Hidden symmetries of DNA molecule.

Despite the fact that DNA molecule is studied up and down, we know very little about the role of DNA triplets in coding amino acids and stop-codons. The paper aims to fill this gap through attracting spintronic ideas and carrying out QM/MM computations on a full-turn DNA fragment. The computations reveal two hidden symmetries: the spin splitting (the Rashba effect), confined within each triplet, and the quantum "phase" link between the triplet nature (in total, 64 triplets) and the corresponding amino acid and three stop-codons. The hidden symmetries become evident upon binding the magnesium cofactor to DNA triplets in 5'-3' and 3'-5' directions.

Magnesium cations assist with unpairing hydrogen-bonded 2-deoxyribose trinucleotides.

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.

Spin symmetry transitions make DNA strands separate. New insight into the mechanism of transcription.

The DFT:B3LYP (6-31G** basis set) method, including the hyperfine and spin-orbit couplings (HFC and SOC, respectively), is used to study the separation of two complementary trinucleotide sequences, (dC-dG-dA)-(dG-dC-dT), upon the action of two Mg(2+) cofactors (a simplified model). The computations reveal a crossing of the singlet (S) potential energy surface by the triplet (T) surface at two distinct points. Within the crossing region the T curve lies below the S curve. Adhering to the concept of the minimal energy path, one can assume that the T path is more favorable compared to that of the S path. The T path is not simple; it consists of two, T+ and T-, curves initially separated by the HFC and SOC. On reaching the second crossing point, both curves merge into the T0 state, which facilitates the T â†’ S transfer. Totally, the process of the two trinucleotide separation (the first step of transcription) appears as the S â†’ T â†’ S symmetry conversion.

New horizons of adenosinetriphosphate energetics arising from interaction with magnesium cofactor.

MD DFT:B3LYP (6-31G** basis set, T = 310 K) method is used to study interactions [singlet (S) and triplet (T) reaction paths] between adenosinetriphosphate, ATP(4-), and [Mg(H(2)O)(6)](2+) in water environment, modeled with 78 water molecules. Computations reveal the appearance of low and high-energy states (stable, quasi-stable, and unstable), assigned to different spin symmetries. At the initial stage of interaction, ATP donates a part of its negative charge to the Mg complex making the Mg slightly charged. As a result, the original octahedral Mg complex loses two (S state) or four (T state) water molecules. Moving along S or T potential energy surfaces (PESs), Mg(H(2)O)(4 )or Mg(H(2)O)(2) display different ways of complexation with ATP. S path favors the formation of a stable chelate with the O1-O2 fragment of ATP triphosphate tail, whereas T path favors producing a single-bonded complex with the O2. The latter, being unstable, undergoes a further conversion into a spin-separated complex, also unstable, and two metastable S complexes, which finally arise in two stable, low-energy and high-energy, chelates. The spin-separated complex experiences rapid decomposition resulting in the production of a highly reactive adenosinemonophosphate ion-radical *AMP, early observed in the CIDNP experiment (Tulub 2006). Biological consequences of the findings are discussed.

Molecular dynamics DFT:B3LYP study of guanosinetriphosphate conversion into guanosinemonophosphate upon Mg2+ chelation of alpha and beta phosphate oxygens of the triphosphate tail.

A molecular dynamics DFT:B3LYP (6-31G(**) basis set) study is used to elucidate the mechanism of guanosinetriphosphate (GTP) conversion into guanosinemonophosphate (GMP) upon the action of Mg(2+) (magnesium cofactor). The computations are carried out at 310 K in a volume of 178 water molecules, which surround the Mg(2+)-GTP complex and imitate the effect of solution. Over 5 ps, Mg(2+)-GTP appears to be fully decomposed, yielding five final products: two hydrated molecules of inorganic phosphate Pi, a hydrated Mg(2+), atomic oxygen (which in the course of a couple of subsequent reactions gains two hydrogens and converts into a water molecule) and a highly active *GMP radical. The radical production is linked to presence of Mg(2+), which initiates a radical mechanism of GTP cleavage. At the initial stage, Mg(2+) undergoes reduction to Mg(+), accompanied by the formation of an ion-radical pair with GTP, (+)Mg*-*GTP(3-). Without Mg(2+), an inert form of GMP (the ionic mechanism of GTP hydrolytic cleavage) rather than GMP is produced. *GMP production, which is similar to that of *AMP (adenosinemonophosphate), *CMP (cytidinemonophosphate), TMP (thymidinemonophosphate) and *UMP (uridinemonophosphate), plays a crucial role in DNA and RNA single chain synthesis.

DFT:B3LYP ab initio molecular dynamics study of the Zundel and Eigen proton complexes, H5O2+ and H9O4+, in the triplet state in gas phase and solution.

DFT:B3LYP ab initio molecular dynamics (MD) approach is used to elucidate the properties of the Zundel and Eigen, H5O2+ and H9O4+, proton complexes in the triplet state. The simulation considers the complexes in the gas phase (isolated complexes) and inside the clusters composed of 32, 64, and 128 water molecules, mimicking the behavior of aqueous solutions. MD simulations reveal three distinct periods. For the complex in solutions, the periods are smoothed out. The H5O2+ and H9O4+ complexes in the triplet state undergo structural rearrangements, which eventually result in hydrogen elimination. For the H5O2+, the hydrogen is eliminated from the center of the water cluster, whereas for the H9O4+ it is removed from a near-surface water molecule. The rate of hydrogen elimination decreases with increasing the number of water molecules surrounding the complex.

Activation of tubulin assembly into microtubules upon a series of repeated femtosecond laser impulses.

Tubulin, a globular protein, mostly distributed in nature in the dimeric alpha, beta form, can polymerize in vivo and in vitro into microtubules-longitudinal dynamic assemblies, involved in numerous cellular functions, including cell division and signaling. Tubulin polymerization starts upon binding Mg(2+) with the tubulin guanosine triphosphate (GTP) site. In the current study we show that a series of repeated femtosecond laser impulses activate the same site without adding Mg(2+). GTP site activation (without GTP no polymerization occurs) produces hydrated electrons (they are detected by the UV spectra), which are trapped in the shell of biological water, surrounding the tubulin. These electrons generate an additional, nonlinear by nature, polarization effect, responsible for the second harmonic generation at lambda=365 nm (the first harmonic is centered at lambda=730 nm) and manyfold increase in strength of the initial electric field. The results are supported by model calculations, based on the assumption of positive (negative) feedback, appearing on interaction of charge transfer exciton dipoles with the applied electromagnetic field.