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Buffer effects on high affinity [3H]-prazosin binding in brain and spinal cord.

[3H]-Prazosin binding was characterized in cortical and spinal membranes from Fischer 344N and Sprague-Dawley rats. Estimates of Bmax and Kd values were comparable with earlier studies of these regions in the central nervous system (CNS). However, the Kd obtained using Tris buffer system was greater than when HEPES or phosphate buffer was used. These data indicate that high affinity [3H]-prazosin binding in the homogenates of tissue from the CNS is affected critically by buffer selection.

Animals↗

Electron paramagnetic resonance and difference ultraviolet studies of Mn2+ binding to serum transferrin.

Serum transferrin is the mammalian protein whose normal function is to transport ferric ions through the blood among sites of absorption, storage, and utilization. It has two specific metal-binding sites that bind a variety of metal ions in addition to ferric ion. The macroscopic equilibrium constant for the binding of the first equivalent of Mn2+ to apotransferrin has been determined by electron paramagnetic resonance spectroscopy (EPR) to be logKM1 = 4.06 +/- 0.13 at pH 7.4 in 0.1 M N-(2-hydroxyethyl)piperazine-N'-2-ethanesulfonic acid (Hepes). An equilibrium constant for nonspecific binding of Mn2+ to apotransferrin of logKns = 2.93 +/- 0.13 has also been obtained by using EPR. Binding of Mn2+ to apotransferrin and to both C- and N-terminal nonferric transferrin has also been studied by difference UV spectroscopy. The second stepwise macroscopic equilibrium constant for the formation of Mn2Tf is logKM2 = 2.96 +/- 0.13. The site-specific microconstants for Mn2+ binding are logkN = 3.13 +/- 0.09 for the N-terminal site and logkC = 3.80 +/- 0.09 for the C-terminal site. There does not appear to be any significant cooperativity between the two sites with respect to metal binding. An equilibrium model for the speciation of Mn2+ in serum has been developed which estimates that almost 90% of Mn2+ is bound to serum proteins, but only approximately 1% is bound to transferrin. The weak binding of Mn2+ to apotransferrin and the obvious inability of transferrin to compete with albumin indicates that the appearance of Mn-transferrin as a major serum species in vivo must involve oxidation of the metal to form the much more stable Mn(3+)-transferrin complex. The computer model confirms that albumin has a sufficient binding affinity to complex most of the Mn(II) in serum in competition with the common low molecular weight ligands in serum. However, there is insufficient data to rule out the possibility that some other protein, such as alpha 2-macroglobulin, may compete with albumin for Mn(II).

Animals↗

Sweet potato feathery mottle potyvirus (C1 isolate) virion and RNA purification.

A procedure for the purification of a Peruvian isolate (C1) of sweet potato feathery mottle potyvirus (SPFMV) and infective RNA has been developed. The use of Hepes [N-(2-hydroxyethyl)piperazine-N'-2-ethanesulfonic acid] buffer containing urea and sodium EDTA as a base for tissue extraction and virus suspension enabled good yields of virus (35-50 mg/100 g) to be obtained from Nicotiana benthamiana L. Domin. A short RNA isolation procedure yielded infectious RNA, from which ds cDNA of nearly genome size could be obtained. Sweet potato feathery mottle potyvirus, Purification, RNA isolation, cDNA synthesis.

Buffers↗

Small diamines as modifiers for phosphatidylcholine/phosphatidylserine coatings in capillary electrochromatography.

Greater stability of liposome coatings and improved resolution of model steroids in capillary electrochromatography (CEC) were sought by adding small diamines (ethylenediamine, diaminopropane, bis-tris-propane, or N-(2-hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid, HEPES)) to the liposome solution before coating of fused silica capillaries. The phospholipid coatings consisted of 1 mM of 8:2 mol% phosphatidylcholine (PC)/phosphatidylserine (PS) and 5 mM of modifier in buffer solutions (acetate, phosphate, or Tris) at pH 4.0-7.4. The coating was based on a published procedure, and five steroids were used as neutral model analytes in evaluation of the coating. The results showed that under optimal conditions, the small linear diamines increased the packing density of anionic phospholipids, leading to improved separations. In addition, the choice of buffer for the liposome coating and separation appeared to influence the performance of the coatings. While buffers with amino groups take part in the phospholipid bilayer formation, buffers like phosphate may even have negative effect on coating formation. The factors affecting phospholipid coatings with diamines as modifiers are clarified.

Buffers↗

Formation of monofunctional cisplatin-DNA adducts in carbonate buffer.

Carbonate in its various forms is an important component in blood and the cytosol. Since, under conditions that simulate therapy, carbonate reacts with cisplatin to form carbonato complexes, one of which is taken up and/or modified by the cell [C.R. Centerwall, J. Goodisman, D.J. Kerwood, J. Am. Chem. Soc., 127 (2005) 12768-12769], cisplatin-carbonato complexes may be important in the mechanism of action of cisplatin. In this report we study the binding of cisplatin to pBR322 DNA in two different buffers, using gel electrophoresis. In 23.8mM HEPES, N-(2-hydroxyethyl)-piperazine-N'-2-ethanesulfonic acid, 5mM NaCl, pH 7.4 buffer, cisplatin produces aquated species, which react with DNA to unwind supercoiled Form I DNA, increasing its mobility, and reducing the binding of ethidium to DNA. This behavior is consistent with the formation of the well-known intrastrand crosslink on DNA. In 23.8mM carbonate buffer, 5mM NaCl, pH 7.4, cisplatin forms carbonato species that produce DNA-adducts which do not significantly change supercoiling but enhance binding of ethidium to DNA. This behavior is consistent with the formation of a monofunctional cisplatin adduct on DNA. These results show that aquated cisplatin and carbonato complexes of cisplatin produce different types of lesions on DNA and they underscore the importance of carrying out binding studies with cisplatin and DNA using conditions that approximate those found in the cell.

Buffers↗

The HOPE-technique permits Northern blot and microarray analyses in paraffin-embedded tissues.

There is an increasing demand for tissue samples that, after having been used for conventional histologic examination, are also suited for molecular analyses. As to formalin-fixed, paraffin embedded (FFPE) tissue, the latter applications are very limited. The HOPE (Hepes-Glutamic acid buffer mediated Organic solvent Protection Effect) technique comprises a new protection-solution with an organic buffer, with acetone as the only dehydrating agent, and pure paraffin of 52-54 degrees C melting temperature, allowing for all pathologic routine investigations. In contrast to FFPE tissue, the HOPE-technique allows for the application of molecular methods, such as high molecular DNA and RNA isolation, which can be used for PCR and reverse transcription PCR (RT-PCR). In this study, we investigated whether RNA from HOPE-fixed tissue samples is suitable for Northern blot and microarray analyses. RNAs of two HOPE-fixed breast cancer specimens of different histologic grade were used to carry out an array experiment. It turned out that RNA from HOPE-fixed tissue is of high quality and can be successfully used for array experiments. In addition, by detecting GAPDH and high mobility group protein gene B1 (HMGB1)-specific transcripts, we were able to demonstrate that RNA from HOPE-fixed tissue can also be used for Northern blot hybridization.

Blotting, Northern↗

Buffering limits plasma HCO3- dehydration when red blood cell anion exchange is inhibited.

Theory suggests that HCO3- dehydration in the plasma of rainbow trout is limited by both the absence of carbonic anhydrase (CA) activity and the low non-bicarbonate buffer capacity of the plasma (betaplasma). The potential for betaplasma to limit plasma HCO3- dehydration was assessed in rainbow trout in which HCO3- dehydration via the red blood cell (RBC) was inhibited using the anion exchange blocker 4,4'-diisothiocyanostilbene-2,2'-disulphonic acid (DIDS). DIDS administration reduced the rate of RBC HCO3- dehydration by 68-80% for at least 6h, resulting in the elevation of arterial CO2 tension (PaCO2) by 3.07 +/- 0.45 Torr (N = 6). Addition of bovine CA to the circulation of DIDS-treated trout caused PaCO2 to decrease significantly. This effect was increased significantly in rainbow trout in which betaplasma was elevated experimentally by intravascular injection of N-[2-hydroxyethyl]piperazine-N'-[2-ethanesulfonic acid] (HEPES), supporting the hypothesis that CA-catalysed HCO3- dehydration in the plasma of rainbow trout is limited by proton availability.

4,4'-Diisothiocyanostilbene-2,2'-Disulfonic Acid↗

Spectral study on the binding of gadolinium ions with apoovotransferrin.

The binding of Gd3+ ion to apoovotransferrin (apoOTf) was monitored by means of UV difference spectra in 0.01M Hepes, pH 7.4 at 25 degrees C. Used 2-p-toluidinylnaphthalene-6-sulfonate (TNS) as fluorescence probe the conformational changes of protein were studied while gadolinium ions bound to apoOTf. The results show that Gd3+ binding produces peaks at 244 and 294 nm that is the characteristic of binding at the apoOTf specific metal-binding sites. At 244 nm the molar absorptivity of Gd-apoOTf complex is (1.99+/-0.17)x10(4)cm(-1)M(-1). The apparent binding constants for the complexes of Gd3+ with apoovotransferrin are logK(1)=7.61+/-0.14 and logK(2)=4.96+/-0.26. A very large conformational change of apoovotransferrin appears when Gd3+ is bound to the N-terminal binding site. When Gd3+ is bound to C-terminal binding site there is less conformational change.

Animals↗

Site-specific effects of local pH changes in the substantia nigra pars reticulata on flurothyl-induced seizures.

Local cerebral changes of acid-base balance may interfere with neuronal communication. Acidosis enhances and alkalosis suppresses GABAA receptor neurotransmission while there are opposite effects on NMDA receptor transmission. In this study, we determined site-specific effects of acidified solutions of Na-HEPES-artificial cerebrospinal fluid infused into the anterior or posterior area of the substantia nigra pars reticulata (SNR) in rats. Two levels of pH were compared: 6.7 and 7.4. Rats were challenged with flurothyl and the threshold for clonic and tonic-clonic seizures was determined. In the anterior SNR, there were no differences between the effects of the solution with pH 6.7 and 7.4 on flurothyl seizures. In contrast in the posterior SNR, microinfusions with pH 6.7 had proconvulsant effects. The results suggest that local pH changes may have site-specific effects on seizure susceptibility in vivo.

Animals↗

Phosphate buffer and salt medium concentrations affect the inactivation of T4 phage by platinum(II) complexes.

The initial rate of inactivation of T4 phage by solutions of [Pt(NH3)2Cl2], [PtenCl2] and [Pten(H2O)2] (NO3)2 at fixed values of pH is strongly reduced by phosphate buffer, slightly reduced by acetate buffer and apparently not influenced by bis(2-hydroxyethyl)aminotris(hydroxymethyl)methane (BIS-Tris) buffer and HEPES buffer. The phosphate abolishes the antiphage activity of the platinum complexes probably by some sort of complex formation. This together with dimerization reactions qualitatively explains the tailing off of the phage inactivation rate. High concentrations of NaNO3 as the salt medium give increased phage inactivation rates, which are also strongly pH-dependent.

Buffers↗

Culture media and their components differ in their ability to scavenge reactive oxygen species in the plasmid relaxation assay.

OBJECTIVE: To investigate the modulation of DNA-damaging effects of reactive oxygen species by media composition. DESIGN: In vitro study. SETTING: Academic medical center. PATIENT(S): None. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): Plasmid relaxation. RESULT(S): Ham's F-10 medium, 1% Percoll, superoxide dismutase (1, 10, or 100 IU), and synthetic serum substitute did not affect DNA damage by reactive oxygen species and did not have any effect on plasmid DNA damage. Plasmid DNA damage was partially inhibited in the presence of P-1 and human tubal fluid media. Human serum albumin, phenol red, glucose, polyvinyl alcohol, polyvinylpyrrolidone, sucrose, and HEPES also were found to protect DNA from damage. CONCLUSION(S): In vitro fertilization media and their components vary widely in the way they affect DNA damage by reactive oxygen species.

Catalase↗

Structure and catalytic mechanism of a SET domain protein methyltransferase.

Protein lysine methylation by SET domain enzymes regulates chromatin structure, gene silencing, transcriptional activation, plant metabolism, and other processes. The 2.6 A resolution structure of Rubisco large subunit methyltransferase in a pseudo-bisubstrate complex with S-adenosylhomocysteine and a HEPES ion reveals an all-beta architecture for the SET domain embedded within a larger alpha-helical enzyme fold. Conserved regions of the SET domain bind S-adenosylmethionine and substrate lysine at two sites connected by a pore. We propose that methyl transfer is catalyzed by a conserved Tyr at a narrow pore connecting the sites. The cofactor enters by a "back door" on the opposite side of the enzyme from substrate, promoting highly specific protein recognition and allowing addition of multiple methyl groups.

Amino Acid Motifs↗

Histological preparation of developing vestibular otoconia for scanning electron microscopy.

The unique nature of vestibular otoconia as calcium carbonate biominerals makes them particularly susceptible to chemical deformation during histological processing. We fixed and stored otoconia from all three otolith endorgans of embryonic, hatchling and adult Japanese quail in glutaraldehyde containing either phosphate or non-phosphate buffers for varying lengths of time and processed them for scanning electron microscopy. Otoconia from all age groups and otolith endorgans processed in 0.1 M phosphate buffer (pH 7.4) showed abnormal surface morphology when compared to acetone fixed controls. Otoconia processed in 0.1 M sodium cacodylate or HEPES buffered artificial endolymph (pH 7.4) showed normal morphology that was similar to controls. The degree of otoconial deformation was directly related to the time exposed to phosphate buffer. Short duration exposure produced particulate deformations while longer exposures resulted in fused otoconia that formed solid sheets. Otoconial surface deformation and fusing was independent of the glutaraldehyde component of the histological processing. These findings should help vestibular researchers to develop appropriate histological processing protocols in future studies of otoconia.

Acetone↗

Interaction of 11 cisplatin analogues with DNA: characteristic pattern of damage with monofunctional analogues.

In this paper the sequence specificity of DNA damage has been determined for 11 cisplatin analogues. A number of the analogues used in this study have been included in clinical trials. A Taq DNA polymerase linear amplification technique was utilised to ascertain the sequence selectivity of cisplatin analogues damage to DNA. The analogues differed in their ability to damage DNA with cisplatin being the most effective DNA damaging agent followed by (in decreasing order): tetraplatin (tetrachloro(1,2-diaminocyclohexane)platinum(IV) (RR isomer)), cis-dichlorobis(isopropylamine)platinum(II), dichloro(1,2-diaminocyclohexane)platinum(II) (SS isomer), dichloro(1,2-diaminocyclohexane)platinum(II) (RR isomer), cis-bis(cyclohexylamine)dichloroplatinum(II), carboplatin, cis-dichlorobis(isopentylamine)platinum(II), and CHIP (cis-dichloro-trans-dihydroxybis(isopropylamine)platinum(IV)). However, the sequence specificity of these analogues was similar in position and relative intensity of damage. We also provide evidence that platinum(IV) complexes can damage DNA without being reduced to platinum(II). It was found that a 10-fold higher concentration of cisplatin was required to damage DNA in Tris-HCl compared to Hepes buffers. In this paper we have detected a characteristic pattern of damage with monofunctional analogues that could be used to determine the mode of binding of a cisplatin analogue with DNA. The monofunctional analogues tested were chloro(diethylenetriamine)platinum(II) and cis-diamminechloro(1-octylamine)platinum(II) as well as transplatin.

Antineoplastic Agents↗

Contributions of protein disulfide isomerase domains to its chaperone activity.

Protein disulfide isomerase (PDI), a member of the thioredoxin (Trx) superfamily, consists of five consecutive domains, a-b-b'-a'-c. Domain combinations, AB, A'C, B'A'C and AB-C, and hybrids of PDI domains with Trx, Trx-C and Trx-B'A'C, have been constructed and expressed in Escherichia coli to examine the contributions of PDI domains to its enzyme and chaperone activities. All the combination and hybrid products are considerably less active than intact PDI in their enzyme activities. Recombinant products containing C, at low concentrations, inhibit the reactivation of lysozyme in HEPES buffer, while those without C do not. Only the intact PDI molecule and the hybrid molecule, Trx-B'A'C, but to a much lower level, show general chaperone activity in assisting the reactivation of denatured D-glyceraldehyde-3-phosphate dehydrogenase. It is suggested that all domains of PDI contribute to the binding of target protein for its chaperone activity.

Buffers↗

Effect of buffering systems on post-thaw motion characteristics, plasma membrane integrity, and acrosome morphology of buffalo spermatozoa.

This study was carried out to identify the suitable buffer for cryopreservation of buffalo semen. Semen was collected with artificial vagina (42 degrees C) from four buffalo bulls. Split pooled ejaculates (n=5), possessing more than 60% visual sperm motility, were extended at 37 degrees C either in tri-sodium citrate (CITRATE), Tris-citric acid (TCA), Tris-Tes (TEST) or Tris-Hepes (HEPEST). Semen was cooled to 4 degrees C in 2 h, equilibrated at 4 degrees C for 4 h, filled in 0.5 ml straws and frozen in a programmable cell freezer before plunging into liquid nitrogen. Thawing of frozen semen was performed after 24 h at 37 degrees C for 15 s. Sperm motion characteristics, plasma membrane integrity, and acrosome morphology of each semen sample were assessed by using computer-assisted semen analyzer (CASA), hypo-osmotic swelling (HOS) assay, and phase-contrast microscope, respectively. Analysis of variance revealed that percent post-thaw visual motility tended (P=0.07) to be higher in HEPEST (61.0+/-2.9) and lowest in CITRATE (48.0+/-2.5). Computerized motility did not vary due to buffering system. Percent post-thaw linear motility tended (P=0.09) to be higher in TCA (78.2+/-5.5) and lower in TEST (52.0+/-6.9). Circular motility (%) was significantly lower (P<0.05) in TCA (11.6+/-2.8) and higher in TEST (29.8+/-5.6). Curvilinear velocity (microm s(-1)) was lower (P<0.05) in TCA (69.4+/-2.0) than in CITRATE (79.0+/-5.8), TEST (87. 2+/-1.6) and HEPEST (82.6+/-3.0). Lateral head displacement (microm) was lowest (P<0.05) in TCA (1.7+/-0.2) and highest in TEST (3.7+/-0. 6). Plasma membrane integrity and normal acrosomes of buffalo spermatozoa did not differ due to buffering system and averaged 40. 0+/-2.7% and 61.4+/-4.6%, respectively. Based upon lower circular motility, curvilinear velocity, and lateral head displacement, it is concluded that post-thaw quality of buffalo semen can be improved using the Tris-TCA buffering system.

Acrosome↗

Effects of surfactants on the spectral behaviour of calcein (II): a method of evaluation.

The spectral behavior of calcein, a water-soluble self quenching fluorescent marker often used in biomedical analysis, can be considerably affected by the presence of surfactants. With this study we intend to obtain further information on the photophysical properties of calcein, in the presence of surfactants and in the concentration range commonly used to investigate the release of such marker from vesicle dispersions. The experiments were carried out both in water and in a physiological buffer (HEPES, pH 7.5), in the presence of Triton X-100, sodium dodecyl sulphate and centyltrimethylammonium bromide, both below and above their critical micelle concentration (c.m.c.). The obtained results confirm that calcein fluorescence can be affected by the presence of surfactants. Thus, environmental conditions must always be carefully checked for the actual quantitative evaluation of this dye. Furthermore, this study sheds some light on the nature and mechanism of calcein quenching.

Cetrimonium↗

Mexiletine-sensitive membrane electrode for medical application.

Response characteristics of mexiletine-sensitive membrane electrodes based on crown ether and ion-exchanger were examined in a physiological saline in order to find an electrode suitable for determining concentrations of this drug under physiological conditions. Among various crown ethers screened, 4',4"(5")-di-tert-butyldicyclohexano-18-crown6 showed the highest sensitivity to mexiletine in physiological saline containing 0.15 M NaCl and 5 mM 4-(2-hydroxyethyl)-2-piperazineethanesulfonic acid (Hepes) NaOH (pH 7.4). However, the detection limit of 30 microM was 10 times higher than that of 3 microM observed with the electrode based on an ion-exchanger, sodium tetrakis[3,5-bis(2-methoxyhexafluoro-2-propyl)phenyl]borate. Having high selectivity against inorganic cations such as Na+ or K+, the electrode using the ion-exchanger enabled us to determine the level of mexiletine in saliva, the monitoring of which is quite effective for controlling the dose of this drug noninvasively. The mexiletine concentrations determined with the mexiletine electrode compared favourably with those determined by high-performance liquid chromatography which requires an additional procedure to extract mexiletine from saliva.

Anti-Arrhythmia Agents↗