Thermodynamic investigation of M-DNA: a novel metal ion-DNA complex

Photoelectric properties in metal ion modified DNA nanostructure

Due to specific or as designed self-assembly, DNA nanostructures gaining popularity in various nanoscale electronic applications. Herein, a novel divalent metal ion-DNA complex known as M-DNA have been investigated for its photoelectric characteristics. The increased conductivity of M-DNA thin films is attributed to the metal ion electrical and optical properties. The gate voltage effect along with illumination on the conductivity of M-DNA demonstrates that M-DNA can be used as an active element of a field-effect transistor. The Zn DNA shows maximum conductivity of 300μS/cm at 480 nm light illumination suggest that M-DNA can be utilized in nano-opto-electronics and bio-sensing applications.

DNA interaction with zinc(II) ions

We focused on interactions of Zn(II) with DNA in this study. These interactions were monitored using UV/vis spectrophotometry and gel electrophoresis. Firstly, we isolated and amplified 498 bp fragment of DNA. Samples were obtained by incubation of DNA fragment with Zn(II) for 60 min at 25 °C. After incubation, the samples were dialyzed and analyzed immediately. In this way, DNA was converted into a metal bound DNA (Zn-DNA). Interaction of Zn(II) with DNA caused change in the absorption spectrum (190-350 nm) and decrease in the melting temperature (Tm) of Zn-DNA. Spectrophotometric (UV/vis) analysis showed that increasing concentrations of zinc(II) ions led to the increase in the absorbance at 200 nm and decrease in absorbance at 251 nm. Application of zinc(II) ions at 5.5 μM concentration caused decrease in Tm for app. 7.5 °C in average in comparison with control (75.5 ± 3 °C). The lowest melting temperature (60.5 ± 2.5 °C) was observed after application of zinc(II) ions at 33 μM concentration. Gel electrophoresis proved significance of Zn(II) in the renaturation of DNA. Samples of Zn-DNA (15 μM DNA+5.5-55 μM Zn(II)) caused significant changes in the renaturation of DNA in comparison with the control, untreated DNA (15 μM DNA).

Effect of Zn2+ and temperature on the conformational equilibrium of single-stranded polyA in neutral solutions

Effect of Zn(2+) ions on the conformation of polyA in cacodilic buffer at pH 7 was investigated by differential UV spectroscopy (DUV) and by thermal denaturation. The shapes of the DUV spectra and melting curves suggest a transition of polyA into a more ordered "metallized", possibly double-helical conformation at Zn(2+) concentrations above 3×10(-5) M. A phase diagram of polyA complexes with Zn(2+) was constructed for the temperature range from 20 °C to 95 °C and Zn(2+) concentrations between 10(-5) M and 5×10(-4) M. It was found that the transition of a single strand into the "metallized" form is possible only if the length of the disordered single-stranded region becomes larger than a certain critical value, ranging between 98% and 78% as the metal concentration increases from 3×10(-5) to 5×10(-4) M.

Synthesis, spectroscopic characterization and DNA nuclease activity of Cu(II) complexes derived from pyrazolone based NSO-donor Schiff base ligands

Two neutral mononuclear Cu(II) complexes have been prepared in EtOH using Schiff bases derived from 4-toluoyl pyrazolone and thiosemicarbazide. Both the ligands have been characterized on the basis of elemental analysis, IR, (1)H NMR, (13)C NMR and mass spectral data. The molecular geometry of one of these ligands has been determined by single crystal X-ray study. It reveals that these ligands exist in amine-one tautomeric form in the solid state. Microanalytical data, Cu-estimation, molar conductivity, magnetic measurements, IR, UV-Visible, FAB-Mass, TG-DTA data and ESR spectral studies were used to confirm the structures of the complexes. Electronic absorption and IR spectra of the complexes suggest a square-planar geometry around the central metal ion. The interaction of complexes with pET30a plasmid DNA was investigated by spectroscopic measurements. Results suggest that the copper complexes bind to DNA via an intercalative mode and can quench the fluorescence intensity of EB bound to DNA. The interaction between the complexes and DNA has also been investigated by agarose gel electrophoresis, interestingly, we found that the copper(II) complexes can cleave circular plasmid DNA to nicked and linear forms.

Metal-complex/DNA conjugates: a versatile building block for DNA nanoarrays

The use of DNA networks as templates for forming nanoarrays of metallic centres shows an exciting potential to generate addressable nanostructures. Inorganic units can be photoactive, electroactive and/or can possess magnetic and catalytic properties and can adopt different spatial arrangements due to their varied coordination nature. All these properties influence both the structure and function of passive DNA scaffolds and provide DNA nanostructures as a new platform for new materials in emerging technologies, such as nanotechnology, biosensing or biocomputing.

Particle stability in polymer-assisted reverse colorimetric DNA assays

"Reverse" colorimetric DNA detection by the formation of core-shell particles upon DNA hybridization is described. Specifically, the assay is based on a strategy to covalently link polymer reaction initiators to suspended nanoparticles upon DNA hybridization. These initiators then prompt polymer chain growth to form a thick polymer shell outside of particles, acting as the physical barrier to keep Au particles apart. Particles without DNA hybridization aggregate, accompanied by a pronounced solution color change from red to blue. The focus of this report is to address reaction kinetics of two co-occurring processes: polymer growth and particle aggregation during the reverse colorimetric DNA assay. The results show that Cu ions used as the polymerization catalyst bind strongly to the bases in DNA molecules, resulting in crosslinking of DNA-attached gold nanoparticles and their subsequent precipitation. Both Cu-ion-assisted particle aggregation and polymer growth are found to depend strongly on Cu ion concentration, salt concentration, and reaction temperature. Under the optimized conditions, faster polymer chain growth on the surface overcomes particle aggregation and preserves particle stability via steric stabilization.

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

M-DNA (a metal complex of DNA with millimolar concentrations of Zn2+, Co2+, or Ni2+ and basic pH) has been proposed to undergo electron transfer over long distances along the helix and has generated interest as a potential building block for nanoelectronics. We show that DNA aggregates form under solvent conditions favorable for M-DNA (millimolar zinc and pH = 8.6) by fluorescence correlation spectroscopy. We have performed steady-state Förster resonance energy transfer (FRET) experiments with DNA oligomers conjugated with 6-carboxyfluorescein and tetramethylrhodamine to the opposite ends of double-stranded DNA (dsDNA) molecules. Enhanced acceptor emission is observed for distances larger than expected for identical DNA molecules with no zinc. To avoid intermolecular FRET, the fluorescently labeled dsDNA is diluted with a 100-fold excess of unlabeled dsDNA. The intramolecular FRET efficiency increases 25-fold for a 30-mer doubly labeled duplex DNA molecule upon addition of millimolar concentrations of zinc ions. Without zinc, this oligomer has less than 1% FRET efficiency. This dramatic increase in the FRET efficiency points to either significant changes in the Förster radius or fraying of the ends of the DNA helices. The latter hypothesis is supported by our experiments with a 9-mer that show dissociation of the duplex by zinc ions.

DNA-Metal Base Pairs

Recent developments show encouraging results for the use of DNA as a construction material for nanometer-sized objects. Today, however, DNA-based molecular nanoarchitectures are constructed with mainly unmodified or at best end-modified oligonucleotides, thus shifting the development of functionalized DNA structures into the limelight. One of most recent developments in this direction is the substitution of the canonical Watson-Crick base pairs by metal complexes. In this way "metal-base pairs" are created, which could potentially impart magnetic or conductive properties to DNA-based nanostructures. This review summarizes research which started almost 45 years ago with the investigation of how metal ions interact with unmodified DNA and which recently culminated in the development of artificial ligand-like nucleobases so far able to coordinate up to ten metal ions inside a single DNA duplex in a programmable fashion.

Synthesis, characterization and in vitro biological activity studies of Cu–M (M=Cu2+, Co2+, Ni2+, Mn2+, Zn2+) bimetallic complexes

Six new bimetallic complexes of the type CuCu, CuCo, CuNi, CuZn and CuMn were prepared. The structures of these complexes and the ligand have been proposed on the basis of FAB mass, elemental analysis, UV-vis, IR, EPR and CV studies. All the complexes completely cleave pBS (SK-) DNA at a concentration of 10 microM; however, even at lower concentrations of 2 microM and 0.1 microM, the complexes (I and Ia) showed partial cleavage. The results of the fluorescence binding studies of the metal complexes with CT-DNA showed that the presence of aliphatic ligands added additional binding effects including electrostatic, hydrogen binding and vander Waals interactions. Complexes (I, Ia) showed 50% inhibition of COX-1 and COX-2 activities at as low a concentration as 12.5 microM, 13.5 microM, 14 microM and 14.5 microM. Inhibition assay of top I and top II by different complexes in mutant yeast strains (JN394, JN394 t(-1) and JN394 t(2-5)) with all the complexes showed significant inhibition of topoisomerase at 5 microM concentration. Complexes I and Ia exhibited good anti-microbial activities against all human pathogens tested except Klebsiella pneumoniae. The following studies showed that among the synthesized bimetallic complexes, complexes I and Ia seem to be promising candidates possessing DNA cleavage activities besides anti-microbial and anti-inflammatory properties to serve as chemical nucleases and chemotherapeutic agents.

Synthesis, physico-chemical and DNA interaction studies of homo- and hetero-trinuclear complexes

Synthesis and characterization of three new trinuclear metal complexes of type Cu3, Cu2Zn and Cu2Ni have been achieved by assembling simple mononuclear complexes, namely 2,2'-bipyridyl 3,4-dihydroxo benzaldehyde copper(II) complex and diethylenetriamine complexes of copper(II), nickel(II) and zinc(II) ions, through the reaction of coordinated ligands. The FAB mass spectra for the complexes show fragmentation pattern in accordance with the molecular formula. The frozen electron paramagnetic resonance (EPR) spectrum of tricopper complex shows two sets of parallel lines with approximately 2:1 ratio. The simulation has been carried out by considering dipolar interaction between the two types of copper ions present in the complex. The trimetallic complexes, Cu3, Cu2Ni and Cu2Zn show strong intercalation type of interaction with Calf thymus DNA in 0.02 mol L(-1) of phosphate buffer containing 60 mmol sodium chloride at pH 7.0 at room temperature. The binding constant is found to be in the order Cu3<Cu2Zn<Cu2Ni. The enhanced binding capability of Cu2Ni complex is attributed to the increased symmetry in the overall structure of the complex and the pronounced binding character of positively charged Ni(II) ions with the purines.

M-DNA: A novel metal ion complex of DNA studied by fluorescence techniques

M-DNA, a complex formed in solution between divalent metal ions (M) and duplex DNA, has been studied extensively using fluorescence quenching. This review examines the methods used to examine the formation of M-DNA, and its ability to serve as a pathway for electron transfer between donor and acceptor chromaphores. A mass action model for M-DNA formation is presented based upon the results of fluorescence quenching studies using fluorescein/QSY-7 labeled duplexes. From the mass action analysis, it was determined that approximately 1.4 protons are released per base pair, with k(eq) on the order of 10(-8), indicative of a strong interaction. As resonance energy transfer is shown to be unlikely over the distances involved in this work, the observed quenching in M-DNA is discussed in terms of an electron hopping mechanism for electron transfer, with k(hop)=2.5 x 10(11)s(-1).

Effect of divalent metal ions on DNA studied by capillary electrophoresis

Divalent metal ions, such as Zn(2+), Co(2+), and Ni(2+), are capable of incorporating into DNA under certain conditions to form complexes termed M-DNA. To better understand the effects of these cations on DNA we used capillary electrophoresis (CE). The presence of these metal ions in a typical genotyping buffer led to broad peaks with low fluorescence intensities. In addition, some of the metal-complexed DNA molecules had different electrophoretic mobilities than their normal DNA counterparts. It is likely that the mobility shifts observed in the electropherograms of these affected fragments are due to the divalent cations causing structural changes in the single-stranded DNA. However, as can be seen from the resulting peak shapes, the structure, charge, and/or mass changes due to metal binding are not conserved among all of the DNA fragments. The extent of both peak-broadening and mobility shifts were found to be dependent on the metal cation and its concentration, the length of time that the DNA sample existed in formamide prior to injection into the capillary, and also the fragment size and sequence. These results suggest that the presence of metal ions might be responsible for the poor CE performance that occurs when genotyping certain kinds of DNA samples.

Thermodynamics of the interaction of aluminum ions with DNA: Implications for the biological function of aluminum

Aluminum is a known neurotoxic agent and its neurotoxic effects may be due to its binding to DNA. However, the mechanism for the interaction of aluminum ions with DNA is not well understood. Here, we report the application of isothermal titration calorimetry (ITC), fluorescence spectroscopy, and UV spectroscopy to investigate the thermodynamics of the binding of aluminum ions to calf thymus DNA (CT DNA) under various pH and temperature conditions. The binding reaction is driven entirely by a large favorable entropy increase but with an unfavorable enthalpy increase in the pH range of 3.5-5.5 and at all temperatures examined. Aluminum ions show a strong and pH-dependent binding affinity to CT DNA, and a large positive molar heat capacity change for the binding, 1.57 kcal mol(-1) K(-1), demonstrates the burial of the polar surface of CT DNA upon groove binding. The fluorescence of ethidium bromide bound to CT DNA is quenched by aluminum ions in a dynamic way. Both Stern-Volmer quenching constant and the binding constant increase with the increase of the pH values, reaching a maximum at pH 4.5, and decline with further increasing the pH to 5.5. At pH 6.0 and 7.0, aluminum ions precipitate CT DNA completely and no binding of aluminum ions to CT DNA is observed by ITC. Combining the results from these three methods, we conclude that aluminum ions bind to CT DNA with high affinity through groove binding under aluminum toxicity pH conditions and precipitate CT DNA under physiological conditions.

Investigation of pH-dependent DNA-metal ion interactions by surface plasmon resonance

Ni(II) and Zn(II) M-DNA formation and denaturation of double-stranded DNA (dsDNA) by Cd(2+) were monitored by surface plasmon resonance (SPR). When exposed to immobilized 30 bp 50% GC dsDNA, Zn(2+) and Ni(2+) were found to give signals indicative of a conformational change at pH 8.5 but not 7.5, while Mg(2+) and Ca(2+) caused small changes at both pHs. The concentrations that gave 50% of the maximum responses were 0.06 and 0.50 mM for Zn(2+) and Ni(2+), respectively. At pH 8.5, Cd(2+) denatured over 40% of the dsDNA, while other metals denatured less than 5% of the DNA. Smaller pH-dependent signals were induced by Zn(2+), Ni(2+) or Cd(2+) with 50% GC single-stranded DNA (ssDNA), and with a homopolymer of d(T)30. Homopolymers d(A)30 and d(C)30 showed small signals that were largely independent of pH in the presence of Zn(2+) or Ni(2+).

Study of Ni(II) ion–DNA interactions with methylene blue as fluorescent probe

Spectroscopic studies of the interactions of Ni(II) ion with herring sperm DNA have been performed in this contribution using methylene blue (MB) as the fluorescent probe molecule. MB binds to double helical DNA via the intercalative mode, and its fluorescence is efficiently quenched by the DNA nucleobases. The fluorescence intensity of the probe molecule increases distinctly when Ni(II) ion is added to the MB-DNA solution system. These results indicate that the Ni(II) ions may be complexed with the DNA helix and probably bind at N-7 of adenine or guanine; consequently, some intercalated MB molecules are released due to the binding of Ni(II) ions to N-7 nitrogen of the purines. The Ni(II) ion-DNA interactions are further investigated by performing the photobleaching experiments of the MB-DNA complex in the presence and absence of Ni(II) ion. The bi-exponential decay functions of the fluorescence intensity have been observed in both cases and the shortening of the slow decay component when added Ni(II) ion also agrees with the release of MB from the DNA duplex.

A survey of the year 2003 literature on applications of isothermal titration calorimetry

Over the last decade isothermal titration calorimetry (ITC) has developed from a specialist method which was largely restricted in its use to dedicated experts, to a major, commercially available tool in the arsenal directed at understanding molecular interactions. The number of those proficient in this field has multiplied dramatically, as has the range of experiments to which this method has been applied. This has led to an overwhelming amount of new data and novel applications to be assessed. With the increasing number of publications in this field comes a need to highlight works of interest and impact. In this overview of the literature we have attempted to draw attention to papers and issues for which both the experienced calorimetrist and the interested dilettante hopefully will share our enthusiasm.