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Different possibilities of H-bonds formation for formamide-water complexes and dimers of formamide were studied. Potential energy maps were calculated for di-, tri- and tetrapeptides. The maps provide necessary data to explain the relative stability of different oligopeptide conformers and Ramachandran maps for peptides.
Polyadenylate sequences have been found in numerous RNA with messenger function, and in several viruses in which the genome is its own messenger. With rabies virus we observed a fixation of viral RNA on Sepharose poly(U) column in the mRNA region (8-25S) and in the double stranded RNA region (25-35S). These percentages of fixation are very low compared to those of VSV in the same regions, but they are significant compared to the uninfected cells and to Lumbo RNA fixation. In order to determine the nature of the RNA bound to poly(U)-sepharose, fractions of the region 8-25S and 25-35S obtained after elution with formamide were centrifuged through a sucrose gradient. We found in the 8-25S region an RNA profile which was identical to the initial profile of this region. In contrast, the 25-35S region exhibited a heterogenous profile which looked like the total virus RNA profile obtained from infected cells. This may be due to the presence of double-stranded RNA in this region which is partially adsorbed on poly(U) and denatured by formamide in RNA molecules of genome and mRNA size. We conclude from our results that the low percentage of fixation of rabies mRNA on poly(U)-sepharose columns could mean either that a small number of molecules are polyadenylated or that a large number exhibit poly(A) tracts too short to be retained by the poly(U).
Chicken globin mRNA has been purified and partially characterized. Globin-specific sequences are found primarily as 9 S RNA, but also are found with ribosomal RNA, preferentially the 28 S moiety. The chicken globin mRNA preparation has been translated in the wheat germ and Krebs ascites cell-free systems. The products have been identified by sodium dodecyl sulfate-gel electrophoresis as the alpha- and beta-globin polypeptides. The globin mRNA is resolved into two asymmetric peaks by polyacrylamide gel electrophoresis in 98% formamide. The minor rapidly migrating peak consists primarily of alpha message while the major slowly migrating peak contains a mixture of alpha and beta messages. The synthesis of cDNA has been optimized and the products analyzed by polyacrylamide gel electrophoresis in 98% formamide. The products consist primarily of full copy transcripts that can be resolved into three discrete species.
Electron microscopy RNA/RNA in situ hybridization was adjusted to Pleurodeles lampbrush chromosomes. The cRNA probe used was synthesized from genomic DNA sequences which were proven to be moderately repetitive. Preembedding hybridization was performed on lampbrush chromosome preparations, and several fixation and hybridization conditions were tested. Paraformaldehyde and glutaraldehyde were used as fixatives at various concentrations and durations. Hybridization was then performed with or without formamide for various times of incubation. The best results were obtained when hybridization was carried out for 4 h at 42 degrees C in the presence of formamide, with lampbrush chromosomes having been previously fixed overnight in a mixture of paraformaldehyde/glutaraldehyde. Due to the excellent preservation of the ultrastructure and specificity of the signal obtained under these conditions, we were able to demonstrate, at the ultrastructural level, that such RNA expression occurs in two types of lampbrush loop ribonucleoprotein matrices showing a different morphology of their transcripts. Furthermore, a different mapping of the same sequence along the loop DNA axes is strongly suggested by a different labeling distribution in these loops.
The flavin-containing monooxygenases (FMO) are a family of enzymes that contain putative FAD- and NADPH-binding domains within the first 200 residues of their N termini. The cDNAs encoding these enzymes contain an area of relatively high identity over the 5' half of the coding region. Rabbit genomic DNA was probed under low stringency conditions, with a mixture of 5' cDNA fragments encoding rabbit FMO1, FMO2, or FMO5. Bands associated specifically with FMO1, FMO2, or FMO5 were resolved by analysis at high stringency with individual probes. Several bands were detected that could not be assigned to FMO1, FMO2, or FMO5. The behavior of the 5' probes at low versus high stringency was used to facilitate the isolation of cDNAs corresponding to the unknown DNA bands. A cDNA library was constructed from rabbit liver mRNA and screened under low stringency hybridization conditions (30 degrees C, 50% formamide, 1 x SSC, 0.1% SDS) with the mixture of 5' FMO1, FMO2, and FMO5 cDNA probes. A total of 157 clones was detected. Of these, 117 clones remained under high stringency hybridization conditions (65 degrees C, 50% formamide, 0.1 x SSC, 0.1% SDS) and were identified as FMO1 (95 clones) or FMO5 (22 clones). Of the 40 remaining clones, 36 were characterized by sequence analysis as encoding FMO3, previously identified at the protein level by Ozols (Ozols, J. (1991) Arch. Biochem. Biophys. 290, 103-115) as a second rabbit liver FMO. Four clones were shown to encode an FMO not previously described for the rabbit, FMO4. No clones encoding FMO2 were isolated from the liver library. Sequence analysis revealed that FMO3 and FMO4 are 56% identical, and analysis of genomic DNA indicated that each is encoded by a single gene. Message distribution was tissue-, species-, and form-specific. The properties of FMO3 cDNA expressed in Escherichia coli were found to be more similar to those of FMO1 than FMO2, but to differ significantly from both. Rabbit genomic DNA was probed under conditions of low stringency with a mixture of 5' cDNA fragments encoding all five FMO forms and produced results consistent with the possibility of one additional FMO.
Specific complementary DNAs (cDNAs) for the messenger RNAs coding for sheep alpha-, betaA-, betaB-, betaC-, and gamma-globins were prepared by thermal denaturation of heterologous hybrids (e.g. alphabetaB-cDNA-alphagamma-mRNA) followed by hydroxylapatite chromatography. Each cDNA represented a nearly full-length copy of its globin mRNA complement as determined by electrophoretic analysis in polyacrylamide gels containing 98% formamide. The purity of each cDNA fraction was estimated by hybridization analysis and thermal denaturation. The beta- and gamma-cDNAs contained 5 to 20% contaminating alpha-cDNA while the alpha-cDNA was 25 to 30% contaminated with non-alpha-cDNA. The melting temperatures (Tm) of homologous duplexes between each non-alpha chain cDNA and its mRNA complement ranged from 69.5-71.5 degrees in 50% formamide while alpha-alpha duplexes melted with a Tm of 75-76 degrees. The Tm values of heterologous duplexes formed between each non-alpha-cDNA and the various globin mRNAs (e.g. betaB-cDNA-Hb C mRNA) ranged between 64.5 degrees and 68 degrees and thus were only 1.5-5.0degrees below that of homologous duplexes. These results suggest that the nucleotide sequence divergence among the various non-alpha-mRNAs (or cDNAs) is not greatly different from the minimum predicted from the amino acid sequence differences of the corresponding globins. When annealing reactions were performed above the Tm of the heterologous hybrids (68 degrees), each non-alpha-cDNA hybridized only to its own complementary mRNA. Thus the purified cDNAs provide molecular probes for the quantitation of alpha-, beta-, and gamma-globin-specific nucleotide sequences.
We have characterized the selectivity filter of the water channel aquaporin-1 (AQP1) of proximal straight tubules (PST), as an equivalent cylindrical structure with a diameter of approximately 4.5 A, where water molecules single file. We report here efforts to evaluate its length. PST were dissected from rabbit kidneys, held with pipettes in a chamber bathed in a buffered mannitol isosmotic solution (MBS, 295 mOsm/kg). Changes in tubule cell volume with time (dV/Adt), were monitored, on line, with an inverted microscope, a TV camera and an image processor. Osmotic permeability coefficients, Pos, and reflection coefficients (sigma s) were measured with several solutes: mannitol (M), raffinose (R), sucrose (S), glycerol (G), acetamide (A) and urea (U). For this purpose PST were suddenly exposed (in approximately 80 ms and for 20 s) to a hyperosmolality step (delta Cs) achieved by adding to MBS a delta Cs of 35 mOsm/kg of either R, S, M, G, A or U. Cells shrunk within 500 ms of t = 0 to their osmometric volume and remained shrunk for the 20 s of the delta Cs. Pos was measured from the shrinking curves; Pos = 3000 +/- 25 microns/s with either R, S, M, G, A or U. This procedure also allowed to calculate sigma s; sigma s = 1.00 for R, S, M, G, A and U, indicating that these solutes do not penetrate the water channel. In contrast, the shrinking curves produced by a delta Cs = 35 mOsm/kg formamide (F) were 1/5th to 1/6th slower and smaller (subosmometric) than those produced by a delta Cs = 35 mOsm/kg of R, S, M, G, A or U. Furthermore, with F, cells did not remain shrunk. They recovered their original volume within 3 s. Pos (measured with F) is denoted as Pos*; Pos* = 480 +/- 30 microns/s. sigma s, formamide (denoted sigma sp) = 0.16 +/- 0.01. Use of sigma sp and Pos* values in Hill's equations for the bimodal theory of osmosis leads to n = 2-3, n being the number of water molecules single filing within the channel selectivity filter, whose length must lie within 6 to 9 A, a value lower than previous values calculated from the Pos/Pd* ratio.
The author demonstrated column and paper chromatographically that no or very little amylose is extracted when using HAMPEL's method for the colorimetric determination of starch damage ("amylose number"). The actually extracted substances are mainly other starch components which form a violet colour on addition of a dilute iodine solution. Further starch components which form a violet colour on addition of a dilute iodine solution are extracted by rewashing with the different components of HAMPEL's solvent mixture. The most distinct results were obtained with distilled water. It is suggested to rewash the filter residue with distilled water to extract all the damaged starch and to use the combined extracts for the determination. In consideration of the fact that HAMPEL's solvent mixture extracts not only amylose from the damaged starch, the term of "amylose number" should be rejected and replaced by the term of formamide ammonium sulphate sulphosalicylic acid (FAS) method or formamide sodium sulphate sulphosalicylic acid (FNS) method.
Barnhart, Benjamin J. (Johns Hopkins University School of Hygiene and Public Health, Baltimore, Md.). Residual activity of thermally denatured transforming deoxyribonucleic acid from Haemophilus influenzae. J. Bacteriol. 89:1271-1279. 1965.-The level of residual transforming activity of heated deoxyribonucleic acid (DNA) (i.e., 1 to a few per cent of native DNA-transforming activity) was found to be independent of the heating and quenching temperatures and less susceptible than native or renatured DNA to heat inactivation upon prolonged heating above or below the critical melting temperature. Similar dose-response curves were obtained for inactivation by formamide of native and renatured DNA, but the residual-active material was much more resistant. Heating DNA above the T(m) in the presence of 1% formaldehyde resulted in a level of residual activity 4 logs lower than that obtained without formaldehyde. Residual-active material was not inactivated by Escherichia coli phosphodiesterase, but it was susceptible to snake venom phosphodiesterase. A new genetic marker was induced in heated-quenched DNA but not in purified residual-active material following nitrous acid treatment. Residual activity was found to be less susceptible to ultraviolet inactivation and to band at a higher density region in CsCl than native DNA. In conclusion, it is suggested that the residual-active material is a structure formed by intrastrand hydrogen bonding of the separated units of heated-quenched DNA. Such a configuration would result in at least a partially double-stranded structure, which is probably the essential characteristic of the residual-active material endowing it with biological activity.
Single and combination chemotherapy was evaluated for antitumor activity against N-[4-(5-nitro-2-furyl)-2-thiazolyl] formamide (FANFT)-induced bladder carcinoma in syngeneic mice. Two hundred fifty C3H/He mice having ingested FANFT for 10 months were randomly divided into groups of 30, and the following regimens initiated: cyclophosphamide (Cy), cis-diam-minedichloroplatinum (cis-Pt-II), dactinomycin, adriamycin, Cy plus cis-Pt-II, Cy plus 5-fluorouracil, and Cy plus adriamycin. The drugs were administered for 3 weeks. Each regimen was capable of producing a significant reduction in the mean bladder weight (MBW) when compared to a groups not receiving therapy (108.3 mg). Adriamycin (MBW equal 69.5), dactinomycin (49.6), and cyclophosphamide (42.9) were the best single agents, but the greatest inhibition of tumor growth was achieved by the combination of cyclophosphamide with 5-fluorouracil (38.3) or adriamycin (37.3). These combination chemotherapeutic regimens were able to effect a significant reduction in the number of bladders with Stage C tumors. It is hoped that information gained from this new animal model which allows evaluation of many antitumor drugs within a relatively short period of time will lead to therapeutic trials in patients with locally advanced or metastatic bladder cancer.
The effect of the three different surfactants, sodium dodecyl sulfate (SDS), diethylhexyl sodium sulfosuccinate (AOT), and taurodexycholic acid sodium salt (STDC) on the nonaqueous capillary electrophoretic separations of hydrophobic compounds were compared with formamide containing 20 mM K2HPO4 as electrolyte solvent. Separations of all selected uncharged hydrophobic compounds, e.g., p-arylacetophones were shown to be strongly dependent on the kind of surfactant. The electrolyte containing 180 mM SDS provided the best result for the selected samples.
Host-guest interactions can be modelled as a non-bonding recognition process using long-range electrostatic forces. By using molecular isopotential maps the differences between the methotrexate-dihydrofolate reductase and folate-dihydrofolate reductase complexes can be predicted. By extending the technique to molecule-molecule docking the interaction of formamide with the crown ether 18-crown-6 can be simulated with reasonable accuracy. The closely related problem of predicting the separation of enantiomers of chiral molecules by chromatography has been attempted with encouraging results. A preliminary report is presented on the progress being made towards a better model for simulating stacking arrangement of pi systems by charge distribution.
Among various mutation detection methods, constant denaturant capillary electrophoresis (CDCE) is one of the most common techniques for rapid identification of known or unknown mutations. In this report, a CDCE analysis method with homemade linear polyacrylamide (LPA) kit was developed on ABI 310 genetic analyzer, the effect and relationship of various denaturing factors in CDCE analysis were investigated and K-ras gene mutations of 31 coloerctal cancer patients were detected. Results indicate that, with the increase of chemical danaturant concentration, the optimum temperature was lowered, and when the concentration of urea (formamide) was higher than 7 M (40%), the homoduplex and heteroduplex of mutant samples were separated with difficulty. Detection results of K-ras gene in colorectal samples indicated that mutations were present in eight (26%) of 31 patients; most mutations were localized in codon 12, which is thought to be a critical step and plays an important role in human colorectal carcinogenesisas.
We studied the effects of deoxyribonucleases on the detection of 5-bromo-2-deoxyuridine (BrdUrd) by anti-BrdUrd monoclonal antibodies (mAbs). After DNase I treatment, BrdUrd was detected in cells fixed on slides with the anti-BrdUrd mAbs, B44 and BMC9318. The level of detection related to the degree of DNA digestion. DNA digestion of 25-75% resulted in levels of staining comparable to control preparations in which DNA was denatured by heating with formamide. Staining with the mAbs of DNase I-treated cells was abolished with S1 nuclease, a single-stranded DNA-specific nuclease. When exonuclease III was used after DNase I treatment, the staining intensity of cells fixed on slides increased, and BrdUrd could be detected in suspended cells by flow cytometry. Since this enzymatic method leading to the detection of BrdUrd does not involve cell loss, or destruction of either cellular morphology or epitope reactivity, as occurs with traditional DNA denaturation procedures, it is useful for kinetic studies of phenotypically mixed populations. Furthermore, staining with anti-BrdUrd mAb of cells treated with exonuclease III offers a simple approach to quantitation of apoptotic cells, in which an endogenous endonuclease is activated.
A series of analogues of N,N-di-n-propyldopamine (DPDA) in which the 3-hydroxyl group was replaced by bioisosteric groups was prepared and evaluated for D1- and D2-receptor affinity. The 3-methane-sulfonamide analogue (18) had a higher affinity for the D2 receptor than DPDA and was more selective for the D2 receptor. The 3-formamide derivative (15) also retained significant D2 affinity. Both of these compounds demonstrated in vivo cardiovascular and renal profiles in an anesthetized rat model that were consistent with selective D2-receptor agonism.
A method for DNA sequencing that combines limited chemical degradation of 3'-fluorescent-labeled DNA with densitometric analysis using an automatic sequencer is presented. The DNA sequence is determined in a single electrophoretic lane by monitoring the intensities of bands representing products of cleavage at the four bases obtained by solvolysis in hot aqueous piperidine (10%) followed by treatment with hot formamide. An application of the method for the detection of point mutations is reported.
Liposomes that have been labeled externally with a DNA oligomer are used in a capillary-migration, sandwich-hybridization assay for specific DNA target sequences. The liposomes are used in a DNA detection scheme that produces visually observable results in 10 min. The preparation and covalent attachment of a thiol-activated 22-base oligomer to the external surface of dye-containing liposomes is described, and the specificity of the assay toward perfectly complementary target DNA is demonstrated. Several characteristics of DNA-tagged liposomes that allow the use of increased stringency during hybridization are evaluated. These include the effect of temperature, formamide, and salt concentration on both the sandwich-hybridization assay and the liposomes themselves. The effects of several components of a common hybridization solution are determined with regard to both assay performance and liposome stability. Using a solution of 0.02% sodium dodecyl sulfate in 3X standard saline citrate, a visual detection limit of 200 amol of target DNA was obtained.
The goal of this research was to examine the developmental effects on zebrafish embryos (Brachydanio rerio) when cryoprotectants were directly microinjected into the yolk. Our objectives were to: (i) determine the final concentration of propylene glycol (PG) and dimethyl sulfoxide (Me(2)SO) that the embryos could tolerate without causing teratogenic effects; (ii) determine if the toxicity of Me(2)SO could be reduced by the simultaneous presence of various proportions of amides; and (iii) examine whether this intracellular cryoprotectant incorporation could reduce the cryodamage to the yolk syncytial layer (YSL) after vitrification trials. The rationale for conducting these microinjection experiments was to overcome the permeability barrier of the YSL. Intracellular PG produced better survival than Me(2)SO (P < 0.05). Embryos tolerated both 10- and 30-nl microinjections of PG, yielding final concentrations of 2.3 and 5.0 M within the yolk, resulting in 70 +/- 3 and 35 +/- 4% survival at day 5, respectively. In similar experiments with Me(2)SO, survival was lower than PG at 60 +/- 4 and 14 +/- 4% at 2.4 and 5.2 M. Unlike other cellular systems, the presence of amides, specifically acetamide or formamide, did not reduce the toxicity of Me(2)SO in zebrafish embryos (P > 0.05). During vitrification trials, we estimated a 25% dehydration of the yolk, yielding an effective PG concentration of 5.9 M. However, the incorporation of this vitrifiable concentration of PG was not sufficient to improve the postthaw morphology of the YSL (P > 0.05). Clearly, other factors need to be examined in establishing a successful vitrification protocol for zebrafish embryos.