Synthesis, characterization and in vitro DNA binding studies of tin(IV) complexes of tert-butyl 1-(2-hydroxy-1-phenylethylamino)-3-methyl-1-oxobutan-2-yl carbamate

Tin(IV) complexes 1(a and b) and 2(a and b) of valine derived peptide derivatives were synthesized and characterized on the basis of elemental analysis, IR, ¹H, ¹³C, ¹¹⁹Sn NMR, ESI-MS spectra and molar conductance measurements. The C-Sn-C angle was estimated from ^I3C and ¹H NMR data ¹J(¹¹⁹Sn, ^I3C) = 623 Hz; solution ²J(¹¹⁹Sn, ¹H) = 93.04 Hz to be 149.9°. In vitro binding studies of complexes 1 and 2 under physiological conditions at room temperature with CT-DNA were carried out employing UV-visible, fluorescence, circular dichroism and viscometric studies. The binding affinity of the complexes was quantified by calculating the K_b values and it follows the order 2a > 1a > 2b > 1b. To further examine the specific mode of binding, the interaction of complexes 2(a and b) were carried out with 5′GMP and 5′TMP by using absorption and NMR (¹H, ³¹P) spectroscopy. The supercoiled pBR322 plasmid DNA cleavage activity of the complexes was ascertained by gel electrophoresis assay. The complexes cleave supercoiled pBR322 plasmid DNA efficiently into its nicked form at micromolar concentrations.     

Surface modified microarray chip and laser induced fluorescence microscopy to detect DNA cleavage

This work describes a quantitative method to detect DNA damage in the presence of Pb and Cd ions using a surface modified microarray chip and a laser induced fluorescence microscopy (LIFM). The detection was carried out by the immobilization of a single-stranded DNA oligomer, tagged with a Cy5 fluorophore on a polydimethylsiloxane (PDMS) microarray chip followed by LIFM. Sulfosuccinimidyl-4-(N-maleimidomethyl) cyclohexane-1-carboxylate (Sulfo-SMCC) was attached as a cross-linker via the formation of covalent amide bonds. Then, the single-stranded DNA oligomer containing Cy5 as a fluorophore and thiol functional groups at both terminals, was bonded to the linker by reaction with sulfhydryl group. As the DNA oligomers were reacted with metal ions of Pb and Cd, the un-cleaved DNA oligomers were quantitatively identified by monitoring Cy5 fluorescence. Cadmium showed a quenching constant of 0.84 in the Stern–Volmer plot, whereas lead gave 0.22, indicating that cadmium ions suppress fluorescence more than lead ions. When optimized, fluorescence reductions of 23% (± 2.1) for Pb and 25% (± 1.4) for Cd were observed in air and decreased to almost < 5.0% in a radical scavenger of 5 mM. The cleaved DNA was also confirmed by MALDI-TOF-MS. In result, this experimental method using a microarray chip with surface modification provided quantitative determination of DNA oligomer damage with reproducible results, significantly reduced sample volumes and analysis times.     

Enzyme digestion of entrapped single-DNA molecules in nanopores

The real-time digestion of entrapped single-DNA molecules by λ-exonuclease in nanoporous alumina membranes was observed using an epifluorescence microscope. The alumina membrane provides pL (∼10⁻¹² L) containers for confining single-DNA molecules without immobilization. When one end of the DNA molecule was inserted into a nanopore, it was possible to monitor the digestion process outside, near and inside the pore, where the individual DNA molecules exhibited different characteristic digestion modes. The digestion rates calculated from the decrease in fluorescence intensity showed different values according to the location of the individual molecules. Entrapment rather than immobilization allows the DNA strand to be fully exposed to the enzyme and the reaction buffer. These results confirm that the enzymatic digestion of DNA molecules is affected by their three-dimensional (3D) environment.     

Au nanowire-on-film SERRS sensor for ultrasensitive Hg2+ detection

We report an ultrasensitive and selective single nanowire-on-film (SNOF) surface-enhanced resonance Raman scattering (SERRS) sensor for Hg(2+) detection based on structure-switching double stranded DNAs (dsDNAs). Binding of Hg(2+) induces conformational changes of the dsDNAs and let a Raman reporter get close to the SNOF structure, thereby turning on SERRS signal. The well-defined SNOF structure provides a detection limit of 100 pM with improved accuracy in Hg(2+) detection. This sensor is stable over a considerable amount of time and reusable after simple treatment. Since this SNOF sensor is composed of a single Au NW on a film, development of a multiplex sensor would be possible by employing NWs modified by multiple kinds of aptamers.     

Nick sealing by T4 DNA ligase on a modified DNA template: tethering a functional molecule on D-threoninol

Efficient DNA nick sealing catalyzed by T4 DNA ligase was carried out on a modified DNA template in which an intercalator such as azobenzene had been introduced. The intercalator was attached to a D-threoninol linker inserted into the DNA backbone. Although the structure of the template at the point of ligation was completely different from that of native DNA, two ODNs could be connected with yields higher than 90% in most cases. A systematic study of sequence dependence demonstrated that the ligation efficiency varied greatly with the base pairs adjacent to the azobenzene moiety. Interestingly, when the introduced azobenzene was photoisomerized to the cis form on subjection to UV light (320-380 nm), the rates of ligation were greatly accelerated for all sequences investigated. These unexpected ligations might provide a new approach for the introduction of functional molecules into long DNA strands in cases in which direct PCR cannot be used because of blockage of DNA synthesis by the introduced functional molecule. The biological significance of this unexpected enzymatic action is also discussed on the basis of kinetic analysis.     

Photoactive Ru(II) -polypyridyl complexes that display sequence selectivity and high-affinity binding to duplex DNA through groove binding

The duplex-DNA binding properties of a nonintercalating polypyridyl ruthenium(II) complex that incorporates a linear extended ligand with a catechol moiety has been probed with a variety of photo- and biophysical techniques. These studies reveal that the complex groove binds to DNA sequences biphasically, and displays binding constants equivalent to those of high-affinity metallointercalators. The complex also displays preferential binding to AT-rich sequences. Changes in the structure of the coordinated catechol ligand and the incorporation of intercalating ancillary ligands into the complex were found to modulate both the optical-binding response and binding parameters of the system, which indicates that the catechol moiety plays a crucial role in the observed enhancement to binding affinities.     

Molecular-glue-triggered DNA assembly to form a robust and photoresponsive nano-network

A robust and photoresponsive DNA network has been designed and constructed from branched DNA and molecular glue. The molecular glue is photoswitchable and can specifically bind to G-G mismatched double-stranded DNA. The assembly process can be reversibly controlled by manipulating the wavelength of light. The approach is flexible, allowing tuning of the size, morphology as well as the cavity of the network by variation of the molar ratio and the isotropic/anisotropic character of the branched building blocks. The assembled architectures are versatile and heat tolerant. These properties should allow the use of the network in further applications.     

DNA‐Based Peroxidation Catalyst—What Is the Exact Role of Topology on Catalysis and Is There a Special Binding Site for Catalysis?

In the last decade, there has been growing interests in studies aimed at delineating the strategies used by various nucleic acid enzymes to facilitate catalysis. Insights gained from such studies would enable the design of better DNA/RNA catalysts for various applications such as biosensing. DNA and RNA catalysts have been shown to be able to catalyze myriads of reactions, including peroxidation reactions, which are catalyzed by G-quadruplexes. In this report, we provide data that clarifies how G-quadruplex peroxidases achieve catalysis. Firstly, we show that by covalently linking a hemin cofactor to DNAzymes, anti-parallel G-quadruplexes, which have been previously shown to be catalytically inefficient, can be "resurrected" to become good peroxidation catalysts. We also reveal that the relative rates of peroxidation by DNAzyme peroxidases depend on the nature of the organic reductant, arguing for a special binding site in the peroxidase-mimicking DNAzymes for catalysis.     

DNA-templated photonic arrays and assemblies: design principles and future opportunities

Molecular photonics is a rapidly developing and multi-disciplinary field of research involving the construction of molecular assemblies comprising photoactive building blocks that are responsive to a light stimulus. A salient challenge in this field is the controlled assembly of these building blocks with nanoscale precision. DNA exhibits considerable promise as an architecture for the templated assembly of photoactive materials. In this Concept Article we describe the progress that has been made in the area of DNA photonics, in which DNA acts as a platform for the construction of optoelectronic assemblies, thin films and devices.