Double-stranded Backbone Research Articles

Protective effect of baicalein on DNA oxidative damage and its binding mechanism with DNA: An in vitro and molecular docking study

In this work, the protective effect of baicalein on DNA oxidative damage and its possible protection mechanisms were investigated. 2-thiobarbituric acid (TBA) colorimetry and agarose gel electrophoresis study found that baicalein protected the deoxyribose residue and double-stranded backbone of DNA from the damage of hydroxyl radicals. Antioxidant analysis results showed that baicalein has excellent radicals scavenging effects and Fe2+ chelating ability, which might be the mechanism of baicalein protecting DNA. DNA binding studies indicated that baicalein bound to the minor groove of DNA with moderate binding affinity (K = (7.35 ± 0.91) × 103 M−1). Hydrogen bonding and van der Waals forces played a major role in driving the binding process. Molecular docking further confirmed the experimental results. This binding could stabilize DNA double helix structure, thereby protecting DNA from oxidative damage. This study may provide theoretical basis for designing new functional foods of baicalein for DNA damage protection.

Unexpectedly flexible graphene nanoribbons with a polyacene ladder skeleton

A new aromatic ladder polymer with a polyacene skeleton shows an unexpectedly high flexibility of its double-stranded backbone.

Counterintuitive DNA Sequence Dependence in Supercoiling-Induced DNA Melting.

The metabolism of DNA in cells relies on the balance between hybridized double-stranded DNA (dsDNA) and local de-hybridized regions of ssDNA that provide access to binding proteins. Traditional melting experiments, in which short pieces of dsDNA are heated up until the point of melting into ssDNA, have determined that AT-rich sequences have a lower binding energy than GC-rich sequences. In cells, however, the double-stranded backbone of DNA is destabilized by negative supercoiling, and not by temperature. To investigate what the effect of GC content is on DNA melting induced by negative supercoiling, we studied DNA molecules with a GC content ranging from 38% to 77%, using single-molecule magnetic tweezer measurements in which the length of a single DNA molecule is measured as a function of applied stretching force and supercoiling density. At low force (<0.5pN), supercoiling results into twisting of the dsDNA backbone and loop formation (plectonemes), without inducing any DNA melting. This process was not influenced by the DNA sequence. When negative supercoiling is introduced at increasing force, local melting of DNA is introduced. We measured for the different DNA molecules a characteristic force F char, at which negative supercoiling induces local melting of the dsDNA. Surprisingly, GC-rich sequences melt at lower forces than AT-rich sequences: F char = 0.56pN for 77% GC but 0.73pN for 38% GC. An explanation for this counterintuitive effect is provided by the realization that supercoiling densities of a few percent only induce melting of a few percent of the base pairs. As a consequence, denaturation bubbles occur in local AT-rich regions and the sequence-dependent effect arises from an increased DNA bending/torsional energy associated with the plectonemes. This new insight indicates that an increased GC-content adjacent to AT-rich DNA regions will enhance local opening of the double-stranded DNA helix.

Oligoamide Duplexes as Organogelators

Oligoamide duplexes carrying multiple alkyl side chains were found to serve as gelators for aromatic solvents. The double-stranded backbone was essential for the hierarchical self-assembly of the molecular duplex into fibers of high aspect ratios. The demonstrated gelating abilities may be extended to a large family of analogous H-bonded duplexes having different H-bonding sequences, leading to a unique platform for developing a diverse variety of potential gelators based on a supramolecular and/or a dynamic covalent approach.

Towards self-replicating materials of DNA-functionalized colloids

We report the first results of ongoing research that involves the creation of a new class of non-biological materials designed to self-replicate and, as a result, to grow exponentially. We propose a system design that exploits the strong specificity and thermal reversibility of the interactions between colloidal particles functionalized with complementary single-stranded DNA ‘sticky ends’. Here, we experimentally test the fundamentals of the different steps that constitute the self-replication scheme. First of all, we quantitatively study the equilibrium and kinetic aspects of the aggregation–dissociation behavior of the particles. We find that the dissociation transition is very sharp (∼1 °C) and that it occurs at unexpectedly low temperatures, with the dissociation temperature shifting further down when the fraction of sticky ends becomes smaller. The sharpness of the transition and its sensitivity to the sticky end fraction are important control parameters in our self-replication scheme. We further find that for our present purposes it is best to use a DNA construct with a double-stranded backbone, as this largely prevents unwanted hybridization events, such as secondary structure formation. The latter is seen to lead to peculiar aggregation kinetics, due to a competition between inter- and intra-particle hybridization. Finally, we show how one can obtain dual recognition at different temperatures by functionalizing a single particle species with two distinct DNA sequences and we demonstrate the formation of permanent bonds, using the chemical intercalator psoralen and long-wavelength UV exposure.

Tetrakis(pentafluorobenzenethiolato-κS)(triphenylphosphine-κP)osmium(IV): aZ′ = 3 structure with a supramolecular double-stranded backbone

The title complex, [Os(C6F5S)4(C18H15P)], crystallizes with three independent molecules in the asymmetric unit. Two of these have very similar conformations, while in the third, the axial thiolate ligand has a rotation that differs by ca 21.5 degrees . The coordination around the metal atom is trigonal bipyramidal and the supramolecular structure involves an unusual double-stranded backbone.

Structure of poliovirus replicative intermediate RNA: Electron microscope analysis of RNA cross-linked in vivo with psoralen derivative

The structure of the poliovirus replicative intermediate RNA was examined by electron microscopy after cross-linking in vivo with 4′-aminomethyl-4,5′,8-trimethylpsoralen. After purification from infected cells, undenatured RI † † Abbreviations used: RI, replicative intermediate; AMT, 4′-aminomethyl-4,5′,8-trimethylpsoralen; RF, double-stranded poliovirus RNA. appeared as a double-stranded backbone of genome length, with an average of three (and occasionally up to eight) nascent, single-stranded tails. After denaturation, however, only single strands of heterogeneous length were visualized, indicating that the RI in the cell contains little or no duplex structure, and thus nascent chains are only transiently hydrogen-bonded to their template over short regions. The double-stranded backbone of undenatured RI, observed previously by others and in these experiments, is due to collapse of complementary chains during the deproteinization and purification procedures. The effectiveness of the in vivo cross-linking procedure was demonstrated by the complete inhibition of viral RNA synthesis in treated cells and by direct binding of [ 3H]AMT to RI molecules in vivo. Mature polio virions are impermeable to AMT; however, growth of virus in cells incubated with AMT in the dark resulted in normal yields of virus particles containing RNA genomes, whose infectivity could be subsequently photo-inactivated. The frequency of AMT-induced cross-linking was determined by analyses of double-stranded poliovirus RNA (RF). Cross-linking in vitro followed by spreading for electron microscopy under denaturing conditions yielded bubbled duplex structures with a minimum of one interstrand cross-link per 80 base-pairs. RF cross-linked in vivo also showed extensive cross-linking, decreased about fivefold from the in vitro cross-linked value. Thus, the failure to detect cross-linked RI under these conditions indicates that extensive base-pairing does not exist in vivo.

Translational accuracy in vitro

of DNA replication can initiate DNA synthesis with primer-dependent DNA polymerase. A wealth of biochemical and genetic evidence supports a similar model for phage 429 DNA replication (Salas et al., op. cit.). In $29, however, the first nucleotide linked to the terminal protein (~3) is dAMP. A closer look at poliovirus and adenovirus suggests that these viruses have adopted a strikingly similar strategy for genome replication. Although poliovirus starts replication with single-stranded RNA, its replicative intermediate is now considered to have a double-stranded backbone, and strand displacement is thought to be the mechanism of daughter-strand release. Adenovirus, however, initiates on doublestranded DNA, but it can also initiate daughter-strand synthesis on linear single strands, at least in vitro. Both viruses appear to utilize a protein-linked pyrimidine nucleotide as primer. It is difficult to imagine why poliovirus RNA polymerase is primer-dependent, when all other known template-dependent RNA polymerases of both eucaryotes and procaryotes can initiate RNA synthesis de novo. A hypothesis to explain this phenomenon is that the poliovirus RNA polymerase was at one time a DNA polymerase that converted to RNA replication but failed to learn how to initiate polynucleotide synthesis. An analysis of the poliovirus RNA sequence favors the hypothesis that this RNA may have originated from vertebrate DNA. Thus poliovirus and adenovirus may. have taken their strategies of genome replication from a common ancestor. The formation of the covalent linkage between DNA and polypeptide is known to occur in many other systems not discussed here. In some cases the protein-DNA complexes may be transient, serving as intermediates in DNA metabolism. For example, topoisomerases, gyrase or the A gene product of phage 4x174 act under specific conditions as endonucleases, the nicking activity being accompanied by covalent linkage formation of the enzyme to the newly generated terminal phosphate. This process may allow either the DNA to undergo topological isomerization (Gellert, Ann. Rev. Biochem. 50, 879-910, 1981) or a newly generated 3’ hydroxyl group to serve as a primer for DNA polymerases (Kornberg, DNA Replication, W. H. Freeman, 1980). It remains to be seen whether the protein of hepatitis B virus DNA, or the polypeptide found linked to the replicative form of DNA of parvovirus H-l (Revie et al., PNAS 76, 55395543, 1979), belongs in this class of proteins.