Application of Isodesmic Reactions to the Calculation of the Enthalpies of H• and OH• Addition to DNA Bases:  Estimated Heats of Formation of DNA Base Radicals and Hydrates

1997 ◽  
Vol 101 (47) ◽  
pp. 8935-8941 ◽  
Author(s):  
Anny-Odile Colson ◽  
David Becker ◽  
Isaac Eliezer ◽  
Michael D. Sevilla
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.


2003 ◽  
Vol 58 (12) ◽  
pp. 749-755
Author(s):  
Abdullah El-Alali ◽  
Ali A. Marashdeh ◽  
Salim M. Khalil

MINDO-Forces calculations have been performed with complete optimization of the geometries on stepwise fluorinated cyclopropanones and their enols. Increase in the number of fluorine atoms causes destabilization of cyclopropanone. Perfluorinated enol was found to be present in substantial concentration, as was mentioned in previous work. This is supported by calculations of Gibbs free energies and isodesmic reactions. Geometrical parameters, heats of formation, electron densities, dipole moments and orbital energies (HOMO-LUMO) are reported.


2005 ◽  
Vol 60 (1-2) ◽  
pp. 47-53
Author(s):  
Bareehan M. Salim ◽  
Salim M. Khalil

MINDO-Forces calculations with complete geometry optimization have been performed on nitromethane, aci-nitromethane and X-substituted nitromethane and aci-nitromethane (X = F, OH, NH2, CH3, CN, CF3, NO2, CHO). It is found that nitromethane is more stable than aci-nitromethane by 9.337 kcal/mol. This agrees with theoretical calculations. Thermodynamically, substituted aci-nitro tautomers are more stable than the corresponding nitromethane, except in case of the substituent F. Geometrical parameters, heats of formation, electron densities, Gibbs free energies and isodesmic reactions are reported.


2005 ◽  
Vol 109 (8) ◽  
pp. 1621-1628 ◽  
Author(s):  
R. Sivaramakrishnan ◽  
Robert S. Tranter ◽  
K. Brezinsky

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.


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

1983 ◽  
Vol 61 (3) ◽  
pp. 503-505 ◽  
Author(s):  
Richard Fuchs ◽  
John H. Hallman

The following heats of vaporization at 25 °C (ΔHv0) have been measured by vaporization calorimetry: cyclopropyl methyl ketone (39.41 ± 0.09 kJ mol−1). methyl cyclopropanecarboxylate (41.27 ± 0.06 kJ mol−1), cyclobutyl cyanide (44.34 ± 0.20 kJ mol−1), methyl cyclobutanecarboxylate (44.72 ± 0.09 kJ mol−1), ethylcyclobutane (31.24 ± 0.03 kJ mol−1), and cyclopentyl cyanide (48.12 ± 0.09 kJ mol−1). Values of ΔHv0 of the last four compounds have been combined with liquid state heats of formation to give new values of the gaseous state heats of formation (ΔHf(g)).When cyclobutyl cyanide, ethylcyclobutane, and cyclobutylamine are involved in hypothetical isodesmic reactions with ethane to give propane and isopropyl derivatives, the enthalpies of reaction are −102.1 ± 1.7 kJ mol−1 (−24.4 ± 0.4 kcal/mol), 8.3 kJ mol−1 (2.0 kcal/mol) less exothermic than the value for cyclobutane. Possible origins of this difference are discussed.


2011 ◽  
Vol 21 (10) ◽  
pp. 3063-3071 ◽  
Author(s):  
L. V. YAKUSHEVICH ◽  
S. GAPA ◽  
J. AWREJCEWICZ

The rotational oscillations of the DNA bases around the sugar-phosphate chains make an important contribution to the process of DNA base pairs opening that in turn plays a crucial role in the process of the DNA-protein recognition. As a result, the study of these oscillations helps to understand better the dynamical mechanisms of the biological activity of the DNA molecule. In this work, we study rotational oscillations of two coupled DNA bases that form a base pair: adenine-thymine (AT) or guanine-cytosine (GC). We show that the problem can be reduced to the mechanical problem of two coupled nonsymmetrical nonlinear pendulums oscillating in the horizontal plane. We obtain the Lagrange equations, estimate the values of the coefficients of the equations and use the results of estimations to construct the potential energy surface. We consider in detail the case of small amplitudes of angular displacements, find the general solution of corresponding Lagrange equations and present graphs using Maple 13.


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