Complexes of silver ion with natural and synthetic polynucleotides

Daune, Michel; Dekker, Charles A.; Schachman, H. K.

doi:10.1002/bip.1966.360040107

Cited by 137 publications

(83 citation statements)

References 48 publications

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“…Furthermore, at pH I 7, Ag' binding is linearly related to the base composition of DNA [3], whereas at pH 2 8 sequence effects on the binding are evident (21 (and below). It should also be added that the overall affinity of Ag' for DNA is lower at pH s 7 [4,5]; this explains why under these conditions the effect of rf on buoyant density is lower and the choice of the initial density of Cs2S04 is less critical. Fig.…”

Section: Conditions For the Optimal Resolution Of D N A Components Inmentioning

confidence: 99%

An Analysis of the Bovine Genome by Density‐Gradient Centrifugation

Macaya

Cortadas

Bernardi

1978

European Journal of Biochemistry

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The dG + dC-rich fractions obtained by density gradient centrifugation of bovine DNA in Cs2S04/ BAMD [J. Cortadas, G. Macaya & G. Bernardi (1977) Eur. J. Biochem. 76, were centrifuged in Cs2S04/Ag+ density gradients. These experiments led to the preparation of the DNA Components which had been detected (by analytical centrifugation in CsCl) in the Cs2S04/BAMD fractions, and also of DNA components which had identical behaviors in CszSO4/BAMD gradients and identical buoyant densities in CsCl. A total of eight satellite components and 11 minor components, accounting for 23 % and 4 % of the bovine genome, respectively, were thus isolated and characterized in their relative amounts and buoyant densities. The implications of these results on the interpretation of renaturation kinetic data on the bovine genome are discussed.Centrifugation of calf thymus DNA in preparative Cs2S04/BAMD density gradients has led to the separation of dG + dC-rich fractions which have been analyzed in terms of DNA components by analytical centrifugation in CsCl [l]. In the present work, we have prepared these components by submitting the CszS04/BAMD fractions to further centrifugations in Cs2S04/Ag' density gradients. This has also led to the preparation of DNA components having the same behavior in CSZSO~/BAMD density gradients and the same buoyant density in CsCl. A precise assessment of the buoyant density and relative amount of eight satellite components and 11 minor components so isolated from the bovine genome has thus been possible.As in other recent papers from this laboratory, (quoted in [I]), we call here DNA components the populations of genome fragments which can be separated from each other by density gradient centrifugation techniques. We distinguish three groups of DNA components according to their nucleotide sequence patterns and relative amounts in the genome as follows. (a) Satellite components are formed by short repeated nucleotide sequences ; each satellite component usually represents a small percentage of the genome. (b) Minor components each account for less than 3 % of the genome; they are not formed by short repeated nucleotide sequences, yet they may contain rf, molar ratio of ligand to DNA phosphate. The different features of nucleotide sequences in these three classes of DNA components allow a distinction to be made on the basis of a number of physical and chemical properties. Suffice it to mention here that the electrophoretic patterns of fragments produced by different restriction enzymes provide a rapid criterion for such a distinction (see following paper). Satellite components are characterized by banding patterns in which the molecular weights of the fragments reveal the underlying repetitive organization of the nucleotide sequences. Major components show continuous distributions of fragment sizes, in which no bands are detected. Minor components either show simple banding patterns due to the tandem repetition of gene-spacer units or continuous distributions of fragments. A detailed discussion of the prope...

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Section: Conditions For the Optimal Resolution Of D N A Components Inmentioning

confidence: 99%

An Analysis of the Bovine Genome by Density‐Gradient Centrifugation

Macaya

Cortadas

Bernardi

1978

European Journal of Biochemistry

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“…Even though AgSu is a sulfonamide drug, its antibacterial activity is not a function of the sulfonamide moiety because its effectiveness is not reversed by p-aminobenzoic acid (10). Silver nitrate (AgNO3) reacts with deoxyribonucleic acid (DNA) in vitro (14, 31; see also 3 and 33); hence, it has been suggested (10) that AgSu reacts with the cellular DNA and that this forms the basis of its antibacterial action. It has been proposed further (10) that when AgSu reacts with the cellular DNA it dissociates and that only the silver ion becomes associated with DNA while the sulfadiazine portion is released.…”

mentioning

confidence: 99%

“…8) that the AgNO3-DNA complex had a buoyant density higher than that of the control DNA; this confirms the earlier finding of Jensen and Davidson (14) and presumably reflects the increased molecular weight of the silver nucleate . (3,14,33). The AgSu-DNA complex, on the other .0 20 hand, showed a decreased buoyant density in 0 Cs2SO4 (Fig.…”

mentioning

confidence: 99%

Silver Sulfadiazine: Interaction with Isolated Deoxyribonucleic Acid

Rosenkranz

1972

Antimicrob Agents Chemother

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Silver sulfadiazine (AgSu) was found to interact with isolated deoxyribonucleic acid (DNA) to form nondissociable complexes. These complexes differ in physical and chemical properties from those that are established when silver nitrate is added to DNA. The reaction between AgSu and DNA is visualized as occurring in two stages: (i) a weak and reversible interaction (intercalation) between DNA and the sulfadiazine moiety and (ii) a tight binding involving the silver atom. In the first stage, sodium sulfadiazine competes with AgSu for the DNA.Silver sulfadiazine (AgSu) was synthesized by Fox, who also established its effectiveness for the prevention and treatment of burn infections due to pseudomonads (8)(9)(10)28). Even though AgSu is a sulfonamide drug, its antibacterial activity is not a function of the sulfonamide moiety because its effectiveness is not reversed by p-aminobenzoic acid (10). Silver nitrate (AgNO3) reacts with deoxyribonucleic acid (DNA) in vitro (14, 31; see also 3 and 33); hence, it has been suggested (10) that AgSu reacts with the cellular DNA and that this forms the basis of its antibacterial action. It has been proposed further (10) that when AgSu reacts with the cellular DNA it dissociates and that only the silver ion becomes associated with DNA while the sulfadiazine portion is released. However, data on both the in vivo and in vitro effects of AgSu are scarce, and therefore an examination of its mode of action was undertaken. The present study shows that in vitro AgSu forms a complex with DNA which is unlike that formed when DNA is mixed with AgNO3; but it is also shown (25; (20), and bacteriophage DNA was isolated from Klebsiella phage E-1, currently under investigation in this laboratory. 3H-labeled DNA derived from chicken embryos was prepared as described previously (13). All DNA specimens were dissolved in 0.005 M NaNO3 and extensively dialyzed against 0.005 M NaNO3 to remove all traces of chloride (capable of reacting with AgNO3 to form AgCl).JSulfadiazines. AgSu (29.1% silver) and sodium sulfadiazine (NaSu) were generously provided by Marion Laboratories, Inc., Kansas City, Mo. Only freshly prepared solutions (in 0.005 M NaNO3) were used.Chemical analysis. The phosphorus content of DNA specimens was determined by the procedure of Fiske and Subbarow (7).Spectral analysis. The spectra of DNA solutions were taken with a Carey model 11 recording spectrophotometer, and the absorbance at selected wavelengths was checked with a Beckman DU-2 spectrophotometer.Centrifugal procedures. Sedimentation velocity studies were carried out on dilute solutions in 12-mm Kel-F centerpiece centrifuge cells. A Spinco model E analytical ultracentrifuge equipped with an ultraviolet optical system was operated at 50,740 rev/min, and pictures were taken at 2-min intervals. The photographs were traced with a Joyce-Loebl Mark III B microdensitometer, and sedimentation coefficients (S5".) and distributions of sedimentation co-

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“…Moreover, the proton of the exocyclic amino group of cytosine is dissociated at pH ²7.0 in the presence of silver ions. 19 The emerged anionic charge on cytosines would partially cancel the effect of the silver ions because of electrostatic repulsion to provide a slightly lower melting temperature of 42°C at pH 7.0. These results are consistent with previously reported data.…”

Section: ¹1mentioning

confidence: 99%

Alteration of DNAzyme Activity by Silver Ion

et al. 2014

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The thermal stability of the parallel motif triple helix DNA containing CG.CH + base triplets is improved by silver ions. The N3 protons of cytosines on the third strand are replaced by the ions to form CG.CAg + , which are stable regardless of the pH values. The activity of the DNAzyme that binds its substrate DNA through triple helix formation was examined in the presence of silver ions. The DNAzyme activity was retained even at neutral pH with the assistance of silver ions.Ribozymes and DNAzymes are a class of functional nucleic acids obtained by molecular evolution. The parallel motif structure of a DNA triplex containing CG.CH + base triplets is stable only under weak acidic conditions, because the N3 position of the cytosines (pK a μ 4.5) on the third strand needs to be protonated for complementarity with the Hoogsteen side of guanines.11 Previously, we reported that silver ions stabilized the parallel motif structure of a DNA triplex even under weak basic conditions.12 The N3 protons of CG.CH + base triplets were quantitatively substituted by silver ions to form silver ion-mediated stable base triplets, CG.CAg + ( Figure 1a). Judging from the experimental conditions, the binding affinity of the silver ion was rather high; the apparent dissociation constant of the silver ion from the binding pocket in CG.C seemed to be less than 10 ¹6 M ¹1. Several applications have been made for some analytical and engineering purposes. The molecular beacon 13 and DNA array 14 that targets the specific sequences in duplexes were proposed based on the stable triplex formation in the presence of silver ions. Luminous Ag clusters were successfully prepared using the DNA triplex as a template, on which silver ions were allocated at defined position as CG.CAg + . 15Recently, specific interactions with certain metal ions have been used for regulating the functions of biomolecules. Here, we intended to regulate the activity of a DNA-cleaving DNAzyme by silver ions. The DNAzyme used in this study was Cu 2+ -dependent and first reported by Breaker et al. 17 The DNAzyme consists of a hairpin duplex and a short singlestranded regions for capturing single-stranded DNA substrates. Thus, the DNAzyme binds the substrate DNA through the cooperative formation of a triple helix and a short duplex. Silver ions were found to significantly stabilize the triple helix of the parallel motif.12a Therefore, the pH profile of the catalytic activity of the DNAzyme would be altered by the addition of silver ions through specific interactions with CG.C base triplets. The sequences of the DNAs used in this study are shown in Figure 1b. Two DNAzymes Dz1 and Dz2 carrying different hairpin-arm sequences and the substrate for Dz1 (S) were prepared to examine the substrate binding specificity through triplex formation.18 Figure 2 shows the results of UV melting experiments of the complex, DNAzyme-substrate (Dz1-S), in the absence (a) and presence (b) of silver ions. The experiments were carried out in buffer solutions at three different pH values (50-mM MES...

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Complexes of silver ion with natural and synthetic polynucleotides

Cited by 137 publications

References 48 publications

An Analysis of the Bovine Genome by Density‐Gradient Centrifugation

An Analysis of the Bovine Genome by Density‐Gradient Centrifugation

Silver Sulfadiazine: Interaction with Isolated Deoxyribonucleic Acid

Alteration of DNAzyme Activity by Silver Ion

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