Acceleration of DNA renaturation rates

The rate of renaturation of DNA may be increased by altering the effective solvent volume available for DNA in solution. Accelerations are demonstrated when neutral and anionic dextran polymers are used to exclude volume in DNA solutions. The logarithm of the DNA renaturation rate constant is shown to be proportional to the concentration of dextran polymer and to be proportional to the intrinsic viscosity of a series of dextran polymers of identical chemical composition. A theory is proposed to account for these results.     

Quantitation and interaction of glycosaminoglycans with Alcian blue in dimethyl sulfoxide solutions.

An improved method is described for the quantitation of glycosaminoglycans separatedon cellulose acetate, stained with Alcian blue, and dissolved in a dimethyl sulfoxide solution. Standard curves are shown for all eight glycosaminoglycans. It is shown that absorption at the Alcian blue orthochromatic E_max is depressed under conditions which favor formation of dye-glycosaminoglycan complexes. The interaction between Alcian blue and the eight glycosaminoglycans was studied in dimethyl sulfoxide solutions of varying composition. It was shown that the extent of complex formation depends both on the glycosaminoglycan and the composition of the dimethyl sulfoxide solution. A dimethyl sulfoxide solution which contains 0.094 m H₂SO₄ is described which maximizes dye-glycosaminoglycan dissociation and thus the absorbance. Also, an improved staining method is described which improves dye uptake by the glycosaminoglycans and consequently increases the sensitivity of glycosaminoglycan quantitation.     

Excluded volume effects on the rate of renaturation of DNA

The rate of renaturation of T2 DNA hits been investigated by using complementary DNA strands of different length. The length of the shorter strand ranged from 0.02 to 1.0 times the length of the longer strand. An excluded volume theory is developed to include this type of reaction as well as the DNA–RNA hybridization reaction. Experimental and theoretical rates of renaturation of DNA are found to be in agreement. For the cases studied, the rate was never greater than twice that observed for short strands of the same length renaturing with themselves. The products of renaturation reactions are also considered.     

Quantitation of dimethyl sulfoxide in solutions and tissues by high-performance liquid chromatography.

We have developed a rapid and simple method to determine the level of dimethyl sulfoxide (Me2SO) in both solutions and tissue samples. For analysis of Me2SO in a cryopreservation medium, the solution is simply diluted in 10% (vol/vol) methanol and centrifuged. Then an aliquot of the supernatant is assayed by high-performance liquid chromatography. For tissue samples, the wet weight is measured and the intact sample is extracted with 10% (vol/vol) methanol (e.g., 10 ml/g wet wt) in a sealed vial. The extract is then diluted and centrifuged, and an aliquot of the supernatant is assayed. The dry weight of the tissue is measured after the methanol-extracted sample is placed into either for 2 h and air-dried overnight. The water content of the tissue is calculated as the difference between the wet and the dry weights. The concentration of Me2SO in the aqueous compartment of the tissue can then be calculated by taking into account the concentration of Me2SO in the extract and the dilution factor, based on the tissue water volume and the volume of methanol used to extract the Me2SO. The calculated values for porcine myocardium samples correlated 1:1 with the actual Me2SO concentrations in the solutions in which the tissue samples were equilibrated. Finally, we present results documenting the usefulness of this assay by following the time course of Me2SO penetration into core versus peripheral regions of 1-cm3 samples of porcine myocardium.     

DNA melting temperatures and renaturation rates in concentrated alkylammonium salt solutions

DNA melting temperatures and renaturation rates have been determined for Me₂Et₂NBr and a series of RMe₃NBr and REt₃NBr solvents where R is a linear hydrocarbon chain. The point of independence of DNA melting temperature on base composition has been investigated for each solvent system. Renaturation rates are compared with those found in other concentrated salt solutions. Solvent mixtures which accelerate DNA renaturation have also been investigated.     

Studies on the assembly and stability of the metal-thiolate clusters of metallothionein in dimethyl sulfoxide.

Solvent perturbation studies in 100% dimethyl sulfoxide (Me2SO) have been carried out on rabbit liver metallothionein (MT) in an effort to learn more about the factors stabilizing the three-dimensional structure and the mechanism of cluster formation. As indicated by the electronic absorption spectra of Co7-metallothionein, the reconstituted protein preserves its structural integrity in this solvent. Minor spectral differences between water and Me2SO were fully reversible. The titration of apoMT with cobalt(II) in Me2SO, followed by UV-visible-near-infrared electronic absorption, circular dichroism, magnetic circular dichroism, and EPR spectroscopy, indicate that the protein can refold in this solvent. A comparison with the previous titration data in water reveals that the first four titration steps in both solvents are identical, indicating a thermodynamically controlled folding process. However, the reversed order of the cluster completion between Me2SO and water may suggest the involvement of a kinetically controlled folding process in the last three titration steps. A new cluster form developed with approximately nine Co(II) equivalents.     

Conformational changes and inactivation of rabbit muscle creatine kinase in dimethyl sulfoxide solutions.

The effects of dimethyl sulfoxide (DMSO) on creatine kinase (CK) conformation and enzymatic activity were studied by measuring activity changes, aggregation, and fluorescence spectra. The results showed that at low concentrations (< 65% v/v), DMSO had little effect on CK activity and structure. However, higher concentrations of DMSO led to CK inactivation, partial unfolding, and exposure of hydrophobic surfaces and thiol groups. DMSO caused aggregation during CK denaturation. A 75% DMSO concentration induced the most significant aggregation of CK. The CK inactivation and unfolding kinetics were single phase. The unfolding of CK was an irreversible process in the DMSO solutions. The results suggest that to a certain extent, an enzyme can maintain catalytic activity and conformation in water-organic mixture environments. Higher concentrations of DMSO affected the enzyme structure but not its active site. Inactivation occurred along with noticeable conformational change during CK denaturation. The inactivation and unfolding of CK in DMSO solutions differed from other denaturants such as guanidine, urea, and sodium dodecyl sulfate. The exposure of hydrophobic surfaces was a primary reason for the protein aggregation.     

New procedure for DNA transfection with polycation and dimethyl sulfoxide.

A new procedure for DNA transfection has been developed in a system of chicken embryo fibroblast cells and cloned Rous sarcoma virus DNA by using a polycation reagent as a mediator to adsorb DNA to the cell surface and dimethyl sulfoxide as an agent to facilitate the uptake of adsorbed DNA by the cells. In this new, simple, and convenient polycation-dimethyl sulfoxide transfection, which requires no carrier DNA even with small amounts of DNA, the number of transformed cell foci induced by Rous sarcoma virus DNA was proportional to the dose of the transfecting DNA, and chicken embryo fibroblast cells were successfully transformed by v-src-containing subgenomic DNA as well.     

Variation of cooling rate and concentration of dimethyl sulfoxide on rabbit kidney function

Rabbit kidney function was assessed in vitro after cryoprotection with either 3 or 4 M dimethyl sulfoxide. The introduction and removal of the cryoprotectant was carried out in a stepwise progressive manner and the removal in a stepwise progressive manner with hypertonic mannitol solutions. This in vitro model can be shown to respond to various ischemic-like states resulting in poor or absent function. Active tubular transport can be demonstrated. It has been used by many authors as an intermediate step prior to the ultimate test of reimplant and contralateral nephrectomy. Variations in the rate of cooling at cryoprotection levels of 3 and 4 M dimethyl sulfoxide concentration (Me2SO) were carried out. In general, at 3 M concentration of Me2SO, creatinine clearance, sodium and glucose reabsorption are preserved with a fair degree of success after cooling to -10, -15, and -20 degrees C in our model, when the rate of cooling to these levels is 1.0 degree C/min. When a cooling rate of 0.5 degree C/min is used, renal function is significantly reduced whether the final temperature is -10, -15, or -20 degrees C. Control rabbit kidneys will tolerate 4 M concentration of Me2SO and give fairly good function. When cooled to -15 or -20 degrees C, there is poor function at 0.1 and 0.5 degrees C/min. Fair function is obtained at the rate of 1 degree C/min to -10 degrees C. Therefore, at cryoprotectant levels of 3 and 4 M Me2SO, kidney function as assayed by in vitro perfusion, is better when the cooling rate is 1.0 degree C/min.     

Cryopreservation of the common carotid artery of the rabbit: Optimization of dimethyl sulfoxide concentration and cooling rate

This paper describes the continuation of studies that demonstrated the suitability of CP-Tes solution as a medium for the introduction and removal of dimethyl sulfoxide in rabbit common carotid arteries and established the kinetics of cryoprotectant permeation in that tissue. In this paper we report the tolerance of rabbit common carotid artery to dimethyl sulfoxide, in concentrations up to 30% (w/w), using a technique of exposure that was designed to control osmotic stress. The maximum concentration achieved without damage was 15% (w/w). Vessels were then equilibrated with 15% dimethyl sulfoxide and cooled to −80 °C at 0.22, 0.69, 2.15, or 9.63 °C/min: they were then transferred to the gas phase of a liquid nitrogen refrigerator {temperature below −160 °C) for storage. Thawing was carried out in a 37 °C water bath. The optimum rate of cooling for these conditions was found to be 0.69 °C/min. The maximal recovery of contractile force in response to 10⁻⁶ M norepinephrine was 30–40%; relaxation to acetylcholine (an endothelium-mediated function) was 80% of control, and an estimated 71% of endothelial cells survived with minimal ultrastructural change.     

Glass transition behavior of the vitrification solutions containing propanediol, dimethyl sulfoxide and polyvinyl alcohol

Knowledge of the glass transition behavior of vitrification solutions is important for research and planning of the cryopreservation of biological materials by vitrification. This brief communication shows the analysis for the glass transition and glass stability of the multi-component vitrification solutions containing propanediol (PE), dimethyl sulfoxide (Me₂SO) and polyvinyl alcohol (PVA) by using differential scanning calorimetry (DSC) during the cooling and subsequent warming between 25 and −150 °C. The glass formation of the solutions was enhanced by introduction of PVA. Partial glass formed during cooling and the fractions of free water in the partial glass matrix increased with the increasing of PVA concentration, which caused slight decline of glass transition temperature, T_g. Exothermic peaks of devitrification were delayed and broadened, which may result from the inhibition of ice nucleation or recrystallization of PVA.     

DNA methylation by dimethyl sulfoxide and methionine sulfoxide triggered by hydroxyl radical and implications for epigenetic modifications

In this Letter, we demonstrate the formation of m⁵dC from dC or in DNA by dimethylsulfoxide (DMSO) and methionine sulfoxide (MetO), under physiological conditions in the presence of the Fenton reagent in vitro. DMSO reportedly affects the cellular epigenetic profile, and enhances the metastatic potential of cultured epithelial cells. The methionine sulfoxide reductase (Msr) gene was suggested to be a metastatis suppressor gene, and the accumulation of MetO in proteins may induce metastatic cancer. Our findings are compatible with these biological data and support the hypothesis that chemical cytosine methylation via methyl radicals is one of the mechanisms of DNA hypermethylation during carcinogenesis. In addition to m⁵dC, the formation of 8-methyldeoxyguanosine (m⁸dG) was also detected in DNA under the same reaction conditions. The m⁸dG level in human DNA may be a useful indicator of DNA methylation by radical mechanisms.     

Determination of the rate of renaturation of modified DNA by fluorescence depolarization

Fluorescence depolarization was used to measure the rate of renaturation of T2 DNA, which had been modified by chloroacetaldehyde. Rates were measured on DNA samples with 5–15% of the base pairs modified and were found to agree with rates determined by DNA absorbance kinetics at 260 nm. The renaturation rate of a modified T2 DNA was unchanged in the presence of a ninefold abundance of unlabeled calf thymus DNA.     

Effects of microscopic and macroscopic viscosity on the rate of renaturation of DNA

The effect of solvent viscosity on DNA renaturation rates has been investigated as a function of temperature for a number of solvent systems. The results are all consistent with a microscopic viscosity limitation of the rate determining step. Rates of renaturation in perchlorate and quaternary ammonium salt solutions are also discussed. Increasing the macroscopic viscosity with dissolved neutral or anionic polymers increases, rather than decreases, renaturation rates due to the excluded volume of the dissolved polymers.     

Antistress effect of dimethyl sulfoxide in the rat

Administration of scavenger of hydroxyl radicals--dimethylsulfoxide (1 g/kg intraperitoneally, daily for 3 weeks) did not lead to any significant changes in animals behaviour in the open field and in visceral functions (arterial pressure, respiratory rate, heart rate) but prevented shifts of these characteristics caused by chronic 3-week emotional-pain stress. In rats injected with dimethylsulfoxide, an increase was observed of superoxide dismutase activity in the brain and blood serum. Molecular mechanisms are discussed of antistress action of dimethylsulfoxide (scavenge of hydroxyl radicals, activation of superoxide dismutase) and possible role of hydroxyl radicals in realization of damaging action of stress on the organism.     

Thermal stability of aminoacyl-tRNAs in aqueous solutions

Life in hot environments poses certain constraints on the metabolism of thermophilic organisms. Many universal metabolic intermediates are quite labile compounds, and without protection will rapidly decompose at elevated temperatures. Among these are aminoacyl-tRNAs that are necessarily formed upon functioning of the translation apparatus. Aminoacyl-tRNAs are known to be hydrolyzed rapidly even at moderate temperatures under mild alkaline conditions. We studied the thermal stability of phenylalanyl- and alanyl-tRNA in aqueous solutions in order to evaluate a potential threat posed by high temperatures to these components of the translation machinery of thermophiles. Specific second-order rate constants of the aminoacyl-tRNA hydrolysis reaction were determined in the range 20 degrees -80 degrees C. The activation energy of phenylalanyl- and alanyl-tRNA hydrolysis was found to be about 42 and 23 kJ/mol, respectively. The calculated half-lives of aminoacyl-tRNAs at sub-80 degrees C temperatures vary from several seconds to several dozens of seconds at near-neutral pH. The possible mechanisms counteracting the observed thermolability of aminoacyl-tRNAs in vivo are discussed.