Fluorescence Measurements of Duplex DNA Oligomers under Conditions Conducive for Forming M−DNA (a Metal−DNA Complex)

Small DNAs That Specifically and Tightly Bind Transition Metal Ions

Specific DNA-binding to metal ions is a long-standing fundamental research topic with great potential to transform into nano/biotechnology and therapeutics applications. Herein, based on the mobility change of DNA in denaturing gels, we develop a selection strategy to discover a series of 40-45 nt small DNAs that can bind Zn²⁺ and Cd²⁺ specifically and tightly. The Zn²⁺- and Cd²⁺-bound DNA complexes can even tolerate harsh denaturing conditions of 8 M urea and 50 mM EDTA. The discovery not only exposes a new class of transition metal ion-binding DNAs but also provides potentially a new tool for targeting drug therapies based on metal ions.

Small DNAs that Bind Nickel(II) Specifically and Tightly

Metal recognition by nucleic acids provides an intriguing route for biosensing of metal. Toward this goal, a key prerequisite is the acquisition of nucleic acids that can selectively respond to specific metals. Herein, we report for the first time the discovery of two small DNAs that can specifically bind Ni²⁺ and discriminate against similar ions, particularly, Co²⁺. Their minimal effective constructs are 60-70 nucleotides (nt) in length with Ni²⁺ binding even at harsh denaturing conditions of 8 M urea and 50 mM EDTA. Using isothermal titration calorimetry (ITC), we estimated the dissociation constant (K_D) of a representative DNA to be 24.0 ± 4.5 μM, with a 9:1 stoichiometry of Ni²⁺ bound to DNA. As being engineered into nanosized particles, these DNAs can act like nanosponges to specifically adsorb Ni²⁺ from artificial wastewater, demonstrating their potential as a novel molecular tool for high-quality nickel enrichment and detection.

Zn2+ -Dependent DNAzymes: From Solution Chemistry to Analytical, Materials and Therapeutic Applications

Since 1994, deoxyribozymes or DNAzymes have been in vitro selected to catalyze various types of reactions. Metal ions play a critical role in DNAzyme catalysis, and Zn²⁺ is a very important one among them. Zn²⁺ has good biocompatibility and can be used for intracellular applications. Chemically, Zn²⁺ is a Lewis acid and it can bind to both the phosphate backbone and the nucleobases of DNA. Zn²⁺ undergoes hydrolysis even at neutral pH, and the partially hydrolyzed polynuclear complexes can affect the interactions with DNA. These features have made Zn²⁺ a unique cofactor for DNAzyme reactions. This review summarizes Zn²⁺ -dependent DNAzymes with an emphasis on RNA-/DNA-cleaving reactions. A key feature is the sharp Zn²⁺ concentration and pH-dependent activity for many of the DNAzymes. The applications of these DNAzymes as biosensors for Zn²⁺ , as therapeutic agents to cleave intracellular RNA, and as chemical biology tools to manipulate DNA are discussed. Future studies can focus on the selection of new DNAzymes with improved performance and detailed biochemical characterizations to understand the role of Zn²⁺ , which can facilitate practical applications of Zn²⁺ -dependent DNAzymes.

Addressing the properties of "Metallo-DNA" with a Ag(i)-mediated supramolecular duplex

The silver-nucleoside complex [Ag(i)-(N3-cytidine)₂]⁺, 1, self-assembles to form a supramolecular metal-mediated base-pair array highly analogous to those seen in metallo-DNA.

The silver-nucleoside complex [Ag(i)-(N3-cytidine)₂], 1, self-assembles to form a supramolecular metal-mediated base-pair array highly analogous to those seen in metallo-DNA. A combination of complementary hydrogen-bonding, hydrophobic and argentophilic interactions drive the formation of a double-helix with a continuous silver core. Electrical measurements on 1 show that despite having Ag···Ag distances within <5% of the metallic radii, the material is electrically insulating. This is due to the electronic structure which features a filled valence band, an empty conduction band dominated by the ligand, and a band gap of 2.5 eV. Hence, as-prepared, such Ag(i)-DNA systems should not be considered molecular nanowires but, at best, proto-wires. The structural features seen in 1 are essentially retained in the corresponding organogel which exhibits thixotropic self-healing that can be attributed to the reversible nature of the intermolecular interactions. Photo-reduced samples of the gel exhibit luminescence confirming that these poly-cytidine sequences appropriately pre-configure silver ions for the formation of quantum-confined metal clusters in line with contemporary views on DNA-templated clusters. Microscopy data reveals the resulting metal cluster/particles are approximately spherical and crystalline with lattice spacing (111) similar to bulk Ag.

A coordination polymer for the site-specific integration of semiconducting sequences into DNA-based materials

Advances in bottom-up material design have been significantly progressed through DNA-based approaches. However, the routine integration of semiconducting properties, particularly long-range electrical conduction, into the basic topological motif of DNA remains challenging. Here, we demonstrate this with a coordination polymer derived from 6-thioguanosine (6-TG-H), a sulfur-containing analog of a natural nucleoside. The complexation reaction with Au(I) ions spontaneously assembles luminescent one-dimensional helical chains, characterized as {Au^I(μ-6-TG)} _n , extending many μm in length that are structurally analogous to natural DNA. Uniquely, for such a material, this gold-thiolate can be transformed into a wire-like conducting form by oxidative doping. We also show that this self-assembly reaction is compatible with a 6-TG-modified DNA duplex and provides a straightforward method by which to integrate semiconducting sequences, site-specifically, into the framework of DNA materials, transforming their properties in a fundamental and technologically useful manner.Integration of semiconducting properties into the basic topological motif of DNA remains challenging. Here, the authors show a coordination polymer derived from 6-thioguanosine that complexes with Au(I) ions to form a wire-like material that can also integrate semiconducting sequences into the framework of DNA materials.

DNA Adsorption by ZnO Nanoparticles near Its Solubility Limit: Implications for DNA Fluorescence Quenching and DNAzyme Activity Assays

Zinc oxide (ZnO) is a highly important material, and Zn(2+) is a key metal ion in biology. ZnO and Zn(2+) interconvert via dissolution and hydrolysis/condensation. In this work, we explore their interactions with DNA, which is important for biointerface, analytical, and bioinorganic chemistry. Fluorescently labeled DNA oligonucleotides were adsorbed by a low concentration (around 5 μg/mL) of ZnO nanoparticles, near the solubility limit. Right after mixing, fluorescence quenching occurred, indicating DNA adsorption. Then, fluorescence recovered, attributable to ZnO dissolution. The dissolution rate followed A5 > T5 > C5. Dissolution was slower with longer DNA. The adsorption affinity was also measured by a displacement assay to be G5 > C5 > T5 > A5, suggesting that tightly adsorbed DNA can retard ZnO dissolution. Electrostatic interactions are important for DNA adsorption because ZnO is positively charged at neutral pH, and a high salt concentration inhibits DNA adsorption. Next, in situ formation of ZnO from Zn(2+) was studied. First, titrating Zn(2+) into a fluorescently labeled oligonucleotide at pH 7.5 resulted in an abrupt fluorescence quenching beyond 0.2 mM Zn(2+). At pH 6, quenching occurred linearly with the Zn(2+) concentration, suggesting the effect of Zn(2+) precipitation at pH 7.5. Second, a Zn(2+)-dependent DNA-cleaving DNAzyme was studied. This DNAzyme was inhibited at higher than 2 mM Zn(2+), attributable to Zn(2+) precipitation and adsorption of the DNAzyme. This paper has established the interplay between DNA, Zn(2+), and ZnO. This understanding can avoid misinterpretation of DNA assay results and adds knowledge to DNA immobilization.

Ethynyl and π-stacked thymine-Hg2+-thymine base pairs enhanced fluorescence quenching via photoinduced electron transfer and simple and sensitive mercury ion sensing

Ethynyl triggered enhanced fluorescence quenching effect was first reported based on photoinduced electron transfer (PET) between fluorophore and ethynyl. Ethynyl and 6-carboxyl-fluorescein (FAM) were labeled at the 5'- and 3'-termini of a poly d(T) sequence containing three thymine units, respectively. In the presence of Hg(2+), Hg(2+) binds to two thymine residues through T-Hg(2+)-T interactions and the formed T-Hg(2+)-T base pairs bring FAM and ethynyl from two matched sequences into close proximity. On the one hand, π-stacked T-Hg(2+)-T mediates and accepts electron transfer of the excited state of FAM and quenches the fluorescence through PET. On the other hand, π-stacked interactions between ethynyl and FAM also provide a de-excitation process for the excited state of FAM via PET and trigger an enhanced fluorescence quenching. On the basis of fluorescence quenching, a simple, rapid, and sensitive Hg(2+) sensor was constructed; under optimum conditions, a good linear relationship was obtained over the concentration range of 5-150 nM for Hg(2+) and a very low detection limit (0.42 nM) was reached. The developed system was further designed as a cysteine (Cys) sensor based on fluorescence recovery resulted from the strong interaction between Cys and Hg(2+); the proposed Cys sensor has a linear range of 10-550 nM and a detection limit of 2.5 nM. The two sensors were used for analysis of real samples and the satisfactory results were achieved.

Cooperative stabilization of Zn(2+):DNA complexes through netropsin binding in the minor groove of FdU-substituted DNA

The simultaneous binding of netropsin in the minor groove and Zn(2+) in the major groove of a DNA hairpin that includes 10 consecutive FdU nucleotides at the 3'-terminus (3'FdU) was demonstrated based upon NMR spectroscopy, circular dichroism (CD), and computational modeling studies. The resulting Zn(2+)/netropsin: 3'FdU complex had very high thermal stability with aspects of the complex intact at 85 °C, conditions that result in complete dissociation of Mg(2+) complexes. CD and (19)F NMR spectroscopy were consistent with Zn(2+) binding in the major groove of the DNA duplex and utilizing F5 and O4 of consecutive FdU nucleotides as ligands with FdU nucleotides hemi-deprotonated in the complex. Netropsin is bound in the minor groove of the DNA duplex based upon 2D NOESY data demonstrating contacts between AH2 (1)H and netropsin (1)H resonances. The Zn(2+)/netropsin: 3'FdU complex displayed increased cytotoxicity towards PC3 prostate cancer (PCa) cells relative to the constituent components or separate complexes (e.g. Zn(2+):3'FdU) indicating that this new structural motif may be therapeutically useful for PCa treatment. An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:32.

Metal-mediated base pairs in nucleic acids with purine- and pyrimidine-derived nucleosides

Metal-mediated base pairs are transition metal complexes formed from complementary nucleosides within nucleic acid double helices. Instead of relying on hydrogen bonds, they are stabilized by coordinative bonds. The nucleosides acting as ligands do not necessarily have to be artificial. In fact, several examples are known of naturally occurring nucleobases (e.g., thymine, cytosine) capable of forming stable metal-mediated base pairs that are highly selective towards certain metal ions. This chapter provides a comprehensive overview of metal-mediated base pairs formed from natural nucleosides or from closely related artificial nucleosides that are pyrimidine or purine derivatives. It addresses the different strategies that lead to the development of these base pairs. The article focuses on structural models for metal-mediated base pairs, their experimental characterization within a nucleic acid, and on their possible applications.

Retroviral integrases promote fraying of viral DNA ends

In the initial step of integration, retroviral integrase (IN) introduces precise nicks in the degenerate, short inverted repeats at the ends of linear viral DNA. The scissile phosphodiester bond is located immediately 3' of a highly conserved CA/GT dinucleotide, usually 2 bp from the ends. These nicks create new recessed 3'-OH viral DNA ends that are required for joining to host cell DNA. Previous studies have indicated that unpairing, "fraying," of the viral DNA ends by IN contributes to end recognition or catalysis. Here, we report that end fraying can be detected independently of catalysis with both avian sarcoma virus (ASV) and human immunodeficiency virus type 1 (HIV-1) IN proteins by use of fluorescence resonance energy transfer (FRET). The results were indicative of an IN-induced intramolecular conformational change in the viral DNA ends (cis FRET). Fraying activity is tightly coupled to the DNA binding capabilities of these enzymes, as follows: an inhibitor effective against both IN proteins was shown to block ASV IN DNA binding and end fraying, with similar dose responses; ASV IN substitutions that reduced DNA binding also reduced end fraying activity; and HIV-1 IN DNA binding and end fraying were both undetectable in the absence of a metal cofactor. Consistent with our previous results, end fraying is sequence-independent, suggesting that the DNA terminus per se is a major structural determinant for recognition. We conclude that frayed ends represent a functional intermediate in which DNA termini can be sampled for suitability for endonucleolytic processing.

Resonance energy-transfer studies of the conformational change on the adsorption of oligonucleotides to a silica interface

Time-resolved evanescent wave-induced fluorescence studies have been carried out on a series of fluorescently labeled oligonucleotide sequences adsorbed to a silica surface from solution. The fluorescence decay profiles of a fluorescent energy donor group undergoing resonance energy transfer to a nonemissive energy-acceptor molecule have been analyzed in terms of a distribution of donor-acceptor distances to reveal the conformational changes that occur in these oligonucleotides upon adsorption. Evanescent wave-induced time-resolved Förster resonance energy-transfer (EW-TRFRET) measurements indicate that at a high electrolyte concentration, there is localized separation of the oligonucleotide strands, and the helical structure adopts an "unraveled" conformation as a result of adsorption. This is attributed to the flexibility within the oligonucleotide at high electrolyte concentration allowing multiple segments of the oligonucleotide to have direct surface interaction. In contrast, the EW-TRFRET measurements at a lower electrolyte concentration reveal that the oligonucleotide retains its helical conformation in a localized extended state. This behavior implies that the rigidity of the oligonucleotide at this electrolyte concentration restricts direct interaction with the silica to a few segments, which correspondingly introduces kinks in the double helix conformation and results in significant oligonucleotide segmental extension into solution.

Zn2+ selectively stabilizes FdU-substituted DNA through a unique major groove binding motif

We report, based on semi-empirical calculations, that Zn(2+) binds duplex DNA containing consecutive FdU-dA base pairs in the major groove with distorted trigonal bipyramidal geometry. In this previously uncharacterized binding motif, O4 and F5 on consecutive FdU are axial ligands while three water molecules complete the coordination sphere. NMR spectroscopy confirmed Zn(2+) complexation occurred with maintenance of base pairing while a slight hypsochromic shift in circular dichroism (CD) spectra indicated moderate structural distortion relative to B-form DNA. Zn(2+) complexation inhibited ethidium bromide (EtBr) intercalation and stabilized FdU-substituted duplex DNA (ΔT(m) > 15 °C). Mg(2+) neither inhibited EtBr complexation nor had as strong of a stabilizing effect. DNA sequences that did not contain consecutive FdU were not stabilized by Zn(2+). A lipofectamine preparation of the Zn(2+)-DNA complex displayed enhanced cytotoxicity toward prostate cancer cells relative to the individual components prepared as lipofectamine complexes indicating the potential utility of Zn(2+)-DNA complexes for cancer treatment.

Fast molecular beacon hybridization in organic solvents with improved target specificity

DNA hybridization is of tremendous importance in biology, bionanotechnology, and biophysics. Molecular beacons are engineered DNA hairpins with a fluorophore and a quencher labeled on each of the two ends. A target DNA can open the hairpin to give an increased fluorescence signal. To date, the majority of molecular beacon detections have been performed only in aqueous buffers. We describe herein DNA detection in nine different organic solvents, methanol, ethanol, isopropanol, acetonitrile, formamide, dimethylformamide (DMF), dimethyl sulfoxide (DMSO), ethylene glycol, and glycerol, varying each up to 75% (v/v). In comparison with detection in water, the detection in organic solvents showed several important features. First, the molecular beacon hybridizes to its target DNA in the presence of all nine solvents up to a certain percentage. Second, the rate of this hybridization was significantly faster in most organic solvents compared with water. For example, in 56% ethanol, the beacon showed a 70-fold rate enhancement. Third, the ability of the molecular beacon to discriminate single-base mismatch is still maintained. Lastly, the DNA melting temperature in the organic solvents showed a solvent concentration-dependent decrease. This study suggests that molecular beacons can be used for applications where organic solvents must be involved or organic solvents can be intentionally added to improve the molecular beacon performance.

Highly sensitive fluorescent sensor for mercury ion based on photoinduced charge transfer between fluorophore and pi-stacked T-Hg(II)-T base pairs

A novel and simple oligodeoxyribonucleotide-based sensor with single fluorophore-labeled for mercury ion sensing was reported. An oligodeoxyribonucleotide poly(dT) was labeled with fluorescein as donor. Based on the specific binding of Hg(II) to T-T mismatch base pairs, the formation of pi-stacked [T-Hg(II)-T] with "sandwich" structure on the addition of Hg(II) ions facilitates the electron transfer via photoinduced charge transfer (PCT), which creates an additional nonradiative decay channel for excited fluorophore and triggers the fluorescence to be quenched. The pi-stacked [T-Hg(II)-T] functioned not only as mercury ion recognition but also as an electron acceptor to quench the donor. A linear relationship was observed over the range of 0-1.0 microM with the detection limit of 20 nM for mercury ions. The fluorescence quenching phenomenon and quenching mechanism, reliability and selectivity of the system were investigated in detail.