The Effect of Polydeoxyribonucleotide Extracted from Salmon Sperm on the Restoration of Bisphosphonate-Related Osteonecrosis of the Jaw.

Bisphosphonates (BPs) used for treating skeletal diseases can induce bisphosphonate-related osteonecrosis of the jaw (BRONJ). Despite much effort, effective remedies are yet to be established. In the present study, we investigated the feasibility of polydeoxyribonucleotide (PDRN) extracted from salmon sperm for the treatment of BRONJ, in a BRONJ-induced rat model. Compared with BRONJ-induced samples, PDRN-treated samples exhibited lower necrotic bone percentages and increased numbers of blood vessels and attached osteoclast production. Moreover, local administration of PDRN at a high concentration (8 mg/kg) remarkably resolved the osteonecrosis. Findings from this study suggest that local administration of PDRN at a specific concentration may be considered clinically for the management of BRONJ.

Isolation of A-T-rich fragments from calf thymus DNA using the phenol method.

The action of phenol on the products of partial digestion of calf thymus DNA by K2 DNAase causes a loss of 3--5% of the material passing into the phenol phase. This part of DNA can be regained in the aqueous phase by lowering both the temperature and the ionic strength. Among oligonucleotides up to 7 monomers in length, those which are soluble in phenol do not contain guanine residues. Phenol-soluble DNA fragments of the molecular weight of an order of 2000--50,000 appeared to be composed mainly of adenosine phosphate. They also contain some thymine and only traces of guanine and cytosine. Some longer A-T-rich fragments, even up to 5-10(6) daltons, were repeatedly found in the phenol phase, but their base composition has not been determined yet. The method presented here was found very convenient for the isolation of relatively large A-T-rich DNA fragments. The property of DNA or its fragments to dissolve in phenol seems to be dependent on an adequate primary structure, probably similar to that of poly (dA-dT).

Denaturing HPLC purification of tritylated oligonucleotides using tetraethylammonium hydroxide.

Purification of oligonucleotides by HPLC is limited by association between failure sequences and full-length oligonucleotide. We describe a protocol for denaturing purification of 5'-dimethoxytritylated oligonucleotides that ensures that separation of tritylated and non-tritylated species will not be complicated by strand association. Fully denaturing conditions are produced by the use of tetraethylammonium hydroxide, which is a basic reagent with ion-pairing properties similar to triethylammonium acetate. The method also includes two other convenient features: a) the option of loading the crude oligonucleotide without removing concentrated ammonium hydroxide and b) detritylation on the column with separation of dimethoxytrityl alcohol.

Separation of pd(GC)12 from pd(AT)12 by free solution capillary electrophoresis.

The two synthetic self complementary oligonucleotides pd(AT)12 and pd(GC)12 were separated by free solution capillary electrophoresis (CZE) using simple borate buffers. The effects of pH (7.5-9) and the concentration of the buffer (0.03-0.35 M) were investigated. Higher pH values and buffer concentrations led to better resolution and longer migration times, the pH having a more pronounced effect on the separation than the concentration of the buffer. It is proposed that the conformation and effective length of the oligonucleotides may have a role in their separation in free solution capillary electrophoresis.

High capacity organic monoliths for the simultaneous application to biopolymer chromatography and the separation of small molecules.

A method for controlling the mesoporous structure of monolithic organic copolymers is presented by systematic variation in polymerisation time, employing poly(p-methylstyrene-co-1,2-(p-vinylphenyl)ethane) (MS/BVPE) as a representative styrene system. Decreasing the time of polymerisation introduces a considerable fraction of mesopores (up to 20% of the total pore volume), while keeping the support permeability reasonable high ( approximately 1.3x10(-14)m(2)). Monolith structures, prepared in such a manner, enable efficient (typically around 70,000plates/m) and fast separation of low-molecular-weight compounds, whereas their performance towards biopolymers is comparable to column supports, fabricated according to typically used protocols (polymerisation time >12h and thus monomer conversion >98%). The polymerisation time is hence a valuable tool to tailor the fraction of support flow-channels, macropores as well as mesopores, which is shown dramatically to influence the chromatographic separation characteristics of the respective column. This way, the preferred applicability of organic (styrene) monolithic copolymers can be extended to the separation of small molecules beyond biopolymer chromatography.

Pulsed field gel electrophoresis techniques for separating 1- to 50-kilobase DNA fragments.

Conventional agarose gel electrophoresis separates DNA using a static electric field. The maximum size limit for separation of DNA by this method is about 20 kilobase pairs (kb). A number of new electrophoretic techniques which employ periodic reorientation of electric fields permit separation of DNA well beyond this size limit. We sought to determine whether the use of very fast (millisecond) field switching could improve separation of DNA in the size range of 1 to 50 kb. Additionally, we have compared the resolution obtained with each of the different field switching regimens for DNA in this size range. Switching intervals of from 0.2 to 900 ms were used with unidirectional pulsing of a single electric field, with pulsed field gels, and with field inversion gel electrophoresis. Plotting the mobility of DNA as a function of size demonstrates that under the conditions used, each of these techniques offers comparable resolution. We also have examined the separation obtained when field inversion gels are run with forward and reverse fields of equal voltage and different durations, versus using fields of equal duration and different voltages. Field inversion which uses forward and reverse fields of different voltages yields resolution which is superior to the other methods examined.

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.

Selective isolation of highly polymorphic (dC-dA)n.(dG-dT)n microsatellites by stringent hybridization.

We defined a hybridization condition for isolation of clones carrying long (dC-dA)n.(dG-dT)n microsatellites from a genomic plasmid library. By using (dC-dA)20 oligonucleotide as a probe and hybridizing under stringent conditions, more than two-thirds of the obtained plasmid carried the repeats that were longer than (dC-dA)14 and highly polymorphic.

Chromatographic separation of oligodeoxynucleotides with identical length: application to purification of oligomers containing a modified base.

A general procedure is described for separation and purification of oligodeoxynucleotides of identical length but different base composition, in particular, of oligomers containing modified bases such as 4-substituted thymines and 6-substituted guanines, using an anion-exchange column (either Mono Q or NucleoPac). The modified oligomers can be well separated from the analogous oligomers containing unmodified thymine or guanine under the basic conditions of the chromatography. The effects of oligomer length, base composition, and lipophilicity on the separation are discussed. A general rule which can be used for prediction of the order of elution of different oligomers and for estimation of tautomeric form of a modified base in the oligomer is presented.

Rapid nanopore discrimination between single polynucleotide molecules.

A variety of different DNA polymers were electrophoretically driven through the nanopore of an alpha-hemolysin channel in a lipid bilayer. Single-channel recording of the translocation duration and current flow during traversal of individual polynucleotides yielded a unique pattern of events for each of the several polymers tested. Statistical data derived from this pattern of events demonstrate that in several cases a nanopore can distinguish between polynucleotides of similar length and composition that differ only in sequence. Studies of temperature effects on the translocation process show that translocation duration scales as approximately T(-2). A strong correlation exists between the temperature dependence of the event characteristics and the tendency of some polymers to form secondary structure. Because nanopores can rapidly discriminate and characterize unlabeled DNA molecules at low copy number, refinements of the experimental approach demonstrated here could eventually provide a low-cost high-throughput method of analyzing DNA polynucleotides.

Preconcentration and separation of double-stranded DNA fragments by electrophoresis in plastic microfluidic devices.

We have evaluated double-stranded DNA separations in microfluidic devices which were designed to couple a sample preconcentration step based on isotachophoresis (ITP) with a zone electrophoretic (ZE) separation step as a method to increase the concentration limit of detection in microfluidic devices. Developed at ACLARA BioSciences, these LabCard trade mark devices are plastic 32 channel chips, designed with a long sample injection channel segment to increase the sample loading. These chips were designed to allow stacking of the sample into a narrow band using discontinuous ITP buffers, and subsequent separation in the ZE mode in sieving polymer solutions. Compared to chip ZE, the sensitivity was increased by 40-fold and we showed baseline resolution of all fragments in the PhiX174/HaeIII DNA digest. The total analysis time was 3 min/sample, or less than 100 min per LabCard device. The resolution for multiplexed PCR samples was the same as obtained in chip ZE. The limit of detection was 9 fg/microL of DNA in 0.1xpolymerase chain reaction (PCR) buffers using confocal fluorescence detection following 488 nm laser excitation with thiazole orange as the fluorescent intercalating dye.

Synthesis and properties of oligodeoxyribonucleotide-polyethylene glycol conjugates.

Pools of oligonucleotide conjugates consisting of 10-400 different molecular species were synthesized. The conjugates contained a varying number of ethylene glycol units attached to 3'-terminal, 5'-terminal and internal positions of the oligonucleotides. Conjugate synthesis was performed by phosphoramidite solid phase chemistry using suitably protected polyethylene glycol phosphoramidites and PEG-derivatized solid supports containing polydisperse PEGs of various molecular weight ranges. The pools were analyzed and fractionated by chromatographic and electrophoretic techniques, and the composition of isolated conjugates was revealed by matrix-assisted laser desorption/ionization mass spectrometry. The number and attachment sites of coupled ethylene glycol units greatly influence the hydrophobicity of the conjugates, as well as their electrophoretic mobilities. Conjugation had little effect on the hybridization behavior of oligonucleotide conjugates with unmodified complementary oligonucleotide strands. Melting temperatures were between 67 and 73 degrees C, depending on the size and number of coupled PEG chains, compared to 68 degrees C for the unmodified duplex. Conjugates with PEG coupled to both 3'- and 5'-terminal positions showed a more than 10-fold increase in exonuclease stability.

Kinetic investigation of unfolding and partial refolding of a crab satellite (dA-dT)n.

Crab (dA-dT)n was isolated from the testes of Cancer borealis by a procedure involving separation of DNA and segregation of the satellite fraction by Hg2+ binding/Cs2SO4 density gradient ultracentrifugation. The titration of crab (dA-dT)n samples at 10 degrees indicated a sharp absorbance change at pH 11.98 in agreement with the pHm value observed for synthetic poly(dA-dT) under identical conditions. The reversal of the titration, however, resulted only in about 50% recovery of the original absorbance (at 260 nm) in marked contrast to the complete reversibility of the synthetic material. pH-jump experiments were carried out for the purpose of characterizing the rates and mechanisms of conformational transitions brought about by changes in the solution environment. It was found that the disintegration of the putative native structure of crab (dA-dT)n starts with a very fast reaction (occurring within the 6-msec deadtime of the instrument and comprising 65% of the total absorbance change) and it is completed via a slower first-order reaction (k = 66 sec minus 1). It is postulated that the first process is due to the rapid untwisting of end regions and, perhaps, some short hairpin-like helical branches present on the macromolecules. The second reaction is believed to be the end-to-end type unwinding of the double-helical backbone of crab (dA-dT)n. In the presence of low concentration (3 mug/ml) of Hg2+ ions the overall rate of disintegration process decreased drastically. pH jumps from pH values above pHm to values below were used to study the rates of absorbance changes corresponding to the refolding of the strands of denatured crab (DA-dT)n. A concentration independent process consisting of two phases was observed. The first phase was a gradual nonexponential process spanning the first second of the reaction, and the other, a very slow first-order process characterized by the rate constant value of 0.053 sec minus 1. It is proposed that the first part of the process (involving about 24% of nucleotide residues) is an intramolecular formation of helical hairpins (frequently interrupted by mismatching bases) and the second part is a manifestation of some association of the extant unpaired bases during the folding of the branched structure. Refolded crab (dA-dT)n samples when subjected again to pH greater than pHm in the stopped-flow apparatus displayed not the disintegration pattern of the native crab (dA-dT)n but rather that of synthetic poly(dA-dT. The marked facility of crab (dA-dT)n macromolecules for rapid conformational transitions induced by slight changes in the solution environment might be relevant to the biological function of this DNA.

Protection of (dA.dT) cluster regions in the DNAase I cleavage of DNA by specific interaction with netropsin.

The specific DNA binding ligand netropsin selectively blocks dA-dT base pairs in clusters containing two or more consecutive thymine residues at the dNAase I cleavage sites of DNA. Using CD and UV absorption measurements it is shown, that at various ratios of netropsin to nucleotide concentrations and even at satuation of ligand interaction the enzyme cuts along regions containing dG-dC pairs sandwiched between dA-dT pairs. This follows a slow kinetics and is associated with a release of netropsin from those segments. These facts suggests the usefulness of the partial protection of certain DNA sequences in DNAase I cleavage sites in producing DNA fragments in structural studies of the genome. A possible interpretation of the effect of netropsin binding on the enzymatic hydrolysis of phosphodiester bonds of the helix is discussed.

Use of high-molecular-mass polyacrylamides as matrices for microchip electrophoresis of DNA fragments.

DNA fragment analysis requires the use of polymer solutions as sieving matrices. Generally, such matrices are constituted of high-molar-weight polymers employed at a concentration higher than their entanglement threshold concentration. These polymer solutions are highly viscous and difficult to use in the narrow channels of a microchip. Ultralarge polyacrylamides synthesized via a nonconventional method, being the low-temperature plasma-induced polymerization (PIP), were used as DNA sieving matrices for microchip electrophoresis. The distinctive features of these polymers (ultralarge molecular mass and linearity) allow their use at a dilute concentration. Dilute PIP polyacrylamides revealed a constant value of resolution in a broad range of DNA fragment sizes (123 bp-1353 bp), thus proving to be effective in common genotyping applications. Moreover, the low viscosity of the dilute solutions enable it to be easier and faster in filling the channel between runs, thus enhancing the throughput of the microchip devices.

Effect of polydeoxyribonucleotides on human fibroblasts in primary culture.

The effects of a mixture of oligo- and polydeoxyribonucleotides (PDRN) on the growth and protein secretion of cultured human skin fibroblasts were investigated. Both intact and DNAase-digested PDRN stimulated cell proliferation to a similar extent. When cultured fibroblasts were incubated with radioactive amino acids in the presence of intact or digested PDRN the incorporation of the tracer into secreted proteins increased significantly. This stimulation appears to be specific for certain protein components, including fibronectin. These results are interpreted assuming that PDRN and the nucleotides and nucleosides resulting from its degradation, can act as signal transducers or, alternatively, can be internalized and utilized to provide purine and pyrimidine rings for the salvage pathways.

Preparation and duplex-to-single strand transition of the fully complementary duplex of d(G4).d(C4) in aqueous solution.

The d(G4) and d(C4) molecules in the single stranded state were synthesized by the phosphotriester method and purified. The full duplex of tetramer d(G4).d(C4) was prepared by expending about a month. The duplex-to-single strand transition was observed by UV-spectroscopy. A standard hypochromic effect was observed, which is different from some experimental results reported previously.

Preparation of insolubilized-DNA film with three-dimensional network and removal of endocrine disruptors.

A water-insolubilized film was prepared by UV irradiation on a dried DNA film. When a UV-irradiated DNA was examined using a circular dichroism spectroscopy, a double stranded structure was observed as well as that of native DNA. The UV irradiated DNA film was also accumulated intercalating reagents. These results suggested that the double stranded structure was involved in the UV irradiated DNA film with a three-dimensional network. The thymine-thymine dimer formation was suggested to be involved in the cross-linking reactions by the polymerization analysis using poly(dA)-poly(dT) and poly(dG)-poly(dC). We also demonstrate the utilization of the UV-irradiated DNA film as a functional material for the accumulation of harmful DNA intercalating pollutants in aqueous solution. These results suggested that the UV-irradiated DNA film was applicable as a functional material for medical, engineering and environmental sciences.