Solution structural studies of the Ag(I)-DNA complex

Reductant-dependent DNA-templated silver nanoparticle formation kinetics

DNA molecules have been demonstrated to be good templates for producing silver nanoparticles (AgNPs), with the advantages of well-controlled sizes, shapes, and properties. Revealing the formation kinetics of DNA-templated AgNPs is crucial for their efficient synthesis. Herein, using magnetic tweezers, we studied the reduction kinetics of the Ag+-DNA structure and the subsequent nucleation kinetics by adding NaBH4, L-ascorbic acid, and sodium citrate solutions. At [Ag+] = 0.01 mM, the addition of NaBH4 solution with the same concentration resulted in the restoration of DNA. In contrast, by increasing the [NaBH4]/[Ag+] ratio (r) to 10 and 100, the DNA extension initially decreased rapidly and then increased, indicating nucleation-dissolution kinetics. With AgNO3 solutions of higher concentrations (0.1 mM and 1 mM), direct particle nucleation and growth kinetics were observed by adding a tenfold (r = 10) or a hundredfold (r = 100) amount of NaBH4, which were evidenced by a significant reduction in DNA extension. The reductant dependence of the kinetics was further investigated. Addition of L-ascorbic acid to the DNA-Ag+ solution yielded an increase-decrease kinetics that was different from that caused by NaBH4, suggesting that nucleation was not initially favored due to the lack of sufficient Ag atoms; while sodium citrate showed a weak nucleation-promoting ability to form AgNPs. We discussed the findings within the framework of classical nucleation theory, in which the supersaturation of the Ag atom is strongly influenced by multiple factors (including the reducing ability of the reductant), resulting in different kinetics.

A survey of recent unusual high-resolution DNA structures provoked by mismatches, repeats and ligand binding

The structure of the DNA duplex is arguably one of the most important biological structures elucidated in modern history. DNA duplex structure is closely associated with essential biological functions such as DNA replication and RNA transcription. In addition to the classical A-, B- and Z-DNA conformations, DNA duplexes are capable of assuming a variety of alternative conformations depending on the sequence and environmental context. A considerable number of these unusual DNA duplex structures have been identified in the past decade, and some of them have been found to be closely associated with different biological functions and pathological conditions. In this manuscript, we review a selection of unusual DNA duplex structures, particularly those originating from base pair mismatch, repetitive sequence motifs and ligand-induced structures. Although the biological significance of these novel structures has not yet been established in most cases, the illustrated conformational versatility of DNA could have relevance for pharmaceutical or nanotechnology development. A perspective on the future directions of this field is also presented.

Anomeric 5-Aza-7-deaza-2'-deoxyguanosines in Silver-Ion-Mediated Homo and Hybrid Base Pairs: Impact of Mismatch Structure, Helical Environment, and Nucleobase Substituents on DNA Stability

Nucleoside configuration (α-d vs. β-d), nucleobase substituents, and the helical DNA environment of silver-mediated 5-aza-7-deazaguanine-cytosine base pairs have a strong impact on DNA stability. This has been demonstrated by investigations on oligonucleotide duplexes with silver-mediated base pairs of α-d and β-d anomeric 5-aza-7-deaza-2'-deoxyguanosines and anomeric 2'-deoxycytidines incorporated in 12-mer duplexes. To this end, a new synthetic protocol has been developed to access the pure anomers of 5-aza-7-deaza-2'-deoxyguanosine by glycosylation of either the protected nucleobase or its salt followed by separation of the glycosylation products by crystallization and chromatography. Thermal stability measurements were performed on duplexes with α-d/α-d and β-d/β-d homo base pairs or α-d/β-d and β-d/α-d hybrid pairs within two sequence environments, positions 6 or 7, of oligonucleotide duplexes. The respective T_m stability increases observed after silver ion addition differ significantly. Homo base pairs with β-d/β-d or α-d/α-d nucleoside combinations are more stable than α-d/β-d hybrid base pairs. The positional switch of silver-ion-mediated base pairs has a significant impact on stability. Nucleobase substituents introduced at the 5-position of the dC site of silver-mediated base pairs affect base pair stability to a minor extent. Our investigation might lead to applications in the construction of bioinspired nanodevices, in DNA diagnostics, or metal-DNA hybrid materials.

Moderate temperature elevation increase susceptibility of early-life stage of the Mediterranean mussel, Mytilus galloprovincialis to metal-induced genotoxicity

The present study aims to evaluate the effects of copper and silver alone or along with a moderate temperature increase on embryonic development, DNA integrity and target gene expression levels in early life stages of Mytilus galloprovincialis. For this purpose, upon fertilized embryos were exposed to a sub-lethal concentration of Cu (9.54 μg/L), Ag (2.55 μg/L) and to the mixture of the two metals (Cu (6.67 μg/L) + Ag (1.47 μg/L)) along with a temperature gradient (18, 20 and 22 °C). In all experiments, larvae were exposed to stressors for 48 h except for those designed to DNA damage analysis exposed only for 24 h (before shell formation).Our results showed a significant increase in the percentage of malformed D-larvae (p < 0.05) with increasing temperature and exposure to silver and copper alone or in a mixture. Moreover, metal toxicity increased significantly (p < 0.05) with the temperature rise. Genotoxicity was evaluated using classic and modified with Formamidopyrimidine DNA glycosylase (Fpg) Comet assay. Results suggest that co-exposure to metals and temperature significantly increased DNA damage on mussel larvae with a more accentuated oxidative damage. A significant transcription modulation was observed for genes involved in DNA repair and DNA replication (p53, DNA ligase II and topoisomerase II) when larvae are exposed to a single stressor. However, in the case of multiple stresses, caspase involved in the cell apoptosis pathway was overexpressed. Our study suggests that mussel larvae exposed to a moderate increase in temperature may have a compromised ability to defend against genotoxicity. This is particularly relevant in the context of global warming and thermal pollution.

Two-stage DNA compaction induced by silver ions suggests a cooperative binding mechanism

The interaction between silver ions and DNA plays an important role in the therapeutic use of silver ions and in related technologies such as DNA sensors. However, the underlying mechanism has not been fully understood. In this study, the dynamics of Ag⁺-DNA interaction at a single-molecule level was studied using magnetic tweezers. AgNO₃ solutions with concentrations ranging from 1 μM to 20 μM led to a 1.4-1.8 μm decrease in length of a single λ-DNA molecule, indicating that Ag⁺ has a strong binding with DNA, causing the DNA conformational change. The compaction process comprises one linear declining stage and another sigmoid-shaped stage, which can be attributed to the interaction mechanism. Considering the cooperative effect, the sigmoid trend was well explained using a phenomenological model. By contrast, addition of silver nanoparticle solution induced no detectable transition of DNA. The dependence of the interaction on ionic strength and DNA concentration was examined via morphology characterization and particle size distribution measurement. The size of the Ag⁺-DNA complex decreased with an increase in Ag⁺ ionic strength ranging from 1 μM to 1 mM. Morphology characterization confirmed that silver ions induced DNA to adopt a compacted globular conformation. At a fixed [AgNO₃]:[DNA base pairs] ratio, increasing DNA concentration led to increased sizes of the complexes. Intermolecular interaction is believed to affect the Ag⁺-DNA complex formation to a large extent.

Selective and Sensitive Detection of Silver(I) Ion Based on Tetracationic Complex and TGA/GSH Co-capped Quantum Dots as an Effective Fluorescent Sensing Platform

CdTe quantum dots capped with glutathione (GSH) and thioglycolic acid (TGA) were synthesized and the interaction between QDs and tetracationic Fe complex was investigated. Based on the specific interaction between Ag⁺ and cytosine bases (C), we designed a label-free DNA sensor for the detection of Ag⁺ in aqueous solution. Furthermore, tetracationic Fe complex with a higher positive charge is demonstrated to improve the sensitivity of the sensor. A detection limit of 3.3 nmol dm^-3 was obtained, which was lower than in previous reports. This sensor also exhibits promising potential for real sample analysis.

Silver-Mediated Base Pairs in DNA Incorporating Purines, 7-Deazapurines, and 8-Aza-7-deazapurines: Impact of Reduced Nucleobase Binding Sites and an Altered Glycosylation Position

Formation of silver-mediated DNA was studied with oligonucleotides incorporating 8-aza-7-deazapurine, 7-deazapurine, and purine nucleosides. The investigation was performed on non-self-complementary duplexes with one or two modifications and self-complementary duplexes with an alternating dA-dT motif. Homo base pairs as well as base pair mismatches of dA analogues with dC and Watson-Crick pairs with dT were studied by stoichiometric silver ion titration and T_m measurements. N⁸ -Glycosylated 8-aza-7-deazaadenine forms silver-ion-mediated base pairs capturing two silver ions (low silver content) whereas regularly glycosylated 8-aza-7-deazapurine, 7-deazapurine (c⁷ A_d ), and dA do not form comparable structures. Stable silver-mediated "dA-dC" base pair mismatches were detected for all nucleosides. Two silver ions per base pair are bound by 8-aza-7-deazapurine whereas c⁷ A_d binds only one silver ion. The situation is different when the equivalents of silver ions were increased to the number of total base pairs. Surprisingly, in 12-mer duplexes as well as in related 25-mer duplexes every base pair consumed one silver ion.

A rapid and practical technique for real-time monitoring of biomolecular interactions using mechanical responses of macromolecules

Monitoring biological reactions using the mechanical response of macromolecules is an alternative approach to immunoassays for providing real-time information about the underlying molecular mechanisms. Although force spectroscopy techniques, e.g. AFM and optical tweezers, perform precise molecular measurements at the single molecule level, sophisticated operation prevent their intensive use for systematic biosensing. Exploiting the biomechanical assay concept, we used micro-electro mechanical systems (MEMS) to develop a rapid platform for monitoring bio/chemical interactions of bio macromolecules, e.g. DNA, using their mechanical properties. The MEMS device provided real-time monitoring of reaction dynamics without any surface or molecular modifications. A microfluidic device with a side opening was fabricated for the optimal performance of the MEMS device to operate at the air-liquid interface for performing bioassays in liquid while actuating/sensing in air. The minimal immersion of the MEMS device in the channel provided long-term measurement stability (>10 h). Importantly, the method allowed monitoring effects of multiple solutions on the same macromolecule bundle (demonstrated with DNA bundles) without compromising the reproducibility. We monitored two different types of effects on the mechanical responses of DNA bundles (stiffness and viscous losses) exposed to pH changes (2.1 to 4.8) and different Ag⁺ concentrations (1 μM to 0.1 M).

Antimicrobial behavior of biosynthesized silica-silver nanocomposite for water disinfection: a mechanistic perspective

The biosynthesis of nano-silica silver nanocomposite (NSAgNC) and it is as antibacterial effect on gram-negative bacteria viz.Escherichia coli and Pseudomonas aeruginosa has been investigated for disinfection of water. The as-synthesized NSAgNC exhibited antibacterial activity in a dose dependent manner and ∼ 99.9% of E. coli and P. aeruginosa were killed at a concentration of 1.5 mg/mL of NSAgNC (5.1 wt% Ag) within 5h. The NSAgNC showed similar antibacterial activities both in oxic and anoxic conditions. The results further demonstrated that NSAgNC exhibited reactive oxygen species (ROS) independent "particle specific" antibacterial activity through multiple steps in absence of leached out Ag(+) ions. The initial binding of NSAgNC on the cell wall caused loss of cell membrane integrity and leakage of cytoplasmic materials. Inhibition of respiratory chain dehydrogenase by NSAgNC caused metabolic inactivation of the cells and affecting the cell viability. Genomic and proteomic studies further demonstrated the fragmentations of both plasmid and genomic DNA and down regulation of protein expression in NSAgNC treated cells, which leading to the cell death. Thus the biosynthesized NSAgNC has great potential as disinfectant for water purification while minimizing the toxic effects.

Silver (I) as DNA glue: Ag(+)-mediated guanine pairing revealed by removing Watson-Crick constraints

Metal ion interactions with DNA have far-reaching implications in biochemistry and DNA nanotechnology. Ag⁺ is uniquely interesting because it binds exclusively to the bases rather than the backbone of DNA, without the toxicity of Hg²⁺. In contrast to prior studies of Ag⁺ incorporation into double-stranded DNA, we remove the constraints of Watson-Crick pairing by focusing on homo-base DNA oligomers of the canonical bases. High resolution electro-spray ionization mass spectrometry reveals an unanticipated Ag⁺-mediated pairing of guanine homo-base strands, with higher stability than canonical guanine-cytosine pairing. By exploring unrestricted binding geometries, quantum chemical calculations find that Ag⁺ bridges between non-canonical sites on guanine bases. Circular dichroism spectroscopy shows that the Ag⁺-mediated structuring of guanine homobase strands persists to at least 90 °C under conditions for which canonical guanine-cytosine duplexes melt below 20 °C. These findings are promising for DNA nanotechnology and metal-ion based biomedical science.

Silver ions enhance UVB-induced phosphorylation of histone H2AX

Silver (Ag) is used in a wide range of industries including healthcare, food, cosmetics, and environmental industries due to its antibacterial properties. The rapidly expanding use of Ag has raised issues concerning its toxicity in humans. However, studies investigating the effects of Ag on humans are very limited, and the combined effects of Ag and other environmental factors have not yet been determined. Ultraviolet (UV) radiation in sunlight is the most prominent and ubiquitous physical stressor in our natural environment. In this study, we investigated the genotoxic potential of combined exposure to Ag(+) (AgNO3) and UVB in the human keratinocyte cell line, HaCaT, by measuring the generation of phosphorylated histone H2AX, which is currently attracting attention as a biomarker for the detection of genotoxic insults. We found that the generation of γ-H2AX was synergistically enhanced when cells were coexposed to Ag(+) and UVB. Furthermore, we showed that the enhanced generation of γ-H2AX could be attributed to the increased formation of UVB-induced cyclobutane pyrimidine dimers and (6-4) photoproducts. These lesions, if not repaired properly, are the major causal factor for skin carcinogenesis. Our results provide an important insight into influence of Ag on the genotoxic potency of sunlight.

Ag(I)-mediated homo and hetero pairs of guanosine and cytidine: monitoring by circular dichroism spectroscopy

Ag(I)-containing compounds are attractive as antibacterial and antifungal agents. The renewed interest in the application of silver(I) compounds has led to the need for detailed knowledge of the mechanism of their action. One of the possible ways is the coordination of Ag(I) to G-C pairs of DNA, where Ag(+) ions form Ag(I)-mediated base pairs and inhibit the transcription. Herein, a systematic chiroptical study on silver(I)-mediated homo and mixed pairs of the C-G complementary-base derivatives cytidine(C) and 5'-guanosine monophosphate(G) in water is presented. Ag(I)-mediated homo and hetero pairs of G and C and their self-assembled species were studied under two pH levels (7.0 and 10.0) by vibrational (VCD) and electronic circular dichroism(ECD). VCD was used for the first time in this field and showed itself to be a powerful method for obtaining specific structural information in solution. Based on results of the VCD experiments, the different geometries of the homo pairs were proposed under pH 7.0 and 10.0. ECD was used as a diagnostic tool to characterize the studied systems and as a contact point between the previously defined structures of the metal or proton mediated pairs of nucleobases and the systems studied here. On the basis of the obtained data, the formation of the self-assembled species of cytidine with a structure similar to the i-motif structure in DNA was proposed at pH 10.0.

Ag+-mediated DNA base pairing: extraordinarily stable pyrrolo-dC-pyrrolo-dC pairs binding two silver ions

6-Substituted pyrrolo-dC-pyrrolo-dC mismatches selectively capture silver ions to form extraordinarily stable metal-mediated base pairs. One single modification in a 12-mer duplex causes a Tm increase of 36.0 °C relative to the metal-free mismatched duplex. Spectrophotometric titrations as well as ESI mass spectra confirmed the binding of two silver ions per base pair. The Ag(+)-mediated base pairs may permit the construction of metal-responsive DNA with a very high silver loading.

Sensitive and selective detection of silver(I) ion in aqueous solution using carbon nanoparticles as a cheap, effective fluorescent sensing platform

In this Letter, we demonstrate the first use of carbon nanoparticles (CNPs) obtained from carbon soot by lighting a candle as a cheap, effective fluorescent sensing platform for Ag(+) detection with a detection limit as low as 500 pM and high selectivity. We further demonstrate its practical application to detect Ag(+) in a real sample.

Silver ions-mediated conformational switch: facile design of structure-controllable nucleic acid probes

Conformationally constraint nucleic acid probes were usually designed by forming an intramolecular duplex based on Watson-Crick hydrogen bonds. The disadvantages of these approaches are the inflexibility and instability in complex environment of the Watson-Crick-based duplex. We report that this hydrogen bonding pattern can be replaced by metal-ligation between specific metal ions and the natural bases. To demonstrate the feasibility of this principle, two linear oligonucleotides and silver ions were examined as models for DNA hybridization assay and adenosine triphosphate detection. The both nucleic acids contain target binding sequences in the middle and cytosine (C)-rich sequences at the lateral portions. The strong interaction between Ag(+) ions and cytosines forms stable C-Ag(+)-C structures, which promises the oligonucleotides to form conformationally constraint formations. In the presence of its target, interaction between the loop sequences and the target unfolds the C-Ag(+)-C structures, and the corresponding probes unfolding can be detected by a change in their fluorescence emission. We discuss the thermodynamic and kinetic opportunities that are provided by using Ag(+) ion complexes instead of traditional Watson-Crick-based duplex. In particular, the intrinsic feature of the metal-ligation motif facilitates the design of functional nucleic acids probes by independently varying the concentration of Ag(+) ions in the medium.

Transfection of living HeLa cells with fluorescent poly-cytosine encapsulated Ag nanoclusters

The fluorescence of silver clusters encapsulated by single stranded oligo-DNA (24 cytosine base pairs, C(24):Ag(n)) was used to monitor the transfection of this new silver/DNA fluorophore inside living HeLa cells. For this, the C(24):Ag(n) molecules were complexed with a commercially available transfection reagent Lipofectamine and the internalization of C(24):Ag(n) was followed with confocal fluorescence microscopy. Bright near-infrared fluorescence was observed from inside the transfected HeLa cells, when exciting with 633 nm excitation, opening up the possibility for the use of these C(24):Ag(n) clusters for biological labelling and imaging of living cells and for monitoring the transfection process with limited harm to the living cells.

Four-Stranded Coordination Helices Containing Silver−Adenine (Purine) Metallaquartets

This Communication describes structures of a family of silver-adenine (purine) metallaquartets that occur in a four-stranded coordination motif, bearing a close resemblance to nucleic acid quadruplexes. Using modified purine frameworks, it is further demonstrated that subtle variations in nucleobase heterocycle are tolerable and a metallaquartet is obtained irrespective of the substitution, thus suggesting a high-propensity silver-adenine interaction to achieve quartet structures. All of the solid-state structures studied were orthorhombic, belonging to the Fdd2 space group.

DNA-templated Ag nanocluster formation

The high affinity of Ag+ for DNA bases has enabled creation of short oligonucleotide-encapsulated Ag nanoclusters without formation of large nanoparticles. Time-dependent formation of cluster sizes ranging from Ag1 to Ag4/oligonucleotide were observed with strong, characteristic electronic transitions between 400 and 600 nm. The slow nanocluster formation kinetics enables observation of specific aqueous nanocluster absorptions that evolve over a period of 12 h. Induced circular dichroism bands confirm that the nanoclusters are associated with the chiral ss-DNA template. Fluorescence, absorption, mass, and NMR spectra all indicate that multiple species are present, but that their creation is both nucleotide- and time-dependent.

Studies on the interaction between Ag(+) and DNA

The interaction between silver ion and DNA has been followed by submarine gel electrophoresis. When pBR322 plasmid DNA was allowed to interact with silver(I) acetate, it was found to contain Form I and Form II bands whose intensity remained unchanged as the concentration of Ag(+) was increased from 0 to 50 mM. However, the mobility of the bands decreased as the concentration of Ag(+) was increased, indicating the occurrence of increased covalent binding of the metal ion with DNA. When 1:1 mixtures of silver(I) acetate and ascorbate were allowed to interact with plasmid and genomic DNAs, it was found that the mixtures were much more damaging to plasmid as well as genomic DNAs than silver(I) acetate or ascorbate alone. In the case of pBR322 plasmid DNA, the mixture at 12.5 mM concentration was found to be more damaging than the mixtures at both higher and lower concentrations. The increased DNA damage is believed to be due to free radicals produced from the oxidation of ascorbate by molecular oxygen where the metal ion was playing a catalytic role.

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.

DNA base modification: ionized base pairs and mutagenesis

The nature of hydrogen bonding between normal and modified bases has been re-examined. It is proposed that hydrogen-bonding schemes may involve tautomeric, ionized or conformational forms (syn, anti and wobble). Several important cases are presented or reviewed in which physical evidence indicates the existence of ionized base pairs. When thermodynamic values determined in aqueous solution under physiological conditions are considered, it can be argued that base ionization will contribute substantially to the stability of many biologically relevant base pairs containing modified bases. A significant incidence of ionized bases in DNA may have important kinetic ramifications for the further chemical reactivity of both the modified base and its cross-strand pairing partner. Moreover, DNA structure at and surrounding ionized base pairs may be altered. For this reason, the model presented in this study should be useful as DNA-sequence analysis becomes more commonly applied to the study of mutagenesis.

Base pairing and mutagenesis: observation of a protonated base pair between 2-aminopurine and cytosine in an oligonucleotide by proton NMR

2-Aminopurine (AP), a potent mutagenic base analogue, most frequently pairs with thymine. In the AP X T base pair, both bases adopt normal tautomeric forms. The mechanism for the mutagenic activity arises from its observed pairing with cytosine, which has been ascribed to an enhanced tendency to adopt the rare imino tautomeric form. NMR studies in H2O on all the exchangeable protons in an oligonucleotide duplex containing an AP X T base pair show Watson-Crick hydrogen bonding. When the thymine is replaced by cytosine in the duplex, we observe an AP X C base pair. Both amino protons of AP are seen excluding the rare tautomeric form. Although several alternative structures are possible, it is shown that the second hydrogen bond is formed by protonation of the AP X C base pair and that this is the dominant species under physiological conditions.

The infrared spectrum and structure of the type I complex of silver and DNA

Infrared spectroscopy was used to study films of the type I complex of Ag+ and DNA as a function of hydration with the following conclusions. Ag+ binds to guanine residues but not to cytosine or thymine residues. Cytosine becomes protonated as Ag+ binds to guanine. (These conclusions confirm previous models.) The type I complex remains in the B family of structures with slight modifications of the sugar-phosphate geometry. This modified B structure remains stable at lower values of hydration for which pure DNA is in the A form. Binding of Ag+ to PO2-, O-P-O or the deoxyribose oxygen is excluded.

The occurrence and consequences of deoxyuridine in DNA

Deoxyuridine can become resident in the DNA of prokaryotic and eukaryotic cells via two general mechanisms - deamination of cytosine to uracil, and nucleotide pool changes that lead to misincorporation of deoxyuridine in place of thymidine. In this paper we have examined the chemical basis of deamination reactions in DNA and discussed a possible mechanism for an increased rate of deamination by means of cross-strand protonation of cytosine by alkylated guanine. In addition, we have examined the genetic and drug-induced conditions that lead to dUMP misincorporation into DNA in place of thymidine and have presented experimental evidence indicating that the antifolate-induced lesion is a general drug-dose dependent lesion of human blood cells. Finally, the toxic and genetic impact of this lesion has been evaluated within the context of a review of the repair mechanisms elicited by dUMP in DNA.

DNA packing in the filamentous viruses fd, Xf, Pf1 and Pf3

Spectral data for filamentous viruses in the presence and absence of Ag+, together with other parameters, indicate that the DNA structures in two of the viruses, fd and Xf, are similar to each other but that these differ from two quite unusual and different DNA structures in Pf1 and Pf3.

Interaction of actinomycin D, ethidium, quinacrine, daunorubicin, and tetralysine with DNA: 31P NMR chemical shift and relaxation investigation

The binding of actinomycin D, ethidium, quinacrine, daunorubicin, and tetralysine to DNA has been investigated using 31P NMR. Titration of DNA with actinomycin yields a new downfield peak or overlapping peaks as would be expected from the slow dissociation kinetics of this compound. The other intercalators shift the DNA 31P signal downfield as a single exchange averaged peak. Tetralysine causes a slight upfield shift. The chemical shift titration curves for the intercalators are sigmoid curves suggesting that cooperative processes or competing effects on the chemical shift are being observed. The magnitude of the chemical shift change at saturation of DNA with the compounds is found to vary significantly and to be linearly related to the DNA base pair unwinding angle for the compounds. Analysis of 31P spin lattice relaxation times (T1) and linewidths as a function of temperature (below Tm) and titration with the above compounds indicates that T1 does not change significantly while linewidth increases with decreasing temperature and increasing bound intercalator. One interpretation of these results is that in both cases the overall motion of DNA becomes slower while the internal motion is not greatly affected.

Solution structural studies of the A and Z forms of DNA

We report transient electric dichroism studies of short double-helical DNA and poly[d(G-C)] fragments in alcohol/water mixtures. The limiting reduced dichroism and the rotational correlation time changed abruptly in the alcohol concentration range expected for the DNA B-to-A and poly[d(G-C)] B-to-Z transitions. The Z form of poly[d(G-C)] was also induced by mitomycin C crosslinking in aqueous solution. The rotational correlation times observed for A- and Z-DNA were approximately consistent with dimensions determined by crystallographic and fiber diffraction analysis: the estimated rise per base pair was 2.8 A for A-DNA and 3.7 A for Z-DNA in solution. In addition, the observed limiting reduced dichroism values for A- and Z-DNA were close to the theoretical limit of -1.5, requiring a structure in which the base transition moments are effectively perpendicular to the double-helix axis. This is the result expected for any DNA double helix having dyad symmetry in which the base pairs are flat and the base transition moments lie predominantly in the short axis of the base pair and therefore close to a helix dyad axis. Only B-DNA deviates from this rule, strongly reinforcing our earlier conclusion that the base pairs in B-DNA are not flat but are propeller twisted, either statically or as a dynamic average.