title: Magnesium cations assist with unpairing hydrogen-bonded 2-deoxyribose trinucleotides.
abstract: 2-deoxyribose trinucleotides are essential units for storage and transfer of the genetic information. Nucleotide transpositions in trinucleotide sequences affect production of different amino acids. The study focuses on the mechanism of unpairing initially H-bonded trinucleotides. In living cells, the unpairing proceeds through DNA polymerase operating only in the presence of Mg cations. The DNA polymerase is a very complex system to be studied quantum chemically. In our simplistic approach, the polymerase is replaced by two Mg cations attached to both sides of the complementary trinucleotides. A distinguished feature of Mg in cell is in its easiness to accept and donate the electron density. In a particular molecular configuration, this makes Mg singly charged. As to the current case, we observe an unpaired electron on the Mg(+) and an unpaired electron on the trinucleotide - totally, a radical pair which coupling produces either triplet or singlet state. The study, based on the DFT B3LYP (6-311G** basis set) computations, shows that the singlet state energetically is less preferable than the triplet state. The latter is unstable and makes the trinucleotide strands unpair in the region where the singlet and triplet states cross.
authors.affiliation: Argonne National Laboratory, 9700S, Argonne, IL, 60439, USA; St.Petersburg State University, Universitetskaya Nab. 7/9, 199034, St.Petersburg, Russia. Electronic address: atulub@yahoo.co.uk.
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Tulub
mesh_terms: D002412:Cations; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry; D003855:Deoxyribose / Q000737:chemistry*; D004583:Electrons; D006860:Hydrogen Bonding; D008274:Magnesium / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D009711:Nucleotides / Q000737:chemistry*
chemical_list: D002412:Cations; D009711:Nucleotides; D003855:Deoxyribose; D004247:DNA; D004259:DNA-Directed DNA Polymerase; D008274:Magnesium
keywords: Magnesium cations; Nucleotide transpositions; Oxidation states; Trinucleotides; Unpairing