Distance distribution in a dye-linked oligonucleotide determined by time-resolved fluorescence energy transfer

Fluorescence energy transfer is potentially a useful technique for obtaining structural and dynamic information on duplex and branched DNA molecules suitably labeled with donor and acceptor dyes. We have assessed the accuracy and limitations of FET measurements in nucleic acids with respect to the localization of the dyes and the flexibility of the dye-DNA linkages. A nine base-pair duplex oligonucleotide was synthesized with donor and acceptor dyes linked at the opposing 5' termini by alkyl chains. A careful analysis of the fluorescence decay of the donor revealed that the donor-acceptor distance in this molecule was not well defined, but was described by a rather broad distribution. The mean donor-acceptor distance and the distribution of distances have been recovered from the donor decay. Orientational effects on energy transfer have been included in the analysis. The implications of these findings for FET measurements in nucleic acids are considered.

The use of capillary electrophoresis in a micropreparative mode: methods and applications

The ability to collect sufficient quantities of analytes from capillary electrophoresis for subsequent analyses is demonstrated. Fractions collected have been analyzed using the following techniques: capillary electrophoresis, mass spectrometry, and protein sequencing. Fractions can be collected directly into small volumes of buffer or directly onto membrane surfaces. Relevant parameters such as capillary diameter, mass loading, and separation parameters are addressed.

Isoelectric focusing by free solution capillary electrophoresis

A reproducible, quantitative isoelectric focusing method using capillary electrophoresis that exhibits high resolution and linearity over a wide pH gradient was developed. RNase T1 and RNase ba are two proteins that have isoelectric points (pI's) at the two extremes of a pH 3-10 gradient. Site-directed mutants of the former were separated from the wild-type form and pI's determined in the same experiment. The pI's of RNase T1 wild-type, its three mutants, and RNase ba were determined for the first time as 2.9, 3.1, 3.1, 3.3, and 9.0, respectively. The paper describes the protocol for isoelectric focusing by capillary electrophoresis, as well as presenting data describing the linearity, resolution, limits of mass loading, and reproducibility of the method.

Effect of traditional Chinese herbal medicines on the pharmacokinetics of western drugs in Sprague-Dawley rats of different ages (II): Aminophylline-huan shao tan and aminophylline-pu chung yi chi tang

The effect of Chinese herbal medicines (Huan Shao Tan and Pu Chung Yi Chi Tang) and western drugs (sodium phenobarbital and cimetidine) on the serum concentration and pharmacokinetic parameters of theophylline and cytochrome P-450 of Sprague-Dawley (SD) rats of three different ages were examined. The older rats without pretreatment with Chinese herbal medicines and western drugs exhibited higher serum theophylline concentration and lower pharmacokinetic parameters of theophylline than middle-aged and younger rats (P < 0.05), but there was no difference in cytochrome P-450 activity among the three different ages of rats. All rats when pretreated with sodium phenobarbital showed lower serum theophylline concentration and higher pharmacokinetics parameters of theophylline. Also, the activity of cytochrome P-450 was higher (P < 0.05). When cimetidine was pre-administered in SD rats of three age groups, all rats exhibited lower serum theophylline concentration and higher pharmacokinetics parameters (P < 0.05), but the activity of cytochrome P-450 remained unchanged (P > 0.05). The results were opposite to other studies, probably because the dose and dosing intervals were different. No single effect occurred on the younger and middle-aged rats after pretreatment with Huan Shao Tan and Pu Chung Yi Chi Tang: their serum theophylline concentration, pharmacokinetics parameters and cytochrome P-450 activity were the same as the control group. However, the older rats after pretreatment with Huan Shao Tan or Pu Chung Yi Chi Tang showed lower serum theophylline concentration and higher pharmacokinetics parameters than the younger and middle-aged rats pretreated with similar Chinese herbal medicines. This indicates that Huan Shao Tan and Pu Chung Yi Chi Tang may perhaps improve the elimination of theophylline in older rats. This might be attributed to the increase in hepatic blood flow or in liver volume, since the activity of cytochrome P-450 was not affected by the administration of Chinese herbal medicines.

Two-dimensional NMR studies of d(GGTTAATGCGGT).d(ACCGCATTAACC) complexed with the minor groove binding drug SN-6999

The dodecadeoxynucleotide duplex d(GGTTAATGCGGT).d(ACCGCATTAACC) and its 1:1 complex with the minor groove binding drug SN-6999 have been prepared and studied by two-dimensional 1H nuclear magnetic resonance spectroscopy. Complete sequence-specific assignments have been obtained for the free duplex by standard methods. The line widths of the resonances in the complex are greater than those observed for the free duplex, which complicates the assignment process. Extensive use of two-quantum spectroscopy was required to determine the scalar correlations for identifying all of the base proton and most of the 1'H-2'H-2''H spin subsystems for the complex. This permitted unambiguous sequence-specific resonance assignments for the complex, which provides the necessary background for a detailed comparison of the structure of the duplex, with and without bound drug. A series of intermolecular NOEs between drug and DNA were identified, providing sufficient structural constraints to position the drug in the minor groove of the duplex. However, the combination of NOEs observed can only be rationalized by a model wherein the drug binds in the minor groove of the DNA in both orientations relative to the long helix axis and exchanges rapidly between the two orientations. The drug binds primarily in the segment of five consecutive dA-dT base pairs d(T3T4A5A6T7).d(A18T19T20A21A22), but surprisingly strong interactions are found to extend one residue in the 3' direction along each strand to G8 and C23. The observation of intermolecular contacts to residues neighboring the AT-rich region demonstrates that the stabilization of the bis(quaternary ammonium) heterocycle family of AT-specific, minor groove binding drugs is not based exclusively on interactions with dA-dT base pairs.

Locating essential Escherichia coli genes by using mini-Tn10 transposons: the pdxJ operon

The mini-Tn10 transposon (delta 16 delta 17Tn10) confers tetracycline resistance. When inserted between a gene and its promoter, it blocks transcription and prevents expression of that gene. Tetracycline in the medium induces divergent transcription of the tetA and tetR genes within the transposon, and this transcription extends beyond the transposon in both directions into the bacterial genes. If the mini-Tn10 inserts between an essential bacterial gene and its promoter, the insertion mutation can cause conditional growth which is dependent on the presence of tetracycline. Two essential genes in adjacent operons of Escherichia coli have been detected by screening for tetracycline dependence among tetracycline-resistant insertion mutants. These essential genes are the era gene in the rnc operon and the dpj gene in the adjacent pdxJ operon. The pdxJ operon has not been described previously. It consists of two genes, pdxJ and dpj. Whereas the dpj gene is essential for E. coli growth in all media tested, pdxJ is not essential. The pdxJ gene encodes a protein required in the biosynthesis of pyridoxine (vitamin B6).

Conformational studies of the duplex d-(CCAAAAATTTCC).d-(GGAAATTTTTGG) containing a (dA)5 tract using two-dimensional 1H-n.m.r. spectroscopy

A variety of two-dimensional nuclear magnetic resonance (n.m.r.) techniques were utilized for structural studies of the dodecadeoxy-nucleotide duplex d-(CCAAAAATTTCC).d-(GGAAATTTTTGG). Overall, the duplex was found to adopt a conformation of the B-DNA type. Direct measurement of 1H-1H coupling constants of the deoxyribose rings and comparison of nuclear Overhauser effects (NOEs) involving characteristic intra- and inter-nucleotide proton-proton connectivities indicate that the sugar rings are all in predominantly C2'-endo/S-type conformation. The appearance of NOEs between adenine 2H and sugar l'H resonances indicates a narrowing of the minor groove at the 3' end of the (dA)n tracts. Several lines of evidence indicate that a conformational change in the DNA duplex is introduced by the (dA)5 tract, in support of the junction model for curved DNA. The results are compared with previous structural studies of the evidence for curvature in duplex DNA containing (dA)n tracts.

Reduced glutathione, superoxide dismutase contents and malondialdehyde formation in platelets from uremic patients: relation to plasma and platelet zinc

Platelet-reduced glutathione (GSH), superoxide dismutase (SOD) and zinc content as well as malondialdehyde (MDA) formation were studied in 55 healthy volunteers as controls and 49 patients with chronic renal failure. Uremic patients had a significantly lower GSH and SOD content as well as an abnormal MDA formation in their platelets. Their plasma zinc level was sharply below the normal value, but their platelet zinc content was similar to that of normal controls. We also found that the plasma zinc and platelet zinc level was positively correlated to the platelet GSH content in normal controls and uremic patients. Therefore, the results suggest that in uremic patients the decrease in platelet antioxidant agents (GSH and SOD) may be partially related to their low plasma zinc level.

Factors affecting survival of hemodialysis patients utilizing urea kinetic modeling. A critical appraisal of shortening dialysis times

The objective of this study was to analyze risk factors affecting mortality rates (MR) in hemodialysis patients undergoing shortened dialysis time who were regularly kinetically modeled. Over a 14-month period, 180 in-center hemodialysis patients, 54% male, 46% female, 57% Black, 39% Caucasian, and 4% Hispanic, treated with rapid high efficiency dialysis (RHED = 2-3 h, 3 times/week) and conventional dialysis (3-4 h, 3 times/week) were studied. Median patient age was 56.7 years (16-84 years) and dialysis care ranged from 6 months to 18 years (mean +/- SD = 4.0 +/- 4.2 years). The patients underwent monthly urea kinetic modeling. The dialysis prescription was based upon normalizing Kt/V between 0.8 and 1.2 and the protein catabolic rate (PCRn) between 0.9 and 1.1. Thirty-three percent of the patients received recombinant human erythropoietin (r-HuEPO). The effects of various covariates, including primary diagnosis, post/predialysis BUN ratios, creatinine, albumin, calcium, phosphate, cholesterol, hemoglobin, r-HuEPO, Kt/V, and PCRn were analyzed using analysis of variance, chi 2 and linear discriminant function (DF) statistical methods. Several significant factors emerged as influencing outcome. The DF analysis produced a highly statistically significant (p < 0.0001) model to predict mortality based upon certain laboratory and dialysis parameters. Further, the linear DF correctly predicted mortality rate in 86% of cases. The results of the analysis revealed an overall mortality rate of 15.6%; hospitalization rates (HR) were 1.4 +/- 1.8 times/year. Length of dialysis time, i.e., dialysis times between 2 and 4 h, when adjusted for Kt/V has no correlation with MR or HR. Variables associated with survival were higher post/predialysis BUN ratios, normal Kt/V (0.8-1.2), normal albumin levels (> 3.5 g/dl), higher postdialysis BUN, creatinine, and cholesterol levels, and use of r-HuEPO. The use of r-HuEPO when analyzed by DF significantly improved MR, 8.3% as opposed to 19.2%. It is concluded that urea kinetic modeling permits shortening dialysis times without affecting mortality or hospitalization rates, and that low postdialysis BUN, post/predialysis BUN ratios, creatinine, and albumin values are correlated with a lower chance of survival.

[Photic maculopathy by low energy laser beam. A case report]

The authors report a case of photic maculopathy that developed in a 30-year-old laboratory worker after repeated, consecutive exposure to low energy He-Ne laser. Pigmented foveal change and a small central scotoma in the right eye with window defect on fluorescein angiography characterized this maculopathy. Photochemical damage is considered to be the cause of the maculopathy.

Studies on the photochemical and photocytotoxic properties of the new PDT photosensitizer aluminum sulfonated phthalocyanine

The properties of photosensitization of sulfonated aluminum phthalocyanine (ALSPC), a new photosensitizer of potential use in cancer photodynamic therapy (PDT) was studied on both the molecular and cellular levels. The mechanism of ALSPC photosensitization on the molecular level was investigated by testing its efficiency of singlet oxygen (1O2) production, using the method of tryptophan degradation and that of ESR spectroscopy and observing the enhancing effect of D2O and the quenching effect of NaN3. Results of all these experiments confirmed the important role of the Type II or 1O2 mechanism in ALSPC photosensitization. In our in-vitro experiments, ALSPC's incorporation into cells and its photocytotoxic effect were investigated on a human liver cancer cell line. The cell incorporation was illustrated by the laser-excited fluorescence spectra emitted both from cell homogenate and cell monolayers incubated with ALSPC aqueous solution. The position of fluorescence peak observed, implied that ALSPC exists in the cells mainly as monomers. The efficiency of cell killing of ALSPC photosensitization was estimated by counting surviving cells with the method of trypan blue staining and by the method of radioisotope labelling. Experiments using the latter method also showed DNA damage caused by ALSPC photosensitization.

[Acetylcholine receptor antibody titer, sensitivity to curare electromyogram and disease severity in myasthenia gravis]

All of 39 rabbits immunized with acetylcholine receptors invariably formed anti-AChR Abs and some of them developed muscular weakness or flaccid paralysis. Pharmacological, physiological and ultrastructural studies indicated that the pathology of experimental autoimmune myasthenia gravis in rabbits resembled that of human myasthenia gravis. The titer of anti-AChR Abs correlated poorly with disease severity and did not simply predicted the muscular weakness. The results ruled out the possibility that antigenic modulation of AChR was sufficient to account for the induction of myasthenia gravis. There was a close relationship between the sensitivity to curare and disease severity, but only part of immunized animals appeared electromyogram change. This led us to conclude that serum anti-AChR concentration would not be the single pathological factor in myasthenia gravis and disease severity may correlate with amount of normal AChR.

Effect of traditional Chinese herbal medicines on the pharmacokinetics of western drugs in SD rats of different ages. I. Aminophylline-Tin chuan Tang and aminophylline-Hsiao Ching Long Tang

The effect of the traditional Chinese herbal medicines (Tin Chuan Tang and Hsiao Ching Long Tang) on the serum concentrations and pharmacokinetics of aminophylline was examined in three different ages of SD rats. Each traditional Chinese herbal medicine was orally preadministered to SD rats for one week and then aminophylline was administered intravenously. The serum concentrations and pharmacokinetic parameters of theophylline were estimated by a two-compartment open model. The liver isolated after the last blood sampling was homogenized and the activity of hepatic cytochrome p-450 was determined. Significant difference was found in some pharmacokinetic parameters of theophylline such as K10, t 1/2, Cl and Vd for three different ages of SD rats without pretreatment with Chinese herbal drugs (p less than 0.05). However, pretreatment with Tin Chuan Tang or Hsiao Ching Long Tang did not affect the pharmacokinetic parameters of theophylline in three different ages of SD rats (p greater than 0.05). We also found that there was no correlation between age and activity of cytochrome p-450 of SD rats (p greater than 0.05). The decline in some pharmacokinetic parameters of theophylline in the elderly rats perhaps might be attributed to the decrease in hepatic blood flow and liver volume. It is concluded that there was no drug interaction between theophylline and Tin Chuan Tang or Hsiao Ching Long Tang in the different ages of SD rats.

Two-dimensional 1H NMR studies of synthetic immobile Holliday junctions

Two 32 base pair, four-arm immobile Holliday junctions have been prepared and studied by two-dimensional 1H nuclear magnetic resonance (NMR) spectroscopy. Two-quantum spectroscopy provides scalar (through bond) correlations for the 1'H, 2'H, and 2''H resonances of the deoxyribose sugar rings and the nonlabile cytosine and thymine base protons. Assignments in the deoxyribose sugars are extended to the 3'H resonances principally from relayed connectivities in total correlation spectra. Severe overlap of resonances in the standard regions of two-dimensional nuclear Overhauser enhancement (NOE) spectra necessitated the use of a unique approach for obtaining sequence-specific assignments of duplex DNA, wherein all possible NOE connectivities in the spectra are analyzed. These studies of 64-residue structures represent a substantial step forward with respect to the size of oligonucleotide for which virtually complete assignments are obtained. The assignments form the critical background for the detailed analysis of Holliday junction structure and dynamics that is required to address key issues in understanding the role of Holliday junctions in genetic recombination and repair.

Renal excretion of citrate in patients with chronic renal failure or nephrolithiasis

Using a specific citrate lyase method, renal excretion of citrate was studied in 32 normal Chinese males, 30 nondialysed uremic male patients and 35 male subjects who had a history of nephrolithiasis. Patients with uremia or nephrolithiasis were found to have a lower urinary citrate excretion. Tubular reabsorption of citrate was markedly decreased in uremic patients, but in stone patients, the increased renal tubular reabsorption of citrate was only found in patients with hypocitraturia, whose renal citrate excretion was below 650 mumol/day and whose urinary magnesium was also low. Hypocitraturia was found in 45% (16/35) of the patients with renal stones whether their filtered load of citrate was normal or subnormal. Urinary citrate excretion was correlated with renal creatinine clearance in both normal subjects and in patients with renal stones or chronic renal failure. However, urinary phosphate correlating with urinary citrate was only found in normal subjects and in patients with kidney stones. In normal subjects, we found a positive correlation between urinary citrate and phosphate, but in stone patients, we found a negative correlation. Hypercalciuria and hyperoxalaturia were noted in some stone formers, who had, moreover, a lower urinary citrate and ascorbate excretion level. Mean urinary ascorbate excretion in patients with renal stones was markedly below that in normal subjects. Thus, we suggest that low urinary citrate excretion may be prevalent in patients with renal stones or chronic renal failure, and that hypocitraturia can be found in some stone formers, whose tubular reabsorption of citrate may be increased.

[Clinical correlation of anti-receptor antibody titer, sensitivity to curare and electromyographic changes in experimental autoimmune myasthenia gravis]

Experimental autoimmune myasthenia gravis (EAMG) was studied in 39 rabbits which were repeatedly immunized with purified membrane-bound Torpedo (Nacine timilei) acetylcholine receptor (N-AchR). These rabbits invariably formed anti-AChR antibodies and some of them developed muscular weakness or flaccid paralysis. Pharmacological, physiological and ultrastructural studies showed that the pathological features of EAMG in rabbits closely resembled those of human myasthenia gravis. Antibody titer to AChR of the rabbit sera was determined with ELISA. In some of the rabbits, a rise in antibody Level occurred without appearance of weakness, while it is still likely that AChR antibody could be necessary for the induction of neuromuscular blockage. The sensitivity to curare was found to correlates closely with the severity of the disease. Typical electromyographic changes were found only in some of the EAMG rabbits with these studies. It was considered that anti-AChR concentration would not be the single pathological factor in EAMG.

Renal excretion of oxalate in patients with chronic renal failure or nephrolithiasis

This study was carried out in order to investigate renal oxalate excretion in a group of normal subjects (n = 40), a group of patients with uremia (n = 52) and a group with nephrolithiasis (n = 34). We found that the mean concentrations of oxalate in the 24-hour urine specimens of both patient groups were below the normal range. Although the renal creatinine clearance (CCR) was significantly decreased in some stone patients (n = 14), decreased renal oxalate clearance was noted only in those patients with severe renal failure. Thus, plasma oxalate was found to be elevated only in patients with chronic renal failure (mean +/- SD, 49.7 +/- 12.4 mumol/l), while the normal value was 17.0 +/- 6.7 mumol/l. The mean tubular excretion fraction of oxalate was also found to increase markedly in uremia with a mean of 26.3 +/- 17.3% (in normal subjects, 11.7 +/- 7.5%), but their mean daily urinary excretion of oxalate decreased to 63.2 mumol/day (mean value of 232.6 mumol/day in normal subjects). A positive correlation was observed between oxalate and creatinine, and between oxalate and calcium excretion, which was not found in normal subjects or patients with kidney stones. In nephrolithiasic patients, the daily excretion of oxalate, calcium and phosphate had no discernible increment and the mean excretory ratio of oxalate, calcium or phosphate to creatinine was all within normal limits. But when the CCR of stone patients was below 80 ml/min, their daily excretion of oxalate and calcium decreased significantly (p less than 0.01) and the excretory ratio of phosphate to creatinine markedly increased.(ABSTRACT TRUNCATED AT 250 WORDS)

Renal excretion of zinc in patients with chronic uremia

Though uremic patients have been reported to have subnormal zinc levels in plasma and an abnormal zinc metabolism, data on their renal excretion of zinc are still unavailable. In our study, 55 nondialyzed uremic patients had a markedly lower concentration of zinc in plasma and a lower urinary zinc excretion. They had a higher excretory fraction of zinc in the renal tubules and a higher ratio of zinc to creatinine excretion than normal subjects. We found that the total daily excretion of zinc, calcium, phosphate and ammonia was reduced, and that the ratio of calcium or ammonia to creatinine excretion decreased in uremic patients. Urinary zinc excretion was correlated with renal creatinine clearance (r = 0.50, p less than 0.001) in both normal subjects and uremic patients, but ammonia excretion was correlated with zinc excretion in normal subjects only. In uremia, urinary zinc excretion was correlated with urinary calcium (r = 0.55, p less than 0.001) and urinary phosphate excretion (r = 0.30, p less than 0.05). We conclude that the increased ratio of zinc to creatinine excretion and the excretory fraction of zinc in the renal tubules of uremic patients may increase the urinary zinc excretion, but a severe diminution of the glomerular filtered load of zinc may be the major factor in decreasing the urinary zinc excretion in uremia.

Expression and characterization of RNase III and Era proteins. Products of the rnc operon of Escherichia coli

The synthesis rates of ribonuclease III (RNase III) and Era proteins are relatively low, and expression of the era gene is translationally coupled with expression of the rnc gene. Expression of both genes is negatively controlled by RNase III itself. We have constructed plasmids that overproduce RNase III and/or Era proteins under the control of the lambda PL promoter. A plasmid with the rnc gene under PL control expresses RNase III at levels greater than 40% of total cellular protein. Another plasmid with the era gene under PL control and a modified translation-initiation signal produces up to 80% of total cell protein as Era. Each protein has been purified using simple and rapid procedures. Purified RNase III protein specifically processes mRNA transcripts containing known RNase III sites. The purified Era protein binds GDP and GTP and has GTPase activity. Kinetic analysis shows that one molecule of GTP or GDP is bound/Era peptide with a Kd of 5.5 microM for GTP binding and 1.0 microM for GDP binding. The Km of the Era GTPase is 9.0 microM, and the maximum catalyzed rate of GTP hydrolyzed/min/mol of Era protein at 37 degrees C is 9.8 mmol.

Risk factors for stroke in rural areas of the People's Republic of China: results of a case-control study

A case-control study on stroke was carried out in 1985 in conjunction with a prevalence survey on neurologic disorders in 22 rural communities of the People's Republic of China. 585 cases of stroke, detected from the survey, together with an equal number of matched controls were investigated. The statistically significant factors associated with stroke in this study were: hypertension (history, findings at examination); high salt intake; family member(s) with cerebrovascular disease and/or hypertension; heart disease (history, abnormal findings at examination); history of transient ischemic attacks, and arteriosclerotic funduscopic findings. These factors were analyzed separately for hemorrhagic and ischemic strokes.

Interferometric measurements of the thickness of nematic liquid crystal films with a free surface

We demonstrate two interferometric methods for measuring the thickness of nematic liquid crystal films with a free surface. The accuracy of either method is better than +/-1 %.

Autoregulation of RNase III operon by mRNA processing

RNase III has been implicated in the control of gene expression by the processing of mRNA. We have found that the rnc operon is autoregulated; rnc- mutant strains oversynthesize the operon's mRNA and protein products. A site in the 5'-noncoding region of the operon's message is cleaved by RNase III. This site-specific cleavage appears to be the initial step in the functional inactivation of the message, since the half-life of the cut message is dramatically shorter than that of the uncut message.