INTERACTIONS OF METAL IONS WITH POLYNUCLEOTIDES AND RELATED COMPOUNDS. V. THE UNWINDING AND REWINDING OF DNA STRANDS UNDER THE INFLUENCE OF COPPER (II) IONS

Nanoscale Study of DNA-Cu2+ Interactions by Liquid-Cell Electron Microscopy

Metal ions are indispensable constituent elements of the human body, among which Cu²⁺ plays an important role in various biochemical reactions in the human body and is an essential element for maintaining human health. Studying the interaction between Cu²⁺ and DNA can be helpful to further understand the mechanism of Cu²⁺ behavior in organisms. In this paper, we investigated the DNA-Cu²⁺ complex by transmission electron microscopy (TEM) and used in situ liquid-cell TEM to observe the dynamic processes of interactions between DNA and Cu²⁺. Results show that the binding of Cu²⁺ to DNA leads to the bending of the DNA strand and provides an anchor site for activating Cu²⁺ for the nucleation and growth of copper crystals. Bound by the DNA strand, the copper crystals are arranged along the curved strand, showing the same arrangement pattern as guanine on the DNA sequence. It is believed that the study will further elaborate the interaction mechanism by directly observing the DNA-Cu²⁺ complex at the nanometer scale and benefit the related biomedical research studies.

Studies on Copper and Aβ1-16-Induced Conformational Changes in CAG/CTG Trinucleotide Repeats Sequence

DNA conformation and stability are critical for the normal cell functions, which control many cellular processes in life, such as replication, transcription, DNA repair, etc. The accumulation of amyloid-β peptide (Aβ) and Copper (Cu) are the etiological factors for neurodegenerative diseases and hypothesized that they can cause DNA instability. In the current investigation, we studied copper and Aβ_1-16 induced conformation and stability changes in CAG/CTG sequences and found alterations from B-DNA to altered B-conformation. Further, the interaction of the copper and Aβ_1-16 with CAG/CTG sequences was studied by molecular docking modeling and results indicated that the interaction of copper and Aβ_1-16 was through the hydrogen bond formation between adenine, guanine, and cytocine. This study illustrates the role of the copper and Aβ_1-16 in modulating the DNA conformation and stability.

Binding of Al(iii) to synthetic RNA and metal-mediated strand aggregation

Kinetic curve of the binding of aluminum to RNA and metal-induced strand aggregation.

Enhanced nonlinear optical characteristics of copper-ion-doped double crossover DNAs

The modification of deoxyribonucleic acid (DNA) samples by sequencing the order of bases and doping copper ions opens the possibility for the design of novel nanomaterials exhibiting large optical nonlinearity. We investigated the nonlinear characteristics of copper-ion doped double crossover DNA samples for the first time to the best of our knowledge by using Z-scan and four-wave mixing methods. To accelerate the nonlinear characteristics, we prepared two types of unique DNA nanostructures composed of 148 base pairs doped with copper ions with a facile annealing method. The outstanding third-order nonlinear optical susceptibility of the copper-ion-doped DNA solution, 1.19 × 10(-12) esu, was estimated by the conventional Z-scan measurement, whereas the four-wave mixing experiment was also investigated. In the visible spectral range, the copper-ion-doped DNA solution samples provided competent four-wave mixing signals with a remarkable conversion efficiency of -4.15 dB for the converted signal at 627 nm. The interactions between DNA and copper ions contribute to the enhancement of nonlinearity due to structural and functional changes. The present study signifies that the copper-ion-doped double crossover DNA is a potential candidate as a highly efficient novel material for further nonlinear optical applications.

Copper interactions with DNA of chromatin and its role in neurodegenerative disorders

In this study, we have demonstrated the conformational changes to DNA induced by abnormal interactions of copper using circular dichroism, in combination with UV-absorbance and fluorescence spectroscopy. Results confirm that binding of copper to bases of DNA in chromatin is concentration dependent. Binding efficiency of Cu²⁺ ions to DNA is increased in proportion to the degree of unwinding of the double helix induced by denaturation. Altered B-DNA conformation will alter the integrity of DNA which may affect the normal process of DNA replication and transcription. Copper induced DNA damage in the brain may cause neurotoxicity and the neuronal cell death and is implicated in Alzheimer's disease and other neurological disorders.

Alkynyl phosphonate DNA: a versatile "click"able backbone for DNA-based biological applications

Major hurdles associated with DNA-based biological applications include, among others, targeted cell delivery, undesirable nonspecific effects, toxicity associated with various analogues or the reagents used to deliver oligonucleotides to cells, and stability toward intracellular enzymes. Although a plethora of diverse analogues have been investigated, a versatile methodology that can systematically address these challenges has not been developed. In this contribution, we present a new, Clickable, and versatile chemistry that can be used to rapidly introduce diverse functionality for studying these various problems. As a demonstration of the approach, we synthesized the core analogue, which is useful for introducing additional functionality, the triazolylphosphonate, and present preliminary data on its biological properties. We have developed a new phosphoramidite synthon--the alkynyl phosphinoamidite, which is compatible with conventional solid-phase oligonucleotide synthesis. Postsynthesis, the alkynylphosphonate can be functionalized via "Click" chemistry to generate the 1,2,3-triazolyl or substituted 1,2,3-triazolyl phosphonate-2'-deoxyribonucleotide internucleotide linkage. This manuscript describes the automated, solid-phase synthesis of mixed backbone oligodeoxyribonucleotides (ODNs) having 1,2,3-triazolylphosphonate (TP) as well as phosphate or thiophosphate internucleotide linkages and also 2'-OMe ribonucleotides and locked nucleic acids (LNAs) at selected sites. Nuclease stability assays demonstrate that the TP linkage is highly resistant toward 5'- and 3'-exonucleases, whereas melting studies indicate a slight destabilization when a TP-modified ODN is hybridized to its complementary RNA. A fluorescently labeled 16-mer ODN modified with two TP linkages shows efficient cellular uptake during passive transfection. Of particular interest, the subcellular distribution of TP-modified ODNs is highly dependent on cell type; a significant nuclear uptake is observed in HeLa cells, whereas diffuse cytoplasmic fluorescence is found in the WM-239A cell line. Cytoplasmic distribution is also present in human neuroblastoma cells (SK-N-F1), but Jurkat cells show both diffuse and punctate cytoplasmic uptake. Our results demonstrate that triazolylphosphonate ODNs are versatile additions to the oligonucleotide chemist's toolbox relative to designing new biological research reagents.

Can copper(II) mediate Hoogsteen base-pairing in a left-handed DNA duplex? A pulse EPR study

Pulse EPR spectroscopy is used to investigate possible structural features of the copper(II) ion coordinated to poly(dG-dC).poly(dG-dC) in a frozen aqueous solution, and the structural changes of the polynucleotide induced by the presence of the metal ion. Two different copper species were identified and their geometry explained by a molecular model. According to this model, one species is exclusively coordinated to a single guanine with the N7 nitrogen atom forming a coordinative bond with the copper. In the other species, a guanine and a cytosine form a ternary complex together with the copper ion. A copper crosslink between the N7 of guanine and N3 of cytosine is proposed as the most probable coordination site. Moreover, no evidence was found for an interaction of either copper species with a phosphate group or equatorial water molecules. In addition, circular dichroism (CD) spectroscopy showed that the DNA of the Cu(II)-poly(dG-dC).poly(dG-dC) adducts resembles the left-handed Z-form. These results suggest that metal-mediated Hoogsteen base pairing, as previously proposed for a right-handed DNA duplex, can also occur in a double-stranded left-handed DNA.

Snap-to-it probes: chelate-constrained nucleobase oligomers with enhanced binding specificity

We describe snap-to-it probes, a novel probe technology to enhance the hybridization specificity of natural and unnatural nucleic acid oligomers using a simple and readily introduced structural motif. Snap-to-it probes were prepared from peptide nucleic acid (PNA) oligomers by modifying each terminus with a coordinating ligand. The two coordinating ligands constrain the probe into a macrocyclic configuration through formation of an intramolecular chelate with a divalent transition metal ion. On hybridization with a DNA target, the intramolecular chelate in the snap-to-it probe dissociates, resulting in the probe 'snapping-to' and binding the target nucleic acid. Thermal transition analysis of snap-to-it probes with complementary and single-mismatch DNA targets revealed that the transition between free and target-bound probe conformations was a reversible equilibrium, and the intramolecular chelate provided a thermodynamic barrier to target binding that resulted in a significant increase in mismatch discrimination. A 4-6 degrees C increase in specificity (DeltaT(m)) was observed from snap-to-it probes bearing either terminal iminodiacetic acid ligands coordinated with Ni(2+), or terminal dihistidine and nitrilotriacetic acid ligands coordinated with Cu(2+). The difference in specificity of the PNA oligomer relative to DNA was more than doubled in snap-to-it probes. Snap-to-it probes labeled with a fluorophore-quencher pair exhibited target-dependent fluorescence enhancement upon binding with target DNA.

DNA-fiber EPR spectroscopy as a tool to study DNA-metal complex interactions: DNA binding of hydrated Cu(II) ions and Cu(II) complexes of amino acids and peptides

DNA-fiber EPR spectroscopy and its application to studies of the DNA binding orientation and dynamic properties of Cu(II) ions and their complexes with amino acids and peptides are reviewed. Cu(II) ions bind in at least two different binding modes; one mode was mobile while the other mode fixed the orientation of the coordination plane. The hydroxyl groups of L-Ser and L-Thr fixed the coordination plane of their respective Cu(II) complexes parallel to the DNA base pair plane, whereas Cu(II) complexes of Lys and Arg induced several binding modes, depending on the tertiary structure of the DNA and the chirality of the amino acids. Unusually broadened signals observed for the His complex were assigned to a mono-L-His complex stacked stereospecifically along the DNA double helix. In comparison, Cu(II). Xaa-Xaa' -His type complexes oriented in the minor groove with different affinities and extents of randomness depending on the Xaa-Xaa' sequence and the chirality of Xaa or Xaa' while the C-terminal Xaa residues in Cu(II).Arg-Gly-His-Xaa (Xaa=L-Leu or L-Glu) decreased the stereospecificity and the stability of the complexes bound to DNA. In contrast to Xaa-Xaa'- His complexes, the coordination planes of Cu(II).Gly-L-His-Gly and Cu(II).Gly-L-His-L-Lys complexes were found to lie parallel to the DNA-fiber axis. Dinuclear Cu(II).carnosine complexes were also shown to bind to DNA stereospecifically.

Atomic force microscopy study of the interaction of DNA and nanostructured beta-Gallia rutile

The ability to attach DNA molecules to solid planar substrates is desired for imaging the molecule and for building DNA-mediated nanostructures. The deposition of DNA on [001] rutile and beta-gallia rutile (BGR) substrates from buffer solutions containing various divalent cations was studied using tapping mode atomic force microscopy (AFM). beta-Gallia rutile intergrowths were prepared by spin-coating gallium isopropoxide onto [001]-oriented TiO2 single-crystal slabs and heating above 1350 degrees C for >24 h, resulting in the formation of intergrowth lines along the {210} planes in the parent rutile structure. Rutile and BGR intergrowth substrates were exposed to various buffered solutions containing DNA and the following divalent cations: Ca(II), Co(II), Cu(II), Fe(II), Mg(II), Mn(II), Ni(II), and Zn(II). Among all the cations examined, only Ni(II) resulted in the attachment of DNA on the rutile surfaces. DNA attachment to BGR surfaces was strong enough to allow AFM imaging when the deposition buffer contained one of the following cations: Co(II), Mg(II), Mn(II), Ni(II), and Zn(II). For all of these cations, DNA attachment occurred preferentially, but not exclusively, along BGR intergrowth lines. When buffers without cation additions and those containing Ca(II), Cu(II), and Fe(II) were used, DNA failed to bind the BGR surfaces strongly enough to allow AFM imaging. The mechanism(s) by which DNA attaches to the BGR surface is (are) not well understood but may involve the incorporation of divalent cations at the tunnel sites of the BGR intergrowths.

Influence of metal coordination on the mismatch tolerance of ligand-modified PNA duplexes

Recent studies on metal incorporation in ligand-modified nucleic acids have focused on the effect of metal coordination on the stability of metal-containing duplexes or triplexes and on the metal binding selectivity but did not address the effect of the sequence of the nucleic acid in which the ligands are incorporated. We have introduced 8-hydroxyquinoline Q in 10-mer PNA strands with various sequences and have investigated the properties of the duplexes formed from these strands upon binding of Cu(2+). Variable-temperature UV-vis spectroscopy shows that, in the presence of Cu(2+), duplexes are formed even from ligand-modified Q-PNA strands that have a large number of mismatches. Spectrophotometric titrations demonstrate that at any temperature, one Cu(2+) ion binds a pair of Q-PNA strands that each contain one 8-hydroxyquinoline, but below the melting temperature, the PNA duplex exerts a supramolecular chelate effect, which prevents the transformation in the presence of excess Cu(2+) of the 1:2 Cu(2+):Q-PNA complexes into 1:1 complexes. EPR spectroscopy gives further support for the existence in the duplexes of [CuQ(2)] moieties that are similar to the corresponding square planar synthetic complex formed between Cu(2+) and 8-hydroxyquinoline. As PNA duplexes show a preferred handedness due to the chiral induction effect of a C-terminal l-lysine, which is transmitted through stacking interactions within the duplex, only if the metal-containing duplex has complementary strands, does it show a chiral excess measured by CD spectroscopy. The strong effect of the metal-ligand moiety is suggestive of an increased correlation length in PNA duplexes that contain such moieties. These results indicate that strong metal-ligand alternative base pairs significantly diminish the importance of Watson-Crick base pairing for the formation of a stable PNA duplex and lead to high mismatch tolerance, a principle that can be used in the construction of hybrid inorganic-nucleic acid nanostructures.

Interaction of metal ions with caffeine and theophylline: stability and structural features

The interactions of caffeine and theophylline with divalent cadmium, mercury, strontium and barium ions were studied in aqueous solution and physiological pH. Fourier transform infrared spectroscopy (FTIR) and absorption spectra were used to determine the cation binding mode and association constants. Spectroscopic results showed that Cd(2+), Hg(2+), Sr(2+) and Ba(2+) bind strongly to caffeine and theophylline. Direct and indirect (through metal hydration shell) interactions were observed for caffeine and theophylline with Cd(2+), Hg(2+), Sr(2+) and Ba(2+) through O6 and N9 (caffeine) and O6, N9 and N7 atoms (theophylline). The overall binding constants are:k(Cd-caffeine) = 1.24 x 10(5) M(-1), k(Hg-caffeine) = 1.74 x 10(5) M(-1), k(Sr- caffeine) = 3.3 x 10(4) M(-1), k(Ba-caffeine) = 1.8 x 10(4) M(-1), k(Cd-theophylline) = 5.75 x 10(5) M(-1), k(Hg-theophylline) = 2.14 x 10(5) M(-1), k(Sr-theophylline) = 4.6 x 10(4) M(-1), k(Ba-theophylline) = 3 x 10(4) M(-1). These k values are evidence for weak and strong cation interactions in these metal complexes.

Studies on the interaction of altromycin B and its platinum(II) and palladium(II) metal complexes with calf thymus DNA and nucleotides

The interaction of the anticancer antibiotic altromycin B and its isostructrural Pt(II) and Pd(II) metal complexes with native calf thymus (CT) DNA was studied using UV-thermal denaturation experiments, circular dichroism spectroscopy and temperature controlled spectrophotometric titrations. Altromycin B stabilizes the double helix by raising the T(m), mainly by intercalation of its chromophore between the base pairs and interacting electrostatically via its sugar moieties with the edges of the DNA helix. Moreover, altromycin B induces a B-->A structural transition of CT DNA. The effect on DNA stability and conformation depends on the metal ion. Pt(II) and Pd(II) complexes induce the B-->A structural transition and stabilize the double helix similarly but they present lower final hyperchromicity due to premelting effects which were caused by intra- and interstrand crosslinking. Thus, a synergic effect of the metal ions to altromycin B-CT DNA interaction is observed in both cases. Altromycin B interacts with 5'-GMP, 5'-AMP and 5'-CMP by electrophilic attack of the opened epoxide ring to the N(7)G, N(1)/N(7)A and N(3)C. Thus, covalent binding between these nucleotides and altromycin B takes place and explain the multiple binding mode suggested by the studies of the interaction of altromycin B and its complexes with DNA. The [Pd(II)-altroB] complex dissociates in the presence of the nucleotides, and various species of Pd(II)-nucleotide complexes, especially with 5'-GMP, are formed. The [Pt(II)-altroB] complex dissociates too, but only one or two species of Pt(II)-nucleotide complexes are formed, and in the case of 5'-AMP interaction the formation of a tertiary altroB-Pt(II)-5'AMP complex is proposed. 5'-TMP reacts very weakly in comparison with the other three nucleotides. These interactions were followed by 1H-NMR.

Raman spectroscopy of DNA-metal complexes. II. The thermal denaturation of DNA in the presence of Sr2+, Ba2+, Mg2+, Ca2+, Mn2+, Co2+, Ni2+, and Cd2+

Differential scanning calorimetry, laser Raman spectroscopy, optical densitometry, and pH potentiometry have been used to investigate DNA melting profiles in the presence of the chloride salts of Ba2+, Sr2+, Mg2+, Ca2+, Mn2+, Co2+, Ni2+, and Cd2+. Metal-DNA interactions have been observed for the molar ratio [M2+]/[PO2-] = 0.6 in aqueous solutions containing 5% by weight of 160 bp mononucleosomal calf thymus DNA. All of the alkaline earth metals, plus Mn2+, elevate the melting temperature of DNA (Tm > 75.5 degrees C), whereas the transition metals Co2+, Ni2+, and Cd2+ lower Tm. Calorimetric (delta Hcal) and van't Hoff (delta HVH) enthalpies of melting range from 6.2-8.7 kcal/mol bp and 75.6-188.6 kcal/mol cooperative unit, respectively, and entropies from 17.5 to 24.7 cal/K mol bp. The average number of base pairs in a cooperative melting unit (<nmelt>) varied from 11.3 to 28.1. No dichotomy was observed between alkaline earth and transition DNA-metal complexes for any of the thermodynamic parameters other than their effects on Tm. These results complement Raman difference spectra, which reveal decreases in backbone order, base unstacking, distortion of glycosyl torsion angles, and rupture of hydrogen bonds, which occur after thermal denaturation. Raman difference spectroscopy shows that transition metals interact with the N7 atom of guanine in duplex DNA. A broader range of interaction sites with single-stranded DNA includes ionic phosphates, the N1 and N7 atoms of purines, and the N3 atom of pyrimidines. For alkaline earth metals, very little interaction was observed with duplex DNA, whereas spectra of single-stranded complexes are very similar to those of melted DNA without metal. However, difference spectra reveal some metal-specific perturbations at 1092 cm-1 (nPO2-), 1258 cm-1 (dC, dA), and 1668 cm-1 (nC==O, dNH2 dT, dG, dC). Increased spectral intensity could also be observed near 1335 cm-1 (dA, dG) for CaDNA. Optical densitometry, employed to detect DNA aggregation, reveals increased turbidity during the melting transition for all divalent DNA-metal complexes, except SrDNA and BaDNA. Turbidity was not observed for DNA in the absence of metal. A correlation was made between DNA melting, aggregation, and the ratio of Raman intensities I1335/I1374. At room temperature, DNA-metal interactions result in a pH drop of 1.2-2.2 units for alkaline earths and more than 2.5 units for transition metals. Sr2+, Ba2+, and Mg2+ cause protonated sites on the DNA to become thermally labile. These results lead to a model that describes DNA aggregation and denaturation during heating in the presence of divalent metal cations; 1) The cations initially interact with the DNA at phosphate and/or base sites, resulting in proton displacement. 2) A combination of metal-base interactions and heating disrupts the base pairing within the DNA duplex. This allows divalent metals and protons to bind to additional sites on the DNA bases during the aggregation/melting process. 3) Strands whose bases have swung open upon disruption are linked to neighboring strands by metal ion bridges. 4) Near the midpoint of the melting transition, thermal energy breaks up the aggregate. We have no evidence to indicate whether metal ion cross-bridges or direct base-base interactions rupture first. 5) Finally, all cross-links break, resulting in single-stranded DNA complexed with metal ions.

The effect of HCl on the solution structure of calf thymus DNA: a comparative study of DNA denaturation by proton and metal cations using Fourier transform IR difference spectroscopy

The interaction of HCl with calf thymus DNA was investigated in aqueous solution at pH 7-2 with H+/DNA(P) (P:phosphate) molar ratios (r) of 1/80, 1/40, 1/20, 1/10, 1/4, 1/2, and 1, using Fourier Transform (FTIR) difference spectroscopy. Correlations between spectral changes, proton binding mode, DNA denaturation, and conformational variations are established. A comparison was also made between the ir spectra of denaturated DNA, in the presence of proton and Cu ions with similar cation concentrations. The FTIR difference spectroscopic results have shown that at low proton concentrations of r = 1/80 and 1/40 (pH 7-5), no major spectral changes occur for DNA, and the presence of H+ results in an increased base-stacking interaction and helical stability. At higher proton concentrations of r > 1/40, the proton binding to the cytosine and adenine bases begins with major destabilization of the helical duplex. As base protonation progresses, a B to C conformational conversion occurs with major DNA spectral changes. Protonation of guanine bases occurs at a high cation concentration r > 1/2 (pH < 3) with a major increase in the intensity of several DNA in-plane vibrations. Copper ion complexation with DNA exhibits marked similarities with proton at high cation concentrations (r > 1/10), whereas at low metal ion concentrations, copper-PO2 and copper-guanine N-7 bindings are predominant. No major DNA conformational transition was observed on copper ion complexation.

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

The interaction of calf thymus DNA with Cu2+ and Pb2+ was studied in aqueous solution at pH 6.5 with metal/DNA (P) (P = phosphate) molar ratios (r) 1/80, 1/40, 1/20, 1/10, 1/4, 1/2, and 1, using Fourier Transform ir (FTIR) spectroscopy. Correlations between the ir spectral changes, metal ion binding mode, DNA condensation, and denaturation, as well as conformational features, were established. Spectroscopic evidence has shown that at low metal/DNA (P) molar ratios 1/80 and 1/40, copper and lead ions bind mainly to the PO2- of the backbone, resulting in increased base-stacking interaction and duplex stability. The major copper ion base binding via G-C base pairs begins at r > 1/40, while the lead ion base binding occurs at r > 1/20 with the A-T base pairs. The denaturation of DNA begins at r = 1/10 and continues up to r = 1/2 in the presence of copper ions, whereas a partial destabilization of the helical structure was observed for the lead ion at high metal ion concentration (r = 1/2). Metal-DNA binding also results in DNA condensation. No major departure from the B-family structure was observed, upon DNA interaction with these metal ions.

Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd

Interactions of divalent metal cations (Mg2+, Ca2+, Ba2+, Sr2+, Mn2+, Co2+, Ni2+, Cu2+, Pd2+, and Cd2+) with DNA have been investigated by laser Raman spectroscopy. Both genomic calf-thymus DNA (> 23 kilobase pairs) and mononucleosomal fragments (160 base pairs) were employed as targets of metal interaction in solutions containing 5 weight-% DNA and metal:phosphate molar ratios of 0.6:1. Raman difference spectra reveal that transition metal cations (Mn2+, Co2+, Ni2+, Cu2+, Pd2+, and Cd2+) induce the greatest structural changes in B-DNA. The Raman (vibrational) band differences are extensive and indicate partial disordering of the B-form backbone, reduction in base stacking, reduction in base pairing, and specific metal interaction with acceptor sites on the purine (N7) and pyrimidine (N3) rings. Many of the observed spectral changes parallel those accompanying thermal denaturation of B-DNA and suggest that the metals link the bases of denatured DNA. While exocyclic carbonyls of dT, dG, and dC may stabilize metal ligation, correlation plots show that perturbations of the carbonyls are mainly a consequence of metal-induced denaturation of the double helix. Transition metal interactions with the DNA phosphates are weak in comparison to interactions with the bases, except in the case of Cu2+, which strongly perturbs both base and phosphate group vibrations. On the other hand, the Raman signature of B-DNA is largely unperturbed by Mg2+, Ca2+, Sr2+, and Ba2+, suggesting much weaker interactions of the alkaline earth metals with both base and phosphate sites. A notable exception is a moderate perturbation by alkaline earths of purine N7 sites in 160-base pair DNA, with Ca2+ causing the greatest effect. Correlation plots demonstrate a strong interrelationship between perturbations of Raman bands assigned to ring vibrations of the bases and those of bands assigned to exocyclic carbonyls and backbone phosphodiester groups. However, strong correlations do not occur between the Raman phosphodioxy band (centered near 1092 cm-1) and other Raman bands, suggesting that the former is not highly sensitive to the structural changes induced by divalent metal cations. The structural perturbations induced by divalent cations are much greater for > 23-kilobase pair DNA than for 160-base pair DNA, as evidenced by both the Raman difference spectra and the tendency toward the formation of insoluble aggregates. In the presence of transition metals, aggregation of high-molecular-weight DNA is evident at temperatures as low as 11 degrees C. A relationship between DNA melting and aggregation is proposed in which initial metal binding at major groove sites locally destabilizes the B-DNA double helix, causing displacement of the bases away from one another and exposing additional metal binding sites. Metal cation linkage of two displaced bases would allow separate DNA strands to crosslink. Aggregation is proposed to result from the formation of an extended network of these crosslinks.

Interaction of calf-thymus DNA with trivalent La, Eu, and Tb ions. Metal ion binding, DNA condensation and structural features

The interaction of calf-thymus DNA with La3+, Eu3+ and Tb3+ has been investigated in aqueous solution at pH 6.5, using metal/DNA(P) molar ratios(r) 1/80, 1/40, 1/20, 1/10, 1/4 and 1/2. Correlations between FTIR spectral changes and DNA structural properties have been established. At low metal/DNA(P) (r) 1/80, the metal ions bind mainly to the PO2- groups of the backbone, resulting in increased base-stacking interaction and duplex stability. At (r) 1/40 and 1/20, metal ion binding to the PO2- and the guanine N-7 site (chelation) predominates with minor perturbations of the A-T base pairs. Evidence for this comes from the displacement of the band at 1712 cm-1 (T,G) towards a lower frequency and the PO2- antisymmetric band at 1222 cm-1 towards a higher frequency. At higher metal/DNA(P) ratio, r > 1/20, DNA begins to condensate and drastic structural changes occur, which are accompanied by the shift and intensity changes of several G-C and A-T absorption bands. No major departure from B-DNA conformation was observed before and after DNA condensation even though some local structural modifications were observed. A comparison with the Cu-DNA complexes (denaturated DNA) shows some degree of helical destabilization of the biopolymer in the presence of lanthanide ions.

Zinc ion-DNA polymer interactions

The adjacent GN7-M-GN7 cross-linking and adjacent G-M-G sandwich-complex models for DNA metal ion binding were evaluated both with native DNAs differing in GC content as well as with the synthetic polymers poly [(dGdC)]2, poly[(dAdT)]2, and poly[(dAdC)(dGdT)]. The effect of Zn2+ was studied in depth, and limited studies were also performed with Co2+ and Mg2+. The results were compared to the extensive information available on Cu2+ binding to native DNAs and poly[(dAdT)]2. At high ratios of metal/base (R), Zn2+ caused all native DNAs to denature with the same melting temperature Tm, approximately 61 degrees C. A similar pattern was reported previously for Cu2+, but the typical Tm was approximately 35 degrees C. The extent of renaturation on cooling DNAs denatured in the presence of Zn2+ increased with GC content, as reported previously for Cu2+. These results, together with previously reported similarities, strongly indicate that the DNA binding characteristics of the two cations are similar. By comparison of the Tm values and hyperchromicity changes monitored at 260 and 282 nm, it is clear that, during thermal denaturation in the presence of Zn2+, both AT and GC regions were denatured, even at high R. The Tm vs R profile for the native DNAs was typical. The rise at low R and subsequent decrease at high R were inversely and directly related, respectively, to GC content. Except for poly[(dAdT)]2, where Tm increased with R, the other synthetic polymers exhibited the increase/decrease pattern. Poly[(dAdC)(dGdT)] gave a Tm value at high R of 54 degrees C. In the absence of Zn2+, this polymer exhibited little hypochromicity on cooling of denatured polymer. However, in the presence of Zn2+, nearly complete hypochromicity was observed, although the midpoint of the cooling curve was lower than the Tm value by approximately 15 degrees C at R = 10. These characteristics were similar to those with native DNAs, although viscosity and CD studies suggested that the "renatured" polymer was not identical to the unheated polymer. Furthermore, addition of Zn2+ after denaturation nearly completely reversed the absorption increase. This finding contrasts with those for native DNAs, where the Zn2+ must be present during denaturation in order to reverse the absorption increase nearly completely on cooling. With some caveats, poly[(dAdC)(dGdT)] appears to be a good model for native DNAs since its properties, including CD and uv changes on addition of Zn2+ to premelted and melted polymer, parallel those of the native polymers.(ABSTRACT TRUNCATED AT 400 WORDS)

Polynucleotide cross-linking by aluminum

The observations that there was an increased concentration of Al in the brains of Alzheimer's, Guam-Parkinson, and amyotrophic lateral sclerosis disease patients and that there was an apparent localization of the Al in chromatin led to a study of the interaction of Al(III) with DNA. We have previously shown that Al cross-links calf thymus DNA at low pH (S. J. Karlik, G. L. Eichhorn, P. N. Lewis, and D. R. Crapper, Biochemistry 19, 5991 [1980]). Extended studies indicate that cross-linking occurs in DNAs of all base ratios, including polydAdT and polydGdC. Since Al cross-links prevent renaturation in polydAdT, the decrease in the amount of polymer renatured in the presence of Al becomes a quantitative appraisal of the extent of cross-linking. Saturation of cross-linking occurs at a 0.4 ratio of Al to nucleotide phosphate, indicating that potentially 80% of the base pairs are Al bound. Cross-links are broken at elevated pH and by EDTA.

Morphometric cytochemistry of diminution of catalase-containing peroxisomes in copper-loaded liver

The density of hepatocellular catalase-containing peroxisomes was quantified, utilizing a computer-aided image analysing technique, on 1-micron thick diaminobenzidine-stained sections. Hepatic copper accumulation following intraperitoneal injection of cupric chloride resulted in a dose-dependent reduction in the density of catalase-containing peroxisomes. A significant correlation between the density of peroxisomes and the activity of hepatic catalase indicated that computer-aided image analysis of peroxisomes stained by the diaminobenzidine technique provided a useful estimate of catalase activity in liver injured by copper. Slight treatment-related differences in the mean diameter of peroxisomes were detected in high-dose but not low-dose rats.

A laser Raman spectroscopic study of the interaction of calf-thymus DNA with Cu(II) and Pb(II) ions: metal ion binding and DNA conformational changes

The interaction of calf-thymus DNA with Cu(II) and Pb(II) ions has been investigated in H2O and D2O solutions at physiological pH, using laser Raman spectroscopy. The results confirm the destabilizing effect of Cu2+ ions, which are shown to bind strongly to the guanine and cytidine bases, perturbing the A-T base pairs and disrupting the double-helical structure of DNA, whose conformation is markedly altered by these interactions. Earlier claims that Pb2+ ions destabilize DNA are not supported by the present study. These ions are found to interact only weakly with the nucleic bases, binding to the N7 position of the guanine bases and also interacting with the A-T pairs. Both types of ions are found to interact with the charged phosphate groups of DNA, although these sites are preferred over the nucleic bases by Pb2+ ions.

Irreversible binding of reductively activated streptonigrin to nucleic acids in the presence of metals

The binding of streptonigrin (SN) to nucleic acids was studied in the presence of reducing agents and metals. Incubation of chemically reduced SN with DNA in vitro resulted in irreversible binding and complexes containing 1 mol of SN per 250 nucleotides were obtained. The presence of Zn2+ increased this binding considerably to give complexes containing 1 mol of SN per 80 nucleotides. On the other hand, Mg2+ decreased this binding. More drug was bound to the denatured DNA than to the native DNA. Maximum binding was obtained when SN was reduced in the presence of DNA. Increased binding was also obtained when the fully reduced SN was incubated with DNA. Considerably more SN was bound to DNA when activated enzymatically than with NaBH4. Studies with synthetic polynucleotides in the presence of Zn2+ suggested that while SN has a high affinity for guanine residues, cytosine and adenine residues also serve as excellent substrates. These studies indicate that the active intermediate that binds to nucleic acids is unstable and may be derived from the fully reduced drug. These in vitro studies further suggest that Zn2+ plays an important role in the binding of SN to DNA and may have implications for the biological actions of SN if similar reactions occurred in vivo.

Interaction of aluminum species with deoxyribonucleic acid

Interactions of aluminum with deoxyribonucleic acid (DNA) have been studied by thermal denaturation, circular dichroism, and fluorescent dye binding; a pH- and concentration-dependent alteration in the interaction of aluminum with DNA was observed. Three distinguishable complexes are produced when DNA is denaturated at pH 5.0-7.5 and in aluminum to DNA mole ratios of 0-0.7. Complex I appears at neutral pH and stabilizes a portion of DNA. Complex II is observed at acidic pH, destabilizes a fraction of the DNA double-helical molecule, and produces intrastrand cross-links. Complex III occurs at all pHs, is maximal at intermediate pH values, and is characterized by a noncooperative melting profile and cross-linking at low pH (less than 6.0). The DNA in complexes II and III can be renatured by treatment with either ethylenediaminetetraacetic acid (EDTA) or a high concentration of sodium chloride. The properties of complexes I and II are consistent with what could be expected for DNA complexes of Al(OH)2+ and Al3+, respectively. Complex III has intermediate properties that are consistent with a structure in which both ions bind the DNA simultaneously. The characteristics of complex III depend on the ratio of Al3+/Al(OH)2+ in solution. Aluminum-DNA complexes differ from other metal-DNA complexes in that melting profiles under many conditions are biphasic. Apparently more than one form of DNA can exist at any time in the presence of aluminum. The different DNA-aluminum complexes, which arise from the multiple species of aluminum in aqueous solution, lead to a variety of reactions with DNA.

Denaturation of DNA in the presence of chromous (Cr2+) ions

The effect of Cr2+ ions on the Tm (melting temperature) of DNA has been investigated under appropriate conditions for the stabilization of DNA by Mg2+ ions. A significant lowering of Tm, analogous to that observed for Cu2+ under normal conditions, was found, for Cr2+ at pH = 4.2 and [Mg2+] = 5.3 mol per mole of DNA base pair. Cu2+ also lowers Tm under similar conditions. The similarity of the effects of Cr2+ and Cu2+ under comparable conditions may be related to similarities in their coordination properties. It is proposed that Cr2+ and Cu2+ ions facilitate denaturation by holding together groups on the DNA chains in such a manner that base pairing and base stacking are inhibited. Comparative results for Cr3+ and Co2+ are also given for these low pH/Mg2+ ion conditions.

Metal chelate affinity chromatography. I. Influence of various parameters on the retention of nucleotides and related compounds

The influence of various parameters, such as pH, ionic strength and temperature, on the retention of different nucleotides and related compounds on copper chelate gels has been investigated in order to understand the respective roles played by the different solute constituents (i.e., heterocyclic bases, sugars and phosphate groups) in the interaction and to define optimal conditions for subsequent application to the fractionation of oligo- and polynucleotides.

Fine structure in the thermal denaturation of DNA: high temperature-resolution spectrophotometric studies

Fine structures which appear in the optical melting profile of DNA are examined from both the experimental and theoretical aspects. After a brief historical survey of the DNA melting experiments during the pre-fine-structure era in Section II, the high temperature-resolution experimental techniques which are essential to the investigation of fine structure are described in Section III. Then, the current status of the high-resolution study is reviewed first by a phenomenological description of the melting profile (Section IV) and then of the refolding profile (Section V), where a general idea about the cooperatively melting region and several factors affecting it is given. Sections VI and VII are devoted to the review of current theoretical works. Several well-established theoretical frameworks which correlate the base sequence with the melting phenomena are examined in terms of their rigorousness and usefulness. The molecular thermodynamic parameters concerning the DNA melting which have been evaluated by several research groups are compared and discussed. Finally, in Section VIII, current ideas on the correlation between the fine structure and genetic functions and genetic maps are reviewed. Some future problems relating to the fine structure are also discussed.

Interaction of DNA with anti-cancer drugs: copper-thiosemicarbazide system

The interaction of copper-thiosemicarbazide complexes with DNA was investigated using ultraviolet and infrared spectroscopy. Evidence for the interaction of the complexes with nucleic acid bases and with the phosphate group is presented.