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PubMed1986

Rates of heat-induced pyrimidine alterations in synthetic polydeoxyribonucleotides.

Hydrolytic damages to DNA can occur at physiological conditions. The possible role of DNA conformation on the distribution of such alterations of pyrimidines was investigated. Model compounds used were the synthetic alternating copolymer poly(dG-dC):poly(dG-dC) and the homopolymer poly(dG):poly(dC). Base damages were assayed by paper chromatography using polymers radioactively labeled in cytosine. Conformational changes were assayed by circular dichroic spectral changes. Incubation and heating of the polymers in 1 mM MnCl2 caused the spectral shift reported for the left-handed Z-DNA conformation in the alternating copolymer and the change reported for the triple helix in the homopolymer. After incubation in 85 degrees C, incidences of base damages were compared between the polymers. The presence of manganese reduced depyrimidination in both polymers. Rates of cytosine deamination to uracil were substantial and did not vary among the various conformational states.

Chromatography, Paper↗
PubMed1986

Rates of heat-induced DNA purine alterations in synthetic polydeoxyribonucleotides.

Damage to DNA by heat can occur at physiological conditions. The effects of the varying conformational states adopted by double-stranded DNA on the incidences and distributions of thermally induced hydrolytic purine alterations are unknown. The possible role of conformational changes on damage by heat to purines in DNA polymers was therefore investigated. Model compounds used were the synthetic alternating copolymer poly(dG-dC):poly(dG-dC) and the homopolymer poly(dG):poly(dC). Base damages were assayed by high performance liquid chromatography using polymers radioactively labeled in guanine. Conformational states were assayed by circular dichroic spectral changes. Incubation and heating of the polymers in 1 mM Mn2+ caused the spectral shift reported for the left-handed Z-DNA conformation in the alternating copolymer and the change reported for the triple helix in the homopolymer. After incubation at 85 degrees C., incidences of base damages were compared between the polymers. No deamination of guanine to xanthine was observed under any conditions. The presence of manganese reduced depurination in both polymers. Rates of guanine imidazole ring openings to yield 2,6-diamino-4-hydroxy-5-formamidopyrimidine were increased in the presence of the cation and constituted the chief form of purine damage in the homopolymer. Therefore, the distribution of heat-induced DNA alterations within the genome may be determined by DNA conformational states. This observed opening of purine imidazole rings in the presence of manganese ions may have mutagenic consequences and may be involved in carcinogenesis by metals.

Chromatography, High Pressure Liquid↗
PubMed2003

Polydeoxyribonucleotide (PDRN) promotes human osteoblast proliferation: a new proposal for bone tissue repair.

Several researchers have recently shed new light upon the importance of extracellular nucleotides and nucleosides to stimulate cells growth. PDRN, a mixture of deoxyribonucleotides polymers of different lengths, has recently demonstrated to stimulate "in vitro" fibroblast proliferation and collagen production, probably stimulating the purinergic receptor system. In this work we evaluated the effects of PDRN on human cultured osteoblasts, focusing our attention on cell proliferation and alkaline phosphatase activity. PDRN at a concentration of 100 microg/ml induce an increase in osteoblasts growth after 6 days as compared to control (+21%). The addition of DMPX 50 microM and suramine (P2 inhibitor) 10 microM give different results: suramine has no significant effect, while DPMX reduce, even if partially, the PDRN induced cell growth. The alkaline phosphatase activity shows a gradual enhancement starting from day 0 to day 10, even if PDRN treated cells, examined at day 6, present a sensibly lower phosphatase activity when compared to controls. Our data demonstrate that PDRN acts as an osteoblast growth stimulator. Its action is partially due to a stimulation of the purinergic system mediated by A2 purinoreceptors, however we can not exclude the involvement of other mechanism like salvage pathway.

Alkaline Phosphatase↗
PubMed1986

Sequence-dependent cooperative interactions in A/T-containing oligo- and polydeoxyribonucleotides.

To evaluate the length and sequence dependence of the unusual interaction properties observed for nonalternating A/T sequences in deoxyribonucleic acid (DNA) [Wilson, W. D., Wang, Y. H., Krishnamoorthy, C. R., & Smith, J. C. (1985) Biochemistry 24, 3991-3999], we have synthesized the oligomers d(A-T)6, dA10 X dT10, and d(A6-T6) and evaluated their interaction with the intercalator propidium. Propidium visible spectral shifts on adding all three oligomers are quite similar. Low-temperature spectrophotometric binding measurements indicate that d(A-T)6 has a significantly larger binding constant for propidium than dA10.dT10, as with the analogous alternating and nonalternating DNA polymers. The oligomer dA10.dT10 displays positive cooperativity in its propidium binding isotherm, and its binding constant increases with increasing temperature while d(A-T)6 does not display positive cooperativity, and its binding constant decreases with temperature, again as with the analogous polymers. van't Hoff plots indicate that the propidium binding enthalpies are approximately -9 and +6 kcal/mol for the alternating and nonalternating DNA samples, respectively. The mixed-sequence self-complementary oligomer d(A6-T6) has an unusual low-temperature binding isotherm which suggests a single strong binding site and a larger number of weaker binding sites which bind propidium cooperatively. A van't Hoff plot indicates that the cooperative sites d(A-T)6 have binding constants and binding enthalpies similar to dA10.dT10. Similar rate constants are observed in the sodium dodecyl sulfate driven dissociation reaction of propidium from d(A-T)6 and d(A6-T6), but the association reaction of propidium is significantly slower with d(A6-T6) than with d(A-T)6.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed1987

fd gene 5 protein binds to double-stranded polydeoxyribonucleotides poly(dA.dT) and poly[d(A-T).d(A-T)].

Circular dichroism (CD) data indicated that fd gene 5 protein (G5P) formed complexes with double-stranded poly(dA.dT) and poly[d(A-T).d(A-T)]. CD spectra of both polymers at wavelengths above 255 nm were altered upon protein binding. These spectral changes differed from those caused by strand separation. In addition, the tyrosyl 228-nm CD band of G5P decreased more than 65% upon binding of the protein to these double-stranded polymers. This reduction was significantly greater than that observed for binding to single-stranded poly(dA), poly(dT), and poly[d(A-T)] but was similar to that observed for binding of the protein to double-stranded RNA [Gray, C.W., Page, G.A., & Gray, D.M. (1984) J. Mol. Biol. 175, 553-559]. The decrease in melting temperature caused by the protein was twice as great for poly[d(A-T).d(A-T)] as for poly(dA.dT) in 5 mM tris(hydroxymethyl)aminomethane hydrochloride (Tris-HCl), pH 7. Upon heat denaturation of the poly(dA.dT)-G5P complex, CD spectra showed that single-stranded poly(dA) and poly(dT) formed complexes with the protein. The binding of gene 5 protein lowered the melting temperature of poly(dA.dT) by 10 degrees C in 5 mM Tris-HCl, pH 7, but after reducing the binding to the double-stranded form of the polymer by the addition of 0.1 M Na+, the melting temperature was lowered by approximately 30 degrees C. Since increasing the salt concentration decreases the affinity of G5P for the poly(dA) and poly(dT) single strands and increases the stability of the double-stranded polymer, the ability of the gene 5 protein to destabilize poly(dA.dT) appeared to be significantly affected by its binding to the double-stranded form of the polymer.

Circular Dichroism↗
PubMed1989

Specificity of the binding of fd gene 5 protein to polydeoxyribonucleotides.

The long-wavelength circular dichroism (CD) changes induced by binding of fd gene 5 protein to the alternating DNA sequences poly[d(A-C)] and poly[d(C-T)] were similar to those induced by the protein complexed with the homopolymers poly[d(A)], poly[d(C)], and poly[d(T)]. The fd gene 5 protein showed different binding affinities for the various polymers. The affinity for the alternating sequences was not compositionally weighted with respect to the affinities for the homopolymers, indicating that both base composition and base sequence of the template are important for the binding of fd gene 5 protein.

Bacteriophages↗
PubMed1981

Altered mobility of polydeoxyribonucleotides in high resolution polyacrylamide gels due to removal of terminal phosphates.

We have compared the electrophoretic mobility of a series of polynucleotides differing solely by the presence or absence of a terminal phosphate. As expected, the effect of removal of a single terminal phosphoryl residue on electrophoretic mobility is dependent on the size of the polynucleotide and therefore is not constant. Removal of a phosphoryl residue from polynucleotides shorter than 30 nucleotides reduces the mobility the equivalent of one nucleotide. Between 30 and 50 nucleotides the reduction in mobility is approximately one-half a nucleotide, while above 50 nucleotides in size the effect of phosphate removal approaches zero.

Chemical Phenomena↗
PubMed1982

Action of T4 endonuclease V on polydeoxyribonucleotides with apyrimidinic or apurinic sites.

[3H]Thymine-labeled poly(dA) . poly(dT) carrying many apyrimidinic (AP) sites has been prepared by treating an enzymatically synthesized poly(dA) . poly(dT, dU) with uracil-DNA glycosylase. Incubation of the polymer with a homogeneous preparation of T4 endonuclease V resulted in conversion of the labeled material into acid-soluble forms. Native DNA with apurinic sites was also cleaved by the enzyme. Single-stranded polymers, poly(dT) carrying AP sites or poly(dT) with thymine dimers, were barely attacked by T4 endonuclease V. The polymer whose aldehyde moieties at AP sites were reduced to alcoholic forms was not susceptible to the enzyme. The site of endonucleolytic cleavage was determined by using alternating copolymers whose phosphate groups were differentially labeled. The result is consistent with the view that T4 endonuclease V cleaves a phosphodiester linkage on the 3'-side of AP sites, producing chains terminated at their 3'-ends with base-free deoxyribose and at their 5'-ends with phosphate.

Binding Sites↗
PubMed1965

ANTIBODIES TO DNA AND A SYNTHETIC POLYDEOXYRIBONUCLEOTIDE PRODUCED BY OLIGODEOXYRIBONUCLEOTIDES.

Calf-thymus DNA was degraded into small fragments (oligodeoxyribonucleotides); the fragments were treated with methylated bovine serum albumin, and the complexes so formed were emulsified in complete Freund's adjuvant and injected into rabbits. The serums of the immunized rabbits contained antibodies that reacted with homologous and heterologous unfragmented heat-denatured DNA, and also with a synthetic polydeoxyadenylate-thymidylate. Relatively small DNA fragments (of the order of tetra-hexanucleotide) can thus serve as haptens for the production of DNA antibodies; this finding increases the probability of producing antibodies specific for unique sequences of nucleotides.

Animals↗
PubMed1991

In vitro inhibition by defibrotide of monocyte superoxide anion generation: a possible mechanism for the antithrombotic effect of a polydeoxyribonucleotide-derived drug.

In an attempt to elucidate the antithrombotic potential of defibrotide (D) we have evaluated several functions of monocytes from 7 healthy subjects before and after in vitro incubation of the cells with increasing concentrations of this drug. At concentrations as high as 40 micrograms/ml, D hardly affected the expression of both the procoagulant activity of monocytes and the formation of superoxide anion in response to 1 mg/ml zymosan (STZ). In contrast, at concentrations that may be achieved in vivo following the administration of the drug (5-20 micrograms/ml), D impaired in a dose-dependent manner (p less than 0.05) the generation of O-2 in response to N-formyl-L-methionyl-L-leucyl-L-phenylalanine (FMLP, 1 microM) or calcium ionophore A23187 (10 microM). Regardless of the agonist employed, at concentrations between 1 and 5 mM, extracellular Ca2+ had little effect on the impairment of superoxide anion generation by D. In contrast, the inhibitory effect was time-dependent, the maximum impairment (greater than 30%) being observed when the cells were preincubated with the drug for 20 h. These data support the concept that the antithrombotic potential of D involves the ability of the drug to affect the generation of free radicals by leukocytes and suggest that future in vivo studies for the evaluation of the activity of D should take into account the role of monocytes in hemostasis and thrombosis.

Adult↗