The influence of oxoG on the electronic properties of ds-DNA. Damage versus mismatch: A theoretical approach |
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| Institution: | 1. Laboratory of Environmental Research, Department of Toxicology, Poznan University of Medical Sciences, Poznań, Poland;2. Department of Bionics and Bioimpedance, Poznan University of Medical Sciences, Poznań, Poland;3. Department of Computer Science and Statistics, Poznan University of Medical Sciences, Poznań, Poland;4. Department of Clinical Pharmacology, Poznan University of Medical Sciences, Poznań, Poland;5. Chair and Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznań, Poland;6. Department of General and Endocrine Surgery and Gastrointestinal Oncology, Poznan University of Medical Sciences, Poznań, Poland;1. Laboratory of Biophysics, Department of Physics, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon;2. Institute of Theoretical and Computational Physics, Department of Physics, College of Sciences, Botswana International University of Science and Technology, P/Bag 16 Palapye, Botswana;3. Institute of Theoretical Physics, Department of Physics, Faculty of Science, University of Stellenbosch, Private Bag X1 Matieland, Stellenbosch 7602, South Africa;4. The African Institute for Mathematical Sciences, 6-8 Melrose Rd, Muizenberg 7945, South Africa;5. Laboratory of Mechanics, Department of Physics, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon;1. School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded-431 606, MS, India;2. Gramin Science (Vocational) College, Vishnupuri, Nanded-431 606, MS, India;3. DD Bhoyar College of Arts and Science Mouda, Nagpur, 441104, MS, India;4. Bioinformatics Centre, Savitribai Phule Pune University, Pune, 411007, India;5. Organic Chemistry Research Laboratory, Department of Chemistry, Institute of Science, Nagpur, MS, India;6. Department of Biotechnology, Savitribai Phule Pune University, Pune, 411007, MS, India;1. Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA;2. The Center for Advanced Computer Studies, University of Louisiana at Lafayette, Lafayette, LA 70504, USA;3. High Performance Computing, 329 Frey Computing Services Center, Louisiana State University, Baton Rouge, LA 70803, USA;1. Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, ?wi?cickiego 4, PL 60-781 Poznań, Poland;2. Laboratory of Environmental Research, Department of Toxicology, Poznan University of Medical Sciences, Dojazd 30, PL 60-631 Poznań, Poland;3. Department Farmaco-Biologico, School of Pharmacy, University of Messina, Viale Annunziata, 98168 Messina, Italy;4. Department of Analytical Chemistry, Jagiellonian University, R. Ingardena 3, PL 30-060 Kraków, Poland;5. Department of Maternal and Child Health, Poznan University of Medical Sciences, Polna 33, PL 60-535 Poznań, Poland;6. Central Laboratory, Gynecology and Obstetrics Hospital, Poznan University of Medical Sciences, Polna 33, PL 60-535 Poznań, Poland |
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| Abstract: | The seed of life is concealed in the base sequence in DNA. This macromolecule is continuously exposed to harmful factors which can cause it damage. The stability of genetic information depends on the protein efficiency of repair systems. Glycosylases are the scouts which recognize and remove damaged bases. Their efficiency depends on how rapidly they recognize DNA lesions. One theory states that charge transfer is involved in protein cross talking through ds-DNA. For these reasons a comparative analysis of ds-oligo containing a mismatched base pair dA:::dG and a damaged dA::dGOXO is proposed. Additionally, the electronic properties of the short ds-oligo in the context of non-equilibrated and equilibrated solvent modes were taken into theoretical consideration. All energetic calculations were performed at the M062x/6-31++G** level of theory, while for geometry optimized ONIOM methodology was used. The lowest adiabatic ionization potential was assigned for DNA containing a dA:dGOXO pair. Moreover, the adiabatic electron affinity was assigned at the same level for the mismatched and lesioned ds-oligo. Surprisingly, in the non-equilibrated mode, a significantly higher vertical electro affinity was found for lesioned DNA. The higher VEA in a non-equilibrated solvent state supported faster recognition in the A:GOXO base pair than A:G by MutY glycosylases under electron transfer mechanism. |
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| Keywords: | DNA damage MutY DFT Electronic properties NE/EQ-PCM |
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