The effects of Cu2+ and Pb2+ on the solution structure of calf thymus DNA: DNA condensation and denaturation studied by Fourier transform ir difference spectroscopy

Molecular mechanisms underlying the toxicity and detoxification of trace metals and metalloids in plants

Plants take up a wide range of trace metals/metalloids (hereinafter referred to as trace metals) from the soil, some of which are essential but become toxic at high concentrations (e.g., Cu, Zn, Ni, Co), while others are non-essential and toxic even at relatively low concentrations (e.g., As, Cd, Cr, Pb, and Hg). Soil contamination of trace metals is an increasing problem worldwide due to intensifying human activities. Trace metal contamination can cause toxicity and growth inhibition in plants, as well as accumulation in the edible parts to levels that threatens food safety and human health. Understanding the mechanisms of trace metal toxicity and how plants respond to trace metal stress is important for improving plant growth and food safety in contaminated soils. The accumulation of excess trace metals in plants can cause oxidative stress, genotoxicity, programmed cell death, and disturbance in multiple physiological processes. Plants have evolved various strategies to detoxify trace metals through cell-wall binding, complexation, vacuolar sequestration, efflux, and translocation. Multiple signal transduction pathways and regulatory responses are involved in plants challenged with trace metal stresses. In this review, we discuss the recent progress in understanding the molecular mechanisms involved in trace metal toxicity, detoxification, and regulation, as well as strategies to enhance plant resistance to trace metal stresses and reduce toxic metal accumulation in food crops.

Single Molecular Chelation Dynamics Reveals That DNA Has a Stronger Affinity toward Lead(II) than Cadmium(II)

Lead ions can bind to DNA via nonelectrostatic interactions and hence alter its structure, which may be related to their adverse effects. The dynamics of Pb²⁺-DNA interaction has not been well understood. In this study, we report the monomolecular dynamics of the Pb²⁺-DNA interaction using a magnetic tweezers (MT) setup. We found that lead cations could induce DNA compaction at ionic strengths above 1 μM, which was also confirmed by morphology characterization. The chelation behavior of the Pb²⁺-DNA and the Cd²⁺-DNA complex solutions after adding EDTA were compared. The results showed that EDTA chelated with the bound metal ions on DNA and consequently led to restoring the DNA to its original length but with different restoration speeds for the two solutions. The fast binding dynamics and the slower chelation dynamics of the Pb²⁺ scenario compared to that of Cd²⁺ suggested that Pb²⁺ was more capable to induce DNA conformational change and that the Pb²⁺-DNA complex was more stable than the Cd²⁺-DNA complex. The stronger affinities for DNA bases and the inner binding of lead cations were two possible causes of the dynamics differences. Three agents, including EDTA, sodium gluconate, and SDBS, were used to remove the bound lead ions on DNA. It was shown that EDTA was the most efficient, and sodium gluconate could not fully restore DNA from its compact state. We concluded that both EDTA and SDBS were good candidates to restore the Pb²⁺-bound DNA to its original state.

Switchable inhibitory behavior of divalent magnesium ion in DNA hybridization-based gene quantification

Mg2+ ion is a switchable inhibitor that can cause either under or over-estimation at different concentrations in DNA hybridization based gene quantification.

Eu3+ as a luminescence probe in DNA studies: Structural and conformational implications

Lanthanide ions are widely used as luminescent probes for structural studies of various biomolecules, including DNA. Latest developments of circularly polarized luminescence (CPL) methodology further boosted interest to luminescence techniques. However, an effect of the lanthanide probes themselves on the DNA structure and conformation was investigated only partially and not for all lanthanides. In the present work, we performed a detailed spectroscopic study of Eu³⁺ complexes with native double-stranded DNA and compared them to the relevant complexes with single-stranded DNA. We employed infrared (IR), vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopic methods to investigate Eu³⁺ effect on DNA structure and conformational transitions. It was shown that Eu³⁺ ions can induce significant alteration of the native DNA structure at the concentrations often used in luminescence studies. While no DNA denaturation was observed at these metal ion concentrations, significant unstacking of the base pairs and disordering of the sugar-phosphate backbone, partial appearance of the A-form backbone geometry, and DNA transition into condensed ψ-type form took place. Eu³⁺ binding to single-stranded DNA was more pronounced than the binding to double-stranded DNA. We detected the main Eu³⁺ binding sites and determined the metal ion concentration range in which DNA geometry remains largely unaltered. The results obtained in the current study could be used for tuning the luminescence and CPL structural studies of DNA utilizing Eu³⁺ ions as probes.

Europium (III) as a Circularly Polarized Luminescence Probe of DNA Structure

We report as a proof-of-concept the first application of circularly polarized luminescence (CPL) measured with a Raman optical activity (ROA) spectrometer to differentiate several DNA structures without need of sensitizing complexes. The ROA/CPL approach provides sufficiently high CPL intensity to use hydrated Eu³⁺ ions, thus avoiding DNA structural changes associated with binding of sensitizers and overcoming the sensitizer quenching issue. We showed that deoxyguanosine monophosphate (dGMP), single- and double-stranded DNA provide different CPL spectra, which could be used for their discrimination. Our results demonstrate that ROA/CPL method is a promising approach to measure CPL spectra of complex biomolecules when the use of sensitizers is not possible. The method can be extended to other biomolecules, such as proteins, lipids, sugars, etc.

Bacterial Resistance and Prostate Cancer Susceptibility Toward Metal-Ion-doped DNA Complexes

DNA nanotechnology has laid a platform to construct a variety of custom-shaped nanoscale objects for functionalization of specific target materials to achieve programmability and molecular recognition. Herein, we prepared DNA nanostructures [namely, synthetic DNA rings (RDNA) and DNA duplexes extracted from salmon (SDNA)] containing metal ions (M²⁺) such as Cu²⁺, Ni²⁺, and Zn²⁺ as payloads for delivery to exterminate highly pathologic hospital bacterial strains (e.g., Escherichia coli and Bacillus subtilis) and prostate cancer cells (i.e., PC3, LNCaP, TRAMP-C1, 22Rv1, and DU145). Morphologies of these M²⁺-doped RDNA were visualized using atomic force microscopy. Interactions between M²⁺ and DNA were studied using UV-vis and Fourier transform infrared spectroscopy. Quantitative composition and chemical changes in DNA without or with M²⁺ were obtained using X-ray photoelectron spectroscopy. In addition, M²⁺-doped DNA complexes were subjected to antibacterial activity studies. They showed no bacteriostatic or bactericidal effects on bacterial strains used. Finally, in vitro cellular toxicity study was conducted to evaluate the effect of pristine DNA and M²⁺-doped DNA complexes on prostate cancer cells. Cytotoxicities conferred by M²⁺-doped DNA complexes for most cell lines were significantly higher than those of M²⁺ without DNA. Cellular uptake of these complexes was confirmed by fluorescence microscopy using PhenGreen FL indicator. On the basis of our observations, DNA nanostructures can be used as safe and efficient nanocarriers for delivery of therapeutics. They have enhanced therapeutic window than bare metals.

Water as a Universal Infrared Probe for Bioanalysis in Aqueous Solution by Attenuated Total Reflection-Surface Enhanced Infrared Absorption Spectroscopy

Monitoring the properties and reactions of biomolecules at their interface has attracted ever-growing interest. Here, we propose an approach of infrared analysis technique that utilizes water molecule as a universal probe for in situ and label free monitoring of interfacial bioevents in aqueous solution with high sensitivity. The strong infrared (IR) signal of O-H stretching vibrations from the repelled water is used to sensitively reveal the kinetics of interfacial bioevents at molecular level based on the steric displacement of water using an attenuated total reflection-surface enhanced infrared absorption spectroscopy. Using interfacial immuno-recognition and DNA hybridization as demonstrations, water IR probe offers 26 and 34 times higher sensitivity and even 200 and 86 times lower detection limit for immunosensing and DNA sensing, respectively, as compared to the traditional IR molecular fingerprints.

Mimicking an Enzyme-Based Colorimetric Aptasensor for Antibiotic Residue Detection in Milk Combining Magnetic Loop-DNA Probes and CHA-Assisted Target Recycling Amplification

A mimicking-enzyme-based colorimetric aptasensor was developed for the detection of kanamycin (KANA) in milk using magnetic loop-DNA-NMOF-Pt (m-L-DNA) probes and catalytic hairpin assembly (CHA)-assisted target recycling for signal amplification. The m-L-DNA probes were constructed via hybridization of hairpin DNA H1 (containing aptamer sequence) immobilized magnetic beads (m-H1) and signal DNA (sDNA, partial hybridization with H1) labeled nano Fe-MIL-88NH₂-Pt (NMOF-Pt-sDNA). In the presence of KANA and complementary hairpin DNA H2, the m-L-DNA probes decomposed and formed an m-H1/KANA intermediate, which triggered the CHA reaction to form a stable duplex strand (m-H1-H2) while releasing KANA again for recycling. Consequently, numerous NMOF-Pt-sDNA as mimicking enzymes can synergistically catalyze 3,3',5,5'-tetramethylbenzidine (TMB) for color development. The aptasensor exhibited high selectivity and sensitivity for KANA in milk with a detection limit of 0.2 pg mL^-1 within 30 min. The assay can be conveniently extended for on-site screening of other antibiotics in foods by simply changing the base sequence of the probes.

An electrochemical aptasensor for multiplex antibiotics detection using Y-shaped DNA-based metal ions encoded probes with NMOF substrate and CSRP target-triggered amplification strategy

An effective electrochemical aptasensor has been developed for the detection of multiplex antibiotics using Y-shaped DNA probes. These probes-based metal ions encoded the nanoscale metal-organic frameworks (NMOF) as a substrate, and circular strand-replacement DNA polymerization (CSRP) target triggered the amplification strategy. The Y-DNA probes (Y-DNA) were assembled using an assisted DNA probe (assisted DNA labeled with magnetic gold nanoparticles) which can hybridize to the captured DNA probe (consisting of aptamer and primer recognition region), and signal tags (NMOF encapsulating signal DNAs and different metal ions such as Pb²⁺ or Cd²⁺). Notably, NMOF was employed as the developed platform with a large specific area to load abundant metal ions that can produce distinguishable signals. In the presence of targets, chloramphenicol (CAP) and oxytetracycline (OTC) as models, the conformational change of the captured DNA can disassemble the Y-DNA probes that can consequently release the signal tags in the supernatant due to the high affinity of targets towards the aptamer domain than its complementary sequences. Subsequently, the exposed sequences of captured DNA serve as the initiators for triggering the target cyclic-induced polymerization with the assistance of Bst DNA polymerase. Thus, numerous signal tags could be detected by square wave voltammetry in the supernatant after magnetic separation, thereby amplifying the electrochemical signals. The proposed strategy exhibited a high sensitivity to antibiotics with a detection limit of 33 and 48 fM (S/N = 3) towards CAP and OTC, respectively. Moreover, this aptasensor showed promising applications for the detection of other analytes.

Multispectroscopic studies on the interaction of a copper(ii) complex of ibuprofen drug with calf thymus DNA

The interaction of copper(II)-ibuprofenato complex with calf thymus DNA (ct-DNA) has been explored following, UV-visible spectrophotometry, fluorescence measurement, dynamic viscosity measurements, and circular dichroism spectroscopy. In spectrophotometric studies of ct-DNA it was found that [Cu(ibp)₂]₂ can form a complex with double-helical DNA. The association constant of [Cu(ibp)₂]₂ with DNA from UV-Vis study was found to be 6.19 × 10⁴ L mol^-1. The values of K_f from fluorescence measurement clearly underscore the high affinity of [Cu(ibp)₂]₂ to DNA. The experimental results showed that the conformational changes in DNA helix induced by [Cu(ibp)₂]₂ are the reason for the fluorescence quenching of the DNA-Hoechst system. In addition, the fluorescence emission spectra of intercalated methylene blue (MB) with increasing concentrations of [Cu(ibp)₂]₂ represented a significant increase of MB intensity as to release MB from MB-DNA system. The results of circular dichroism (CD) suggested that copper(II)-ibuprofenato complex can change the conformation of DNA. In addition, the results of viscosity measurements suggest that copper(II)-ibuprofenato complex may bind with non-classical intercalative mode. From spectroscopic and hydrodynamic studies, it has been found that [Cu(ibp)₂]₂ interacts with DNA by partial intercalation mode which contains intercalation and groove properties.

An electrochemical aptasensor for multiplex antibiotics detection based on metal ions doped nanoscale MOFs as signal tracers and RecJf exonuclease-assisted targets recycling amplification

An ultrasensitive electrochemical aptasensor for simultaneous detection of oxytetracycline (OTC) and kanamycin (KAN) has been developed based on metal ions doped metal organic frame materials (MOFs) as signal tracers and RecJ_f exonuclease-catalyzed targets recycling amplification. The aptasensor consists of capture beads (the anti-single-stranded DNA Antibody, as anti-ssDNA Ab, labeled on Dynabeads) and nanoscale MOF (NMOF) based signal tracers (simplified as Apts-MNM, the NMOF labeled with metal ions and the aptamers). Particularly, the MOF (UiO-66-NH₂), with large internal surface areas, ultrahigh porosity and abundant amine groups in the pores, was employed as substrates to carry plenty of metal ions (Pb²⁺ or Cd²⁺) and label aptamers of OTC or KAN. Thus, the aptasensor is formed by the specific recognition between anti-ssDNA Ab and aptamers. In the presence of targets (OTC and KAN), aptamers prefer to form targets-Apts-MNM complexes in lieu of anti-ssDNA Ab-aptamer complexes, which results in the dissociation of Apts-MNM from capture beads. With the employment of RecJ_f exonuclease, targets-Apts-MNM in supernatant was digested into mononucleotides and liberated the target, which can further participate in the next reaction cycling to produce more signal tracers. After magnetic separation, the enhanced square wave voltammetry (SWV) signals were produced from signal tracers. The aptasensor exhibited a linear correlation in the range from 0.5pM to 50nM, with detection limits of 0.18pM and 0.15pM (S/N=3) toward OTC and KAN respectively. This strategy provides specificity and sensitive approach for multiplex antibiotics detection and has promising applications in food analysis.

Effect of magnesium ions on the structure of DNA thin films: an infrared spectroscopy study

Utilizing Fourier transform infrared spectroscopy we have investigated the vibrational spectrum of thin dsDNA films in order to track the structural changes upon addition of magnesium ions. In the range of low magnesium concentration ([magnesium]/[phosphate] = [Mg]/[P] < 0.5), both the red shift and the intensity of asymmetric PO2 stretching band decrease, indicating an increase of magnesium-phosphate binding in the backbone region. Vibration characteristics of the A conformation of the dsDNA vanish, whereas those characterizing the B conformation become fully stabilized. In the crossover range with comparable Mg and intrinsic Na DNA ions ([Mg]/[P] ≈ 1) B conformation remains stable; vibrational spectra show moderate intensity changes and a prominent blue shift, indicating a reinforcement of the bonds and binding in both the phosphate and the base regions. The obtained results reflect the modified screening and local charge neutralization of the dsDNA backbone charge, thus consistently demonstrating that the added Mg ions interact with DNA via long-range electrostatic forces. At high Mg contents ([Mg]/[P] > 10), the vibrational spectra broaden and show a striking intensity rise, while the base stacking remains unaffected. We argue that at these extreme conditions, where a charge compensation by vicinal counterions reaches 92-94%, DNA may undergo a structural transition into a more compact form.

Groove binding mediated structural modulation and DNA cleavage by quinoline appended chalcone derivative

The present study embodies the detail DNA binding interaction of a potential bioactive quinoline appended chalcone derivative (E)-3-(anthracen-10-yl)-1-(6,8-dibromo-2-methylquinolin-3-yl)prop-2-en-1-one (ADMQ) with calf thymus DNA (ctDNA) and its consequences by UV-Vis absorption, steady state fluorescence spectroscopy, fluorescence anisotropy, circular dichromism, helix melting, agarose gel electrophoresis, molecular docking, Induced Fit Docking (IFD) and molecular dynamics (MD) simulation. The UV-Vis absorption and fluorescence study reveal that the molecule undergoes considerable interaction with the nucleic acid. The control KI quenching experiment shows the lesser accessibility of ADMQ molecule to the ionic quencher (I(-)) in presence of ctDNA as compared to the bulk aqueous phase. Insignificant change in helix melting temperature as well as in circular dichromism (CD) spectra points toward non-covalent groove binding interaction. The moderate rotational confinement of this chalcone derivative (anisotropy=0.106) trapped in the nucleic acid environment, the comparative displacement assay with well-known minor groove binder Hoechst 33258 and intercalator Ethidium Bromide establishes the minor groove binding interactions of the probe molecule. Molecular docking, IFD and MD simulation reveal that the DNA undergoes prominent morphological changes in terms of helix unwinding and bending to accommodate ADMQ in a crescent shape at an angle of 110° in a sequence specific manner. During interaction, ADMQ rigidifies and bends the sugar phosphate backbone of the nucleic acid and thereby shortens its overall length by 3.02Å. Agarose gel electrophoresis experiment with plasmid pBR 322 reveals that the groove binded ADMQ result in a concentration dependent cleavage of plasmid DNA into its supercoiled and nicked circular form. The consolidated spectroscopic research described herein provides quantitative insight into the interaction of a heterocyclic chalcone derivative with relevant target nucleic acid, which may be useful for the future research on chalcone based therapeutic agents.

Determining the mode of interaction of calf thymus DNA with the drug sumatriptan using voltammetric and spectroscopic techniques

The interaction of native calf thymus DNA with sumatriptan(1-[3-(2-dimethylaminoethyl)-1H-indol-5-yl]-N-methyl-methanesulfonamide) at physiological pH was studied by spectrophotometry, circular dichroism, voltammetry and viscosimetric techniques. Sumatriptan molecule intercalated between base pairs of DNA, showed by a sharp increase in specific viscosity of DNA. In cyclic voltammetry, decrease of the peak current and positive shift indicated that this drug is able to intercalate between the DNA base pairs. In addition, the drug induced changes in the CD spectrum of CT-DNA, as well as hypochromism changes in its UV-vis spectrum.

DNA binding, DNA cleavage and cytotoxicity studies of a new water soluble copper(II) complex: the effect of ligand shape on the mode of binding

The interaction of native calf thymus DNA (CT-DNA) with [Cu(ph(2)phen)(phen-dione)Cl]Cl was studied at physiological pH by spectrophotometric, spectrofluorometric, circular dichroism, and viscometric techniques. Considerable hypochromicity and red shift are observed in the UV absorption band of the Cu complex. Binding constants (K(b)) of DNA with the complex were calculated at different temperatures. Thermodynamic parameters, enthalpy and entropy changes were calculated according to Van't Hoff equation, which indicated that reaction is predominantly enthalpically driven. All these results indicate that Cu(II) complex interacts with CT-DNA via intercalative mode. Also, this new complex induced cleavage in pUC18 plasmid DNA as indicated in gel electrophoresis and showed excellent antitumor activity against K562 (human chronic myeloid leukemia) and human T lymphocyte carcinoma-Jurkat cell lines.

Preparation, characterization and scanned conductance microscopy studies of DNA-templated one-dimensional copper nanostructures

The synthesis of one-dimensional metal nanostructures can be achieved through the use of DNA molecules as templates to control and direct metal deposition. Copper nanostructures have been fabricated using this strategy, through association of Cu(2+) ions to DNA templates and reduced with ascorbic acid. Due to the possibility that the reduction of the Cu(2+) can result in the preferential formation of Cu(2)O over metallic Cu(0), X-ray photoelectron spectroscopy and X-ray diffraction have been carried out to establish the chemical identity of the nanostructures. Conclusive evidence is found that reduction of the Cu(2+) ions does result in the formation of the desired metallic Cu(0) structures. The morphology of the nanostructured Cu(0) material has also been observed by atomic force microscopy, showing the structures to have a "beads-on-a-string" appearance and being 3.0-5.5 nm in height. The electrical properties of the structures have been investigated by scanned conductance microscopy, showing the Cu(0) structures exhibit much larger electrical resistance than expected for a metallic nanowire. This is thought to be a consequence of their "beads-on-a-string" morphology and small lateral dimensions (sub-10 nm); both these factors would be expected to increase the electron scattering rate, and, further, there are likely to be significant tunneling barriers at the Cu(0) particle-particle junctions.

Infrared absorption detection of metal ion-deoxyguanosine monophosphate binding: experimental and theoretical study

Metal ion interactions with nucleic acids attract attention because of the environmental and biological consequences. The formation of the complex is often monitored by the vibrational spectroscopy. To identify characteristic binding patterns and marker bands on a model DNA component, infrared absorption spectra of the deoxyguanosine monophosphate complexes with Na(+), Mg(2+), Ca(2+), Ni(2+), Cu(2+), Zn(2+), and Cd(2+) cations were recorded and interpreted on the basis of density-functional computations. The aqueous environment was simulated by continuum and combined continuum-explicit solvent models. For the binding to the N7 position of the guanine base, the computation predicted a characteristic frequency upshift and splitting of the 1578 cm(-1) band, which is in accord with available experimental data. Contrary to the expectation, the modeling suggests that the binding to the carbonyl group might not be detectable, as the metal causes smaller spectral changes if compared to the hydrogen-bound water molecules. The binding to the phosphate group causes significant spectral changes in the sugar-phosphate vibrating region ( approximately 800-1200 cm(-1)), but also notable frequency shifts of the carbonyl vibrations. The Cu(2+) and Zn(2+) ions induced the largest alterations in observed vibrational absorption, which corresponds to the calculated strong interaction energies in the N7-complexes and to previous experimental experience. Additional changes in the vibrational spectra of the copper complexes were observed under high metal concentration, corresponding to the simultaneous binding to the phosphate residue. The two-step Cu(2+) binding process was also confirmed by the microcalorimetry titration curve. The computations and combination of more techniques thus help us to assign and localize spectral changes caused by the metal ion binding to nucleic acids.

Mechanism of copper mediated triple helix formation at neutral pH in Drosophila satellite repeats

The highly repeated Drosophila melanogaster AAGAGAG satellite sequence is present at each chromosome centromere of the fly. We demonstrate here how, under nearly physiological pH conditions, these sequences can form a pyrimidine triple helix containing T.A-T and CCu.G-C base triplets, stabilized by Cu2+ metal ions in amounts mirroring in vivo concentrations. Ultraviolet experiments were used to monitor the triple helix formation at pH 7.2 in presence of Cu2+ ions. Triplex melting is observed at 23 degrees C. Furthermore, a characteristic signature of triple helix formation was obtained by Fourier transform infrared spectroscopy. The stabilization of the C.G-C base triplets at pH 7.2 is shown to occur via interactions of Cu2+ ions on the third strand cytosine N3 atom and on the guanine N7 atom of the polypurine target strand forming CCu.G-C triplets. Under the same neutral pH conditions in absence of Cu2+ ions, the triple helix fails to form. Possible biological implications are discussed.

The effect of manganese(II) on the structure of DNA/HMGB1/H1 complexes: Electronic and vibrational circular dichroism studies

The interactions were studied of DNA with the nonhistone chromatin protein HMGB1 and histone H1 in the presence of manganese(II) ions at different protein to DNA and manganese to DNA phosphate ratios by using absorption and optical activity spectroscopy in the electronic [ultraviolet (UV) and electronic circular dichroism ECD)] and vibrational [infrared (IR) and vibrational circular dichroism (VCD)] regions. In the presence of Mn2+, the protein-DNA interactions differ from those without the ions and cause prominent DNA compaction and formation of large intermolecular complexes. At the same time, the presence of HMGB1 and H1 also changed the mode of interaction of Mn2+ with DNA, which now takes place mostly in the major groove of DNA involving N7(G), whereas interactions between Mn2+ and DNA phosphate groups are weakened by histone molecules. Considerable interactions were also detected of Mn2+ ions with aspartic and glutamic amino acid residues of the proteins.

A Comparative study of Fe(II) and Fe(III) interactions with DNA duplex: major and minor grooves bindings

The involvement of the Fe cations in autoxidation in cells and tissues is well documented. DNA is a major target in such reaction, and can chelate Fe cation in many ways. The present study was designed to examine the interaction of calf-thymus DNA with Fe(II) and Fe(III), in aqueous solution at pH 6.5 with cation/DNA (P) (P = phosphate) molar ratios (r) of 1:160 to 1:2. Capillary electrophoresis and Fourier transform infrared (FTIR) difference spectroscopic methods were used to determine the cation binding site, the binding constant, helix stability and DNA conformation in Fe-DNA complexes. Structural analysis showed that at low cation concentration (r = 1/80 and 1/40), Fe(II) binds DNA through guanine N-7 and the backbone PO(2) group with specific binding constants of K(G) = 5.40 x 10(4) M(1) and K(P) = 2.40 x 10(4) M(1). At higher cation content, Fe(II) bindings to adenine N-7 and thymine O-2 are included. The Fe(III) cation shows stronger interaction with DNA bases and the backbone phosphate group. At low cation concentration (r = 1:80), Fe(III) binds mainly to the backbone phosphate group, while at higher metal ion content, cation binding to both guanine N-7 atom and the backbone phosphate group is prevailing with specific binding constants of K(G) = 1.36 x 10(5) M(-1) and K(P) = 5.50 x 10(4) M(-1). At r = 1:10, Fe(II) binding causes a minor helix destabilization, whereas Fe(III) induces DNA condensation. No major DNA conformational changes occurred upon iron complexation and DNA remains in the B-family structure.

Urea effect on Cu2+-induced DNA structural transitions in solution

Cu(2+) ion interaction with DNA in aqueous solutions containing urea (0-5 M) was studied by IR spectroscopy. It was shown that upon the Cu(2+) ion binding DNA transition into a compact form occurs. This transition is of positive cooperativity. We suppose that the mechanism of Cu(2+)-induced DNA compaction in solutions containing urea is not completely electrostatic. Urea addition to the DNA solution decreases the Cu(2+) ion concentration required to induce DNA compaction. As the urea content in solution rises, the binding constant of Cu(2+) ions interacting with DNA increases, going through the maximum in the case of 2 M solution; further increase of the urea content in solutions leads to decrease of the binding constant. DNA transition into the compact form under the Cu(2+) ion action is determined not only by the effects of the solution dielectric permeability but by the solvation effects; when changes of the dielectric permeability are small the solvation effects may prevail. Urea addition to the DNA solution also decreases cooperativity of the DNA compaction process. Perhaps, cooperativity of the DNA transition into the compact state depends on the ordered spatial structure of water adjacent to the macromolecule and decreases on the structure destruction.

RNA Adducts with Chlorophyll and Chlorophyllin: Stability and Structural Features

Porphyrins and their metal derivatives are strong nucleic acids binders. Some of these compounds have been used for radiation sensitization therapy of cancer and are targeted to interact with cellular DNA. Chlorophyll (Chl) binds DNA via guanine N-7 atom (major groove) and the backbone phosphate group (Neault and Tajmir-Riahi. Biophys. J. 76, 2177, 1999), whereas chlorophyllin (Chln) intercalates into A-T and G-C regions (Neault and Tajmir-Riahi. J. Phys. Chem. B. 102, 1610, 1998). This study was designed to examine the interaction of RNA with chlorophyll a and chlorophyllin in aqueous solution at physiological pH with pigment/RNA(phosphate) ratios (r) of 1/80 to 1/2. Fourier transform infrared (FTIR) and UV-visible difference spectroscopic methods were used to characterize the nature of pigment-RNA interaction and to establish correlation between spectral changes and the pigment binding mode, binding constant, RNA secondary structure and structural variations of pigment-RNA complexes in aqueous solution. Spectroscopic results showed that Chl and Chln bind RNA through G-C and A-U bases and the backbone phosphate group with overall binding constants of KChl = 1.95 x 10(5) M(-1) and KChln = 1.61 x 10(5) M(-1). The larger K value obtained for Chl-RNA complexes is attributed to the formation of more stable five or six-coordinate Mg cation in the RNA adducts, while the four-coordination Cu(II) in Chln can be more stable than that of the five or six-coordinated copper ion in the Chln-RNA complexes. Aggregation of pigment-RNA complexes occurs at high metalloporphyrin concentrations. No biopolymer secondary structural changes were observed upon pigment interaction and RNA remains in the A-family structure in these pigment complexes.

The effect of manganese(II) on DNA structure: electronic and vibrational circular dichroism studies

The interaction of DNA with Mn2+ was studied in absorbance and optical activity in the electronic and vibrational regions. Based on the data, several stages of the interaction were identified. Con formational transition towards the C-form of DNA was observed in solution at the molar ratio Mn2+/DNA-phosphates between 0.1 and 1.5. The exact ratio depended on the ionic strength and increased with increasing NaCl concentration. Although manganese interacted with the phosphates and bases of DNA at higher metal concentrations, it is unlikely that direct chelation occurred. A model for the interaction between manganese ions and DNA mediated by water is suggested destabilizing the double helix and partially breaking the hydrogen bonds between the base pairs. At high Mn2+ concentrations DNA aggregation was observed.

Vibrational circular dichroism and IR absorption of DNA complexes with Cu2+ ions

Vibrational circular dichroism (VCD) spectroscopy and simultaneous IR absorption measurements are applied to study the interaction of natural calf thymus DNA with Cu2+ ions at room temperature in a Cu2+ concentration range of 0-0.4M (a Cu2+/phosphate molar ratio [Cu]/[P] of 0-0.7). In some important instances, VCD provides more detailed insights than previous IR investigations whereas in several others it leads to the same interpretations. The Cu2+ ions bind to phosphate groups at a low metal concentration. Upon increasing the ion concentration, chelates are formed in which Cu2+ binds to the N7 of guanine (G) and a phosphate group. Detectable only by VCD, significant distortion of most guanine-cytosine (GC) base pairs occurs at a [Cu]/[P] ratio of 0.5 with only a minor affect on adenine-thymine (AT) base pairs, which favors a "sandwich" complex in which a Cu2+ ion is inserted between two adjacent guanines in a GpG sequence. The AT base pairs become significantly distorted when the metal concentration is increased to 0.7 [Cu]/[P]. A number of GC base pairs, which are possibly involved in sandwich complexes, remain stacked and paired even at 0.7 [Cu]/[P], preventing complete strand separation. The DNA secondary structure changes considerably from the standard B-form geometry at a [Cu]/[P] ratio of 0.4 and higher. A further transition to some intermediate conformation that is inconsistent with either the A- or Z-form or a completely denatured state is suggested in agreement with other works. In general, VCD proves to be a reliable indicator of the 3-dimensional structure of the DNA-metal ion complexes, which reveals structural details that cannot be deduced from the IR absorption spectra alone.

DNA interaction with Mn2+ ions at elevated temperatures: VCD evidence of DNA aggregation

Interaction of natural calf thymus DNA with Mn(2+) ions was studied at room temperature and at elevated temperatures in the range from 23 degrees C to 94 degrees C by means of IR absorption and vibrational circular dichroism (VCD) spectroscopy. The Mn(2+) concentration was varied between 0 and 1.3M (0 and 10 [Mn]/[P]). The secondary structure of DNA remained in the frame of the B-form family in the whole ion concentration range at room temperature. No significant DNA denaturation was revealed at room temperature even at the highest concentration of metal ions studied. However at elevated temperatures, DNA denaturation and a significant decrease of the melting temperature of DNA connected with a decrease of the stability of DNA induced by Mn(2+) ions occurred. VCD demonstrated sensitivity to DNA condensation and aggregation as well as an ability to distinguish between these two processes. No condensation or aggregation of DNA was observed at room temperature at any of the metal ion concentrations studied. DNA condensation was revealed in a very narrow range of experimental conditions at around 2.4 [Mn]/[P] and about 55 degrees C. DNA aggregation was observed in the presence of Mn(2+) ions at elevated temperatures during or after denaturation. VCD spectroscopy turned out to be useful for studying DNA condensation and aggregation due to its ability to distinguish between these two processes, and for providing information about DNA secondary structure in a condensed or aggregated state.

Persistence length of a strongly charged rodlike polyelectrolyte in the presence of salt

The persistence length of a single, intrinsically rigid polyelectrolyte chain, above the Manning condensation threshold is investigated theoretically in the presence of added salt. Using a loop expansion method, the partition function is consistently calculated, taking into account corrections to mean-field theory. Within a mean-field approximation, the well-known results of Odijk, Skolnick, and Fixman are reproduced. Beyond mean field, it is found that density correlations between counterions and thermal fluctuations reduce the stiffness of the chain, indicating an effective attraction between monomers for highly charged chains and multivalent counterions. This attraction results in a possible mechanical instability (collapse), alluding to the phenomenon of DNA condensation. In addition, we find that more counterions condense on slightly bent conformations of the chain than predicted by the Manning model for the case of an infinite cylinder. Finally, our results are compared with previous models and experiments.

Vibrational CD (VCD) and atomic force microscopy (AFM) study of DNA interaction with Cr3+ ions: VCD and AFM evidence of DNA condensation

The interaction of natural calf thymus DNA with Cr(3+) ions was studied at room temperature by means of vibrational CD (VCD) and infrared absorption (ir) spectroscopy, and atomic force microscopy (AFM). Cr(3+) ion binding mainly to N(7) (G) and to phosphate groups was demonstrated. Psi-type VCD spectra resembling electronic CD (ECD) spectra, which appear during psi-type DNA condensation, were observed. These spectra are characterized mainly by an anomalous, severalfold increase of VCD intensity. Such anomalous VCD spectra were assigned to DNA condensation with formation of large and dense particles of a size comparable to the wavelength of the probing ir beam and possessing large-scale helicity. Atomic force microscopy confirmed DNA condensation by Cr(3+) ions and the formation of tight DNA particles responsible for the psi-type VCD spectra. Upon increasing the Cr(3+) ion concentration the shape of the condensates changed from loose flower-like structures to highly packed dense spheres. No DNA denaturation was seen even at the highest concentration of Cr(3+) ions studied. The secondary structure of DNA remained in a B-form before and after the condensation. VCD and ir as well as AFM proved to be an effective combination for investigating DNA condensation. In addition to the ability of VCD to determine DNA condensation, VCD and ir can in the same experiment provide unambiguous information about the secondary structure of DNA contained in the condensed particles.

Silver(I) complexes with DNA and RNA studied by Fourier transform infrared spectroscopy and capillary electrophoresis

Ag(I) is a strong nucleic acids binder and forms several complexes with DNA such as types I, II, and III. However, the details of the binding mode of silver(I) in the Ag-polynucleotides remains unknown. Therefore, it was of interest to examine the binding of Ag(I) with calf-thymus DNA and bakers yeast RNA in aqueous solutions at pH 7.1-6.6 with constant concentration of DNA or RNA and various concentrations of Ag(I). Fourier transform infrared spectroscopy and capillary electrophoresis were used to analyze the Ag(I) binding mode, the binding constant, and the polynucleotides' structural changes in the Ag-DNA and Ag-RNA complexes. The spectroscopic results showed that in the type I complex formed with DNA, Ag(I) binds to guanine N7 at low cation concentration (r = 1/80) and adenine N7 site at higher concentrations (r = 1/20 to 1/10), but not to the backbone phosphate group. At r = 1/2, type II complexes formed with DNA in which Ag(I) binds to the G-C and A-T base pairs. On the other hand, Ag(I) binds to the guanine N7 atom but not to the adenine and the backbone phosphate group in the Ag-RNA complexes. Although a minor alteration of the sugar-phosphate geometry was observed, DNA remained in the B-family structure, whereas RNA retained its A conformation. Scatchard analysis following capillary electrophoresis showed two binding sites for the Ag-DNA complexes with K(1) = 8.3 x 10(4) M(-1) for the guanine and K(2) = 1.5 x 10(4) M(-1) for the adenine bases. On the other hand, Ag-RNA adducts showed one binding site with K = 1.5 x 10(5) M(-1) for the guanine bases.