Fluorinated DNA Bases as Probes of Electrostatic Effects in DNA Base Stacking

2003 ◽  
Vol 115 (48) ◽  
pp. 6155-6159 ◽  
Author(s):  
Jacob S. Lai ◽  
Jin Qu ◽  
Eric T. Kool
2003 ◽  
Vol 42 (48) ◽  
pp. 5973-5977 ◽  
Author(s):  
Jacob S. Lai ◽  
Jin Qu ◽  
Eric T. Kool

Antioxidants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 97
Author(s):  
Leila Rashki Ghaleno ◽  
AliReza Alizadeh ◽  
Joël R. Drevet ◽  
Abdolhossein Shahverdi ◽  
Mojtaba Rezazadeh Valojerdi

One important reason for male infertility is oxidative stress and its destructive effects on sperm structures and functions. The particular composition of the sperm membrane, rich in polyunsaturated fatty acids, and the easy access of sperm DNA to oxidative damage due to sperm cell specific cytologic and metabolic features (no cytoplasm left and cells unable to mount stress responses) make it the cell type in metazoans most susceptible to oxidative damage. In particular, oxidative damage to the spermatozoa genome is an important issue and a cause of male infertility, usually associated with single- or double-strand paternal DNA breaks. Various methods of detecting sperm DNA fragmentation have become important diagnostic tools in the prognosis of male infertility and such assays are available in research laboratories and andrology clinics. However, to date, there is not a clear consensus in the community as to their respective prognostic value. Nevertheless, it is important to understand that the effects of oxidative stress on the sperm genome go well beyond DNA fragmentation alone. Oxidation of paternal DNA bases, particularly guanine and adenosine residues, the most sensitive residues to oxidative alteration, is the starting point for DNA damage in spermatozoa but is also a danger for the integrity of the embryo genetic material independently of sperm DNA fragmentation. Due to the lack of a spermatozoa DNA repair system and, if the egg is unable to correct the sperm oxidized bases, the risk of de novo mutation transmission to the embryo exists. These will be carried on to every cell of the future individual and its progeny. Thus, in addition to affecting the viability of the pregnancy itself, oxidation of the DNA bases in sperm could be associated with the development of conditions in young and future adults. Despite these important issues, sperm DNA base oxidation has not attracted much interest among clinicians due to the lack of simple, reliable, rapid and consensual methods of assessing this type of damage to the paternal genome. In addition to these technical issues, another reason explaining why the measurement of sperm DNA oxidation is not included in male fertility is likely to be due to the lack of strong evidence for its role in pregnancy outcome. It is, however, becoming clear that the assessment of DNA base oxidation could improve the efficiency of assisted reproductive technologies and provide important information on embryonic developmental failures and pathologies encountered in the offspring. The objective of this work is to review relevant research that has been carried out in the field of sperm DNA base oxidation and its associated genetic and epigenetic consequences.


QRB Discovery ◽  
2020 ◽  
Vol 1 ◽  
Author(s):  
Bengt Nordén ◽  
Masayuki Takahashi

AbstractThe human protein Rad51 is double-edged in cancer contexts: on one hand, preventing tumourigenesis by eliminating potentially carcinogenic DNA damage and, on the other, promoting tumours by introducing new mutations. Understanding mechanistic details of Rad51 in homologous recombination (HR) and repair could facilitate design of novel methods, including CRISPR, for Rad51-targeted cancer treatment. Despite extensive research, however, we do not yet understand the mechanism of HR in sufficient detail, partly due to complexity, a large number of Rad51 protein units being involved in the exchange of long DNA segments. Another reason for lack of understanding could be that current recognition models of DNA interactions focus only on hydrogen bond-directed base pair formation. A more complete model may need to include, for example, the kinetic effects of DNA base stacking and unstacking (‘longitudinal breathing’). These might explain how Rad51 can recognize sequence identity of DNA over several bases long stretches with high accuracy, despite the fact that a single base mismatch could be tolerated if we consider only the hydrogen bond energy. We here propose that certain specific hydrophobic effects, recently discovered destabilizing stacking of nucleobases, may play a central role in this context for the function of Rad51.


2020 ◽  
Vol 49 (14) ◽  
pp. 4266-4276
Author(s):  
Reza Latifi ◽  
Jennifer L. Minnick ◽  
Matthew G. Quesne ◽  
Sam P. de Visser ◽  
Laleh Tahsini

A detailed QM/MM and DFT study into the structure and reactivity of AlkB repair enzymes with alkylated DNA bases is reported. In particular, we investigate the aliphatic hydroxylation and CC epoxidation mechanisms of the enzymes by a high-valent iron(iv)–oxo intermediate.


2015 ◽  
Vol 27 (1) ◽  
pp. 145-158 ◽  
Author(s):  
Tanja van Mourik ◽  
Simon W. L. Hogan
Keyword(s):  

Biopolymers ◽  
1992 ◽  
Vol 32 (2) ◽  
pp. 145-159 ◽  
Author(s):  
Richard A. Friedman ◽  
Barry Honig

2002 ◽  
pp. 500-501 ◽  
Author(s):  
Ishwar Singh ◽  
Walburga Hecker ◽  
Ashok K. Prasad ◽  
Virinder S. Parmar ◽  
Oliver Seitz
Keyword(s):  

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