of other lesions in a ds-DNA structure. In the case of electron transfer, however, the situation is different. An excess electron migration towards (5′S)cdG was found to be preferred in the case of oligo-ScdG, while in the case of oligo-RcdG, OXOdG was favored. The above observation was confirmed by the charge transfer rate constant, vertical/adiabatic ionization potential, and electron affinity energy values, as well as the charge and spin distribution analysis. The obtained results indicate that 5′,8-cyclo-2′-deoxyguanosine, depending on the C5′ atom chirality, can significantly influence the charge migration process through the double helix. The above can be manifested by the slowdown of DNA lesion recognition and removal processes, which can increase the probability of mutagenesis and subsequent pathological processes. With regard to anticancer therapy (radio/chemo), the presence of (5′S)cdG in the structure of formed clustered DNA damage can lead to improvements in cancer treatment.

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Nucleotide Excision Repair in the Three Domains of Life

Cited by 4 publications

References 32 publications

A History of Genomic Structures: The Big Picture

A History of Genomic Structures: The Big Picture

The Influence of Clustered DNA Damage Containing Iz/Oz and OXOdG on the Charge Transfer through the Double Helix: A Theoretical Study

The Influence of 5′,8-Cyclo-2′-Deoxyguanosine on ds-DNA Charge Transfer Depends on Its Diastereomeric Form: A Theoretical Study

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