Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Formamides”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,405 records · Page 78Linked to original sources

Extensive symmetrical transcription of Simian Virus 40 DNA in virus-yielding cells.

Rapidly labeled RNA was extracted from monkey cells after infection with Simian Virus 40 (SV40) and exposure to short pulses of [5-(3)H]uridine late in infection. When this RNA was self-annealed, it became resistant to digestion with ribonuclease. The fraction of RNA that resisted the ribonuclease treatment decreased with increased labeling time, or when a short pulse of radioactivity was followed by incubation with unlabeled uridine and actinomycin D. The RNase-resistant RNA was isolated by chromatography on Sephadex G-100 and shown to be double-stranded by its susceptibility to ribonuclease as a function of salt concentration and temperature. This behavior was not due to RNA-DNA hybrid formation, since deoxyribonuclease had no effect upon the double-stranded molecules, even after their denaturation. The relation of the double-stranded RNA to SV40 was demonstrated by the hybridization of about 50% (corrected value, >90%) of the separated RNA strands with component I of SV40 DNA from plaque-purified virus. After self-annealing in formamide at low temperature, about 10% of the rapidly labeled, viral RNA sedimented at 13 S. This value corresponds in size to about 60% of the SV40 DNA.These observations indicate that late in infection of monkey cells, SV40 DNA is transcribed symmetrically over a considerable portion of its length, and that subsequently some sequences from one or both of the RNA strands are degraded.

Animals↗

Ribonucleic acid components of murine sarcoma and leukemia viruses.

Defective Kirsten murine sarcoma virus was present as leukemia virus pseudotype [Ki-MSV(MLV)] in a 10- to 100-fold excess over its helper, Kirsten murine leukemia virus (Ki-MLV), when the two viruses were propagated in an NRK rat cell line. The s(omega,20) of the fastsedimenting RNA complex of Ki-MLV and of Ki-MSV-(MLV) was 62 S and 55 S, respectively. Gel electrophoresis in buffered aqueous or formamide solution of the dissociated 62S RNA complex of Ki-MLV showed a single major peak of molecular weight about 2.5 x 10(6). Dissociated 55S RNA of Ki-MSV(MLV) was resolved into a major component with a higher electrophoretic mobility than that of Ki-MLV RNA and molecular weight about 2.3 x 10(6). Occasionally, a minor component with the same electrophoretic mobility as Ki-MLV RNA was observed in Ki-MSV(MLV) RNA; it is thought to be the RNA of Ki-MLV present as helper virus in our stocks of Ki-MSV(MLV). The RNA of an endogenous rat C-type RNA virus was electrophoretically different from both Ki-MLV RNA and Ki-MSV(MLV) RNAs. Oligonucleotide fingerprinting of the RNAs digested with RNase T1 indicated that the RNAs of Ki-MSV(MLV) and Ki-MLV are different. However, the extent of the difference between the two RNAs could not be estimated by this method. The heat-dissociated 50-70S RNAs of two other defective murine sarcoma-leukemia viruses; Harvey-MSV(MLV) and Moloney-MSV(MLV) and of defective spleen-focus-forming Friend virus were resolved electrophoretically into two components. The larger components had the same electrophoretic mobility as the RNA of Ki-MLV or Moloney MLV. The smaller were not present in leukemia virus. It is suggested that the small RNA components of the two murine viruses and of Friend virus represent specific genetic information of these replication-defective transforming viruses. Possible relationships between the RNAs of murine leukemia viruses and replication-defective murine sarcoma and Friend viruses are discussed.

Animals↗

Chromosome structure as revealed by a combined chemical and immunochemical procedure.

Human metaphase chromosomes were photooxidized in the presence of methylene blue, a process that destroys guanine residues in DNA. Indirect immunofluorescence showed that such chromosomes reacted with a cytosine-specific antibody revealing a consistent fluorescent banding pattern by which each chromosome could be identified. The observed fluorescent patterns were the reverse of those produced in formamide-denatured chromosomes treated with an antibody specific for adenine and of the patterns obtained with quinacrine and with Giemsa staining by the G-banding techniques. The patterns were identical to Giemsa R-banding patterns. The chromosome banding patterns, therefore, appeared to reflect DNA base composition, indicating the feasibility of a combined chemical-immunochemical investigation of the chemical organization of chromosomes.

Antibodies, Antinuclear↗

A general method of gene isolation.

A general method of gene isolation has been developed that involves the chemical linkage of RNA to cellulose by a water-soluble carbodiimide, and the continuous circulation of DNA containing specific sequences complementary to the RNA. The temperature of the cellulose matrix is maintained at 37 degrees (50% formamide, 0.3 M NaCl-0.03 M Na(3) citrate) to allow efficient DNA-RNA interaction in the stationary phase, while unreacted and any reassociated DNA is denatured at 90 degrees and then recirculated into the hybridization chamber. Between 40 and 45% of fragmented (32)P-labeled simian virus (SV)40 DNA was removed from the circulating solution when cellulosebound SV40-specific RNA, assymmetrically transcribed in vitro with Escherichia coli RNA polymerase, was used. In the presence of 10(4)-fold excess of sheared E. coli DNA, nearly half of the [(32)P]SV40 DNA was recovered from the mixture as a DNA-RNA hybrid with negligible contamination by bacterial DNA. The isolation procedure is almost quantitative for the complementary DNA. The efficiency and selectivity of this method permit the isolation of a defined DNA sequence from a large and complex genome.

Carbodiimides↗

The identification of collagen messenger RNA.

RNA isolated from calvaria of 16- to 18- day-old chick embryos, assayed in rabbit reticulocyte lysates, programs the synthesis of a collagenase-sensitive protein with the molecular weight of collagen pro-alpha-chains. When RNA labeled with [(3)H]uridine for 2 hr and chased for 1 or 2 hr was electrophoresed on aqueous polyacrylamide gels, most of the radioactivity not in 28S or 18S rRNA migrated with an apparent molecular weight of about 1,800,000. After oligo(dT)-cellulose chromotography and analysis in 99% formamide gels, this nonribosomal, rapidly labeled calvaria RNA species migrates at 28S-30S and thus has a molecular weight of at least 1,600,000. Both the ability to program the synthesis of collagenase-sensitive protein in reticulocyte lysates and the presence of a single prominent rapidly labeled 30S peak in acrylamide gels strongly support the deduction that there is only one major mRNA species in calvaria and that this species is collagen messenger RNA.

Animals↗

Isolation of DNA Strand-specific early messenger RNA species in cells infected by human adenovirus 2.

Hybridization to the separated light (L) and heavy (H) strands of adenovirus 2 DNA in 50% formamide at 37 degrees was used to isolate undegraded virus-specific RNA molecules from the polyribosomes of cycloheximide-treated human KB cells early after infection with adenovirus 2. About 20% of polyribosomal RNA labeled with [(3)H]uridine from 4 to 7 hr after infection was virus-specific. Twice as much labeled RNA was homologous to the L strand as to the H strand. Polyacrylamide gel electrophoresis of RNA selected with unfractionated adenovirus DNA resolved a major component of virus-specific RNA in the 19-20 S region of the gel and smaller amounts of viral RNA in two heterogeneous fractions migrating at 15-18 S and 21-26 S. Selection with individual DNA strands showed that the 19-20 S main size class of early mRNA consists of two homogeneous RNA species with slightly different mobilities, the transcripts from the L and H strand having molecular weights of 7.4 x 10(5) and 7.7 x 10(5), respectively. The 15-18 S RNA hybridized with the L strand and the 21-26 S RNA with the H strand.

Adenoviridae↗

A new chemical procedure for 32P-labeling of ribonucleic acids at their 5'-ends after isolation.

A new technique, which utilizes the chemical reaction between [32P]diimidazolidate of orthophosphate and the cetyltrimethylammonium salt of high-molecular-weight RNA in nonaqueous dimethyl formamide, has been developed for the 32P-labeling of RNAs after isolation. The radioactive label of high specific activity is introduced onto a phosphorylated 5'-end of the RNA and renders it suitable for 5'-terminal group analysis. When the labeling reaction was applied to the 70S RNA of avian myeloblastosis virus, a labeled 35S RNA was isolated on sucrose-dimethyl sulfoxide gradients without apparent degradation.

Avian Myeloblastosis Virus↗

In vitro synthesis of full-length DNA transcripts of Rous sarcoma virus RNA by viral DNA polymerase.

Varying the concentration of Triton X-100, a nonionic detergent used to promote the DNA polymerase activity of Rous sarcoma virus in an endogenous reaction, showed a very sharp peak at about 0.02% (vol/vol) for optimal DNA synthesis. The yield of DNA at this concentration of Triton exceeded yields obtained at concentrations above the optimum by a factor of 2-5 for the 90-min reaction. At optimal Triton concentration, about 1-7% of the DNA made in the absence of actinomycin and about 4-10% of the DNA made in the presence of actinomycin was 2.5 X 10(6) daltons or greater, as estimated by formamide polyacrylamide gel electrophoresis and by alkaline sucrose gradient sedimentation. No large DNA was obtained at higher than optimal Triton concentrations. The large DNA molecules were rendered totally resistant to single-strand specific nuclease S1 after hybridization to an excess of viral RNA. It was concluded that at optimal detergent concentration, the viral DNA polymerase can synthesize full-size DNA transcripts of viral RNA.

Avian Sarcoma Viruses↗

Synthesis of DNA complementary to separated human alpha and beta globin messenger RNAs.

Human globulin messenger RNA, purified by oligo(dT)-cellulose column chromatography, is reproducibly separated into two bands by polyacrylamide gel electrophoresis in the presence of 99% formamide. The more rapidly migrating (fast) band is somewhat more abundant than the slow band in normal (nonthalassemic) total reticulocyte globin messenger RNA. In alpha-thalassemic (Hb H disease) messenger RNA, the slow band is 6.5 times more abundant than the fast band, whereas in beta-thalassemic messenger RNA the fast band is three times more abundant than a second band, which has a slightly greater mobility than the slow band of normal and alpha-thalassemic RNA. The RNA bands of nonthalassemic globin messenger RNA were eluted from the gel and efficiently transcribed into DNA copies by use of the RNA-dependent DAN polymerase of avian myeloblastosis virus. Hybridization of these copy DNAs to fast and slow band RANs and to nonfractionated normal, alpha-thalassemic, and geta-thalassemic messenger RNAs revealed that the eluted fast band RNA contains predominantly alpha-chain specific sequences, whereas the eluted slow band RNA contains predominantly beta-chain specific sequences. Nucleotide sequence analysis of 32-P-labeled RNA transcribed from the slow band copy DNA also indicated that the slow band RNA is beta messenger RNA.

Avian Myeloblastosis Virus↗

Partial purification and characterization of the mRNA for rat preproinsulin.

Electrophoretically homogeneous messenger RNA for rat preproinsulin has been prepared from an islet cell tumor by the use of oligo(dT(-cellulose chromatography and sucrose density gradient centrifugation. The molecular weight of the mRNA is about 210,000, as determined by polyacrylamide gel electrophoresis in formamide, and its sedimentation coefficient is 9.3 S in sucrose gradients containing 0.2 M NaCl. These results indicate that the synthesis of preproinsulin is directed by a monocistronic mRNA 600 nucleotides in length and requires approximately 55% of the molecule's coding capacity.

Adenoma, Islet Cell↗

No detectable reiteration of genes coding for mouse MOPC 41 immunoglobulin light-chain mRNA.

RNA fractions rich in immunoglobulin light (L)-chain mRNA were isolated from mouse myeloma MOPC 41 by procedures previously described, and chemically labeled with 125I. These RNA fractions were hybridized with MOPC 41 DNA under conditions of DNA excess. Hybridization conditions were chosen under which the entire sequence of the L-chain mRNA probe, thus including the variable region, remains available for hybridization throughout the reaction. The hybridization (C0t) curve showed double transition kinetics, with one component corresponding to about 250 gene copies and the other to about two to four copies. In contrast, when MOPC 41 L-chain mRNA was further purified as a single band by gel elecptrophoresis in 99% formamide, the hybridization curve showed only a single transition, corresponding to about two to four genes, with the disappearance of the "reiterated" component. That component resulted therefore from contaminating RNA species. The data indicate that no reiteration can be detected by RNase or by hydroxylapatite for the genes corresponding to the entire sequence of MOPC 41 L-chain mRNA, including the untranslated segments, within the limits of detectability of short reiterated segments. It thus appears that there is only one or very few genes corresponding to the 41 L-chain variable region "subgroup" in MOPC 41 DNA. The possibility that the variable genes of plasmocytes might result frm a combination of several nonreiterated germline genes is discussed.

Alleles↗

Structure of a nicked DNA-protein complex isolated from simian virus 40: covalent attachment of the protein to DNA and nick specificity.

A portion of the nicked circular DNA isolated from purified simian virus 40 contains a protein-DNA complex in which protein(s) is covalently attached to the end of a DNA single strand. (Nicked DNA is double-stranded DNA that contains at least one single-strand scission.) The protein was visualized by electron microscopy and labeled in vitro with 125I. The bond between the protein and the DNA is stable in alkali, 4 M guanidine-hydrochloride, 3.86 M hydroxylamine (pH 4,23), and in 98% formamide. Most of the molecules in the nicked circular DNA fraction contained one nick. The nick occurs on either of the two complementary strands; the specific nick sites on the two strands are staggered, but lie within a few hundred nucleotides of each other.

DNA, Circular↗

Heterogeneous nuclear RNA secondary structure: oligo (U) sequences base-paired with poly (A) and their possible role as binding sites for heterogeneous nuclear RNA-specific proteins.

HeLa cell heterogeneous nuclear RNA derived from high-molecular-weight nuclear ribonucleoprotein (RNP) particles contains oligo(U) sequences of 15-50 nucleotides base-paired with poly(A). These duplexes are resistant to pancreatic RNase at 0.5 M NaCl in native RNP, remain so after chemical deproteinization of the RNP digests, and then copurify with poly(A) on oligo(dT)-cellulose chromatography. Oligo(dT)-cellulose binding capacity of the oligo(U)-poly(A) duplexes is abolished by prior titration of the nonduplex poly(A) regions with excess poly(U). The oligo(dT)-purified fraction is 97.5 mole % A + U and the [3H]uridine-labeled component is resistant to redigestion by pancreatic RNase at 0.5 M NaCl but not at 0.01 M NaCl. After thermal denaturation, the [3H]uridine-labeled chains become RNase-sensitive at 0.5 M NaCl. Electrophoresis of [3H]adenosine- or [3H]uridine-labeled material in polyacrylamide gels containing 99% formamide confirms that the oligo(U) sequences are not covalently linked to poly(A). Controls establish that the A-U duplexes are not formed artifactually during isolation of heterogeneous nuclear RNP or subsequent fractionation. The oligo(U)-poly(A) duplexes appear to be associated with protein in native heterogeneous nuclear RNP, as reflected by the differential pancreatic RNase sensitivity of the duplexed oligo(U) in RNP (resistant) and RNA (sensitive), measured at physiological ionic strength.

Base Sequence↗

Pregrowth hormone messenger RNA: glucocorticoid induction and identification in rat pituitary cells.

We have investigated whether the large (5- to 15-fold) stimulation of synthesis of growth hormone (somatotropin) observed upon exposure of a strain of rat pituitary (GH3) cells to dexamethasone (a synthetic glucocorticoid) arises from a stimulation of pregrowth hormone mRNA. A good agreement was observed between the stimulation of growth hormone synthesis and the stimulation of cytoplasmic levels of pregrowth hormone mRNA, assayed by translation in wheat germ extracts. Electrophoresis on formamide-acrylamide gels of oligo(dT)-treated membrane fraction RNA revealed a band that was induced by dexamethasone to about the same extent as was translatable pregrowth hormone mRNA. Elution of the band and translation in wheat germ extracts showed directly that it contained pregrowth hormone mRNA. These results suggest that the dexamethasone induction of growth hormone synthesis in GH3 cells arises from an accumulation of pregrowth hormone mRNA in the cytoplasm of the cells. The pregrowth hormone mRNA band observed by gel electrophoresis had an estimated molecular weight of 3.6 X 10(5), suggesting the existence in this molecule of an untranslated region at least 200 nucleotides in length.

Cell Line↗

Frog oocytes synthesize and completely process the precursor polypeptide to virion structural proteins after microinjection of avian myeloblastosis virus RNA.

After microinjection of Xenopus laevis oocytes with RNA from avian myeloblastosis virus, viral structural proteins p27, p19, p15, and p12 are formed by a sequence of posttranslational cleavages of a high-molecular-weight precursor polypeptide. The 60-70S RNA aggregate or its 30-40S RNA subunits obtained by heat or formamide treatment possess the same ability to serve as template in X. laevis oocytes. The processing pattern of virus-specific precursor polypeptides is the same in X. laevis oocytes as in chick embryo fibroblasts infected with avian myeloblastosis virus, but the processing takes place at a much slower rate.

Animals↗

Separation and infectivity of circular and linear forms of potato spindle tuber viroid.

Potato spindle tuber viroid can be separated into two fractions by polyacrylamide gelelectrophoresis in the presence of formamide and urea. One fraction contains predominantly circular molecules; the second fraction contains almost exclusively linear molecules. The purity of the fractions was estimated by electron microscopy of formaldehyde-denatured molecules. The length distributions of denatured circular and linear molecules were determined. Both circular and linear molecules were found to be infectious.

Electrophoresis, Polyacrylamide Gel↗

Translation and characterization of messenger RNAs in differentiating chicken cartilage.

Total RNA, prepared from chicken limb bud cultures undergoing differentiation to cartilage, has been translated in a wheat germ cell-free protein-synthesizing system. Antibodies against chondroitin sulfate proteoglycan core protein immunoprecipitate a single component which migrates as a protein of 340,000 daltons in sodium dodecyl sulfate/polyacrylamide gels. The messenger RNA for this protein sediments at approximately 27 S in 70% formamide or aqueous sucrose gradients. The 340,000-dalton protein is present in cell-free translation products directed by RNA prepared from limb bud cultures and sternae and is absent in cell-free translation directed by RNA prepared from embryonic calvaria or liver. The level of synthesis of this protein is greatly reduced when RNA prepared from limb bud cultures inhibited from differentiation by BrdUrd is used. (Pre)pro alpha 1(I), -alpha 2(I), and -alpha 1(II) collagen bands have been identified on gels by electrophoresis of collagenase-digested or immunoprecipitated cell-free translation products directed by RNA from differentiating limb bud cultures, embryonic sternae, and embryonic calvaria.

Animals↗

Coupling between oxidation state and hydrogen bond conformation in heme proteins.

In all heme proteins for which crystal structures are available, the N(epsilon) of a histidyl residue is bonded to the heme iron and N(delta) is hydrogen bonded to a carbonyl oxygen of the peptide backbone. We investigate here the possibility that a change in oxidation state of the iron or a change in the geometry of this hydrogen bond might change the hydrogen bond strength in a functionally significant way. Dimerization energies obtained from ab initio molecular orbital calculations on the hydrogen-bonded dimer of imidazole and planar formamide are used to represent the strength of this hydrogen bond in heme proteins. The effect of a change in iron oxidation state is modeled by varying the positive charge on imidazole. The effect of a change in hydrogen bond geometry is studied by employing x-ray coordinates for reduced and oxidized cytochrome c, deoxy- and metmyoglobin, and deoxy- and methemoglobin. Our conclusions are that the strength of this hydrogen bond in heme proteins is sensitive to both the oxidation state of the iron atom and to geometry changes on the order of those obtained from the x-ray coordinates. We speculate that the changes in oxidation state may be functionally coupled with changes in hydrogen bond geometry and that this hydrogen bond represents a feasible pathway to link protein conformation with redox potential or reactivity of the iron atom.

Animals↗