Visualizing Rev1 catalyze protein-template DNA synthesis

During DNA replication, replicative DNA polymerases may encounter DNA lesions, which can stall replication forks. One way to prevent replication fork stalling is through the recruitment of specialized translesion synthesis (TLS) polymerases that have evolved to incorporate nucleotides opposite DNA lesions. Rev1 is a specialized TLS polymerase that bypasses abasic sites, as well as minor-groove and exocyclic guanine adducts. Lesion bypass is accomplished using a unique protein-template mechanism in which the templating base is evicted from the DNA helix and the incoming dCTP hydrogen bonds with an arginine side chain of Rev1. To understand the protein-template mechanism at an atomic level, we employed a combination of time-lapse X-ray crystallography, molecular dynamics simulations, and DNA enzymology on theSaccharomyces cerevisiaeRev1 protein. We find that Rev1 evicts the templating base from the DNA helix prior to binding the incoming nucleotide. Binding the incoming nucleotide changes the conformation of the DNA substrate to orient it for nucleotidyl transfer, although this is not coupled to large structural changes in Rev1 like those observed with other DNA polymerases. Moreover, we found that following nucleotide incorporation, Rev1 converts the pyrophosphate product to two monophosphates, which drives the reaction in the forward direction and prevents pyrophosphorolysis. Following nucleotide incorporation, the hydrogen bonds between the incorporated nucleotide and the arginine side chain are broken, but the templating base remains extrahelical. These postcatalytic changes prevent potentially mutagenic processive synthesis by Rev1 and facilitate dissociation of the DNA product from the enzyme.

The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase

Efficient search for DNA damage embedded in vast expanses of the DNA genome presents one of the greatest challenges to DNA repair enzymes. We report here crystal structures of human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, that interact with the DNA containing the damaged base oxoG and the normal base G while they are nested in the DNA helical stack. The structures reveal that hOGG1 engages the DNA using different protein-DNA contacts from those observed in the previously determined lesion recognition complex and other hOGG1-DNA complexes. By applying molecular dynamics simulations, we have determined the pathways taken by the lesion and normal bases when extruded from the DNA helix and their associated free energy profiles. These results reveal how the human oxoG DNA glycosylase hOGG1 locates the lesions inside the DNA helix and facilitates their extrusion for repair.

Transition Metal Complexes of N-(4-(N-(8-Hydroxyquinolin-5-yl)sulfamoyl)phenyl)acetamide ligand: Synthesis, Characterization, in silico, in vitro Antimicrobial and DNA Binding Studies

A new, N-(4-(N-(8-hydroxyquinolin-5-yl)sulfamoyl)phenyl)acetamide (8HQSPA) ligand and its metal chelates with transition metal salts of Cu(II), Ni(II), Zn(II), Co(II), Fe(II) and Mn(II) was synthesized. The synthesized 8HQSPA ligand was characterized by mass, FT-IR, 1H NMR, 13C NMR and its metal chelates by studying their physico-chemical properties, elemental analysis, FT-IR, thermogravimetric (TG) analysis, UV-visible absorption spectroscopy and magnetic susceptibility. Thermogravimetric analysis result evident presence of two water molecules in the coordination which gives the idea of octahedral geometry and also electronic spectra showed transitions in ligand field and charge transfer bands. in silico ADMET studies was carried out to know the biological potential of synthesized compounds as it helps in development of drug candidate with fewer side effects. Molecular docking studies was carried out on bacterial proteins (PDB ID: 5h67, 3ty7, 3t88 and 5i39) and DNA helix (PDB ID: 1BNA) to predict its inhibitory effect and role on integration of DNA helix. Results showed least binding energy score (kcal/mol), which indicate that their potential of binding is greater in receptor of proteins and binds DNA through intercalation mode, which was further assessed by in vitro experiments. Antibacterial studies were carried out in the form of minimum inhibitory concentration (MIC), the results showed increased biological activity of free ligand on metal complexation in the following order: Cu > Fe > Zn > Ni > Co > Mn > 8HQSPA. Also interaction of complexes with CT-DNA was carried out by viscosity measurement, electronic absorption titration and gel electrophoresis, showed intercalation mode of binding.

Сhiral and Racemic Fields Concept for Understanding of the Homochirality Origin, Asymmetric Catalysis, Chiral Superstructure Formation from Achiral Molecules, and B-Z DNA Conformational Transition

The four most important and well-studied phenomena of mirror symmetry breaking of molecules were analyzed for the first time in terms of available common features and regularities. Mirror symmetry breaking of the primary origin of biological homochirality requires the involvement of an external chiral inductor (environmental chirality). All reviewed mirror symmetry breaking phenomena were considered from that standpoint. A concept of chiral and racemic fields was highly helpful in this analysis. A chiral gravitational field in combination with a static magnetic field (Earth’s environmental conditions) may be regarded as a hypothetical long-term chiral inductor. Experimental evidences suggest a possible effect of the environmental chiral inductor as a chiral trigger on the mirror symmetry breaking effect. Also, this effect explains a conformational transition of the right-handed double DNA helix to the left-handed double DNA helix (B-Z DNA transition) as possible DNA damage.

Recent Developments in the Interactions of Classic Intercalated Ruthenium Compounds: [Ru(bpy)2dppz]2+ and [Ru(phen)2dppz]2+ with a DNA Molecule

[Ru(bpy)2dppz]2+ and [Ru(phen)2dppz]2+ as the light switches of the deoxyribose nucleic acid (DNA) molecule have attracted much attention and have become a powerful tool for exploring the structure of the DNA helix. Their interactions have been intensively studied because of the excellent photophysical and photochemical properties of ruthenium compounds. In this perspective, this review describes the recent developments in the interactions of these two classic intercalated compounds with a DNA helix. The mechanism of the molecular light switch effect and the selectivity of these two compounds to different forms of a DNA helix has been discussed. In addition, the specific binding modes between them have been discussed in detail, for a better understanding the mechanism of the light switch and the luminescence difference. Finally, recent studies of single molecule force spectroscopy have also been included so as to precisely interpret the kinetics, equilibrium constants, and the energy landscape during the process of the dynamic assembly of ligands into a single DNA helix.