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PubMed1983

Efficient recovery of functionally intact mRNA from agarose gels via transfer to an ion-exchange membrane.

A simple method is described for the efficient recovery of intact mRNA from high resolution agarose gels. Fractionation of RNA is accomplished by gel electrophoresis under denaturing conditions using methylmercuric hydroxide. The RNA in the gel is then transferred electrophoretically to a diethylaminoethyl (DEAE)-membrane. After reversing the methylmercuric modification of the RNA, the membrane is sliced into narrow sections and the RNA is eluted at 65 degrees with a high ionic strength buffer containing 6M guanidine hydrochloride. RNA isolated by this procedure is suitable for subsequent enzymatic reactions, including in vitro translation and reverse transcription. The major advantages offered by this procedure are: 1) The membrane-bound RNA is a replica of the high resolution fractionation pattern achieved in the gel. 2) The immobilization and concentration of RNA and the removal of gel matrix contaminants are all accomplished in one step. 3) Small quantities of RNA are efficiently recovered and are suitable for subsequent biochemical manipulations. The method is of general utility for any biological system. We have applied its use to the fractionation, recovery, and analysis of mRNA from Xenopus liver and have identified cDNA clones complementary to albumin mRNA.

Animals↗
PubMed1993

SP6 RNA polymerase efficiently synthesizes RNA from short double-stranded DNA templates.

SP6 DNA-dependent RNA polymerase, like T7 RNA polymerase, can be used to synthesize RNA sequences from short DNA templates which contain the 18 base pair promoter region. Use of SP6 polymerase extends the range of possible 5' sequences of RNA products, since the preferred SP6 start site (of the RNA product) is 5'GAAGA, while T7 polymerase prefers 5'GGGAG. The SP6 start site can be advantageous in large-scale syntheses where high concentrations of RNA can lead to aggregation. Using the limited number of DNA templates described here, there appears to be a significant difference between the two enzymes: SP6 polymerase requires a complete duplex DNA substrate for efficient synthesis, unlike the T7 enzyme which works efficiently when only the 18 base promoter region is double-stranded. SP6 polymerase consistently produces higher yields of RNA than does T7 polymerase, and the reactions can be easily scaled up to produce milligram quantities of RNA.

Bacteriophage T7↗
PubMed1977

DNA-dependent RNA polymerases from Artemia salina. IV. appearance of nuclear RNA polymerase activity during pre-emergence development of encysted embryos.

Dessicated and encysted gastrulae of the brine shrimp Artemia salina remain metabolically dormant until they are rehydrated. At this time development resumes, culminating in the hatching of free swimming nauplius larvae. The resumption of embryogenesis provides a convenient system for studying biochemical events which accompany development of a eukaryotic organism, and in particular Artemia has proven useful for studies of the transcriptional regulation of gene expression. Encysted gastrulae of Artemia yielded only trace amounts of DNA-dependent RNA polymerase activity when crude nuclear pellets were subjected to sonication at high ionic strength. Furthermore, when crude nuclear pellets from encysted gastrulae and developing nauplius larvae were mixed prior to sonication, subsequent solubilization of proteins from the mixture did not yield RNA polymerase activity; sonication of the pellet from nauplii alone resulted in the solubilization of large quantities of RNA polymerases I and II as we have previously found [1]. RNA polymerases I and II were detectable in sonicates of crude nuclear pellets after 1-h incubation of Artemia cysts in sea water. This presents the possibility that dormant gastrulae of the brine shrimp contain RNA polymerase which is inactive, and that the rapid appearance of nuclear enzymatic activity which accompanies the resumption of development may not require de novo synthesis of the polymerase.

Animals↗
PubMed2002

Improvement of molecular monitoring of residual disease in leukemias by bedside RNA stabilization.

The sensitivity of assays designed to monitor minimal residual disease (MRD) by RT-PCR in leukemia depend on quality and quantity of RNA derived from peripheral blood (PB) and bone marrow (BM) leukocytes. Shipment of material may lead to RNA degradation resulting in a loss of sensitivity and, potentially, false negative results. Furthermore, degradation may lead to inaccurate estimates of MRD in positive specimens. We sought to determine feasibility and efficacy of a novel blood collection and processing system which is based on integrated RNA stabilization at the time of phlebotomy (PAXgene Blood RNA Kit) by comparison with standard methods of RNA extraction (cesium chloride gradient ultracentrifugation and RNeasy Mini Kit) using unstabilized EDTA anticoagulated PB. In 26 patients with chronic myelogenous leukemia (CML) on therapy, PB was processed after a storage time at room temperature of 2 and 72 h according to these protocols. BCR-ABL, total ABL and glucose-6-phosphate dehydrogenase (G6PD) mRNA transcripts of PB samples were quantified as a measure for response to therapy and RNA integrity. RNA yield expressed as the ratio of ABL transcripts after a storage time of 72 h/ABL transcripts after a storage time of 2 h at room temperature was significantly higher with the stabilizing method (median 0.40) compared to the RNeasy method using unstabilized PB (median 0.13, P = 0.01). Furthermore, ratios BCR-ABL/ABL after 72 vs 2 h still correlated well using the PAXgene method (r = 0.99, P < 0.0001) in contrast to the standard method which did not (r = 0.65, P = 0.03). Even investigation of complete cytogenetic responders with very low tumor burden showed a good correlation of ratios BCR-ABL/ABL compared to the reference method. Comparable results were achieved using G6PD transcripts as standard. We conclude that the new PAXgene stabilization method could improve RNA quality and the comparability of molecular monitoring within and between multicenter trials.

Adult↗
PubMed2002

Synthesis of the tRNA(Lys,3) anticodon stem-loop domain containing the hypermodified ms2t6A nucleoside.

The synthesis of a protected form of the hypermodified nucleoside, N-[(9-beta-D-ribofuranosyl-2-methylthiopurin-6-yl)carbamoyl]threonine, (ms2t6A) is reported. The hypermodified nucleoside was subsequently elaborated to the protected nucleoside phosphophoramidite using a protecting group strategy compatible with standard RNA oligonucleotide chemistry. The phosphoramidite reagent was then used to synthesize the 17-nucleotide RNA hairpin having the sequence of the anticodon stem-loop (ASL) domain of human tRNA(Lys,3), the primer for HIV-1 reverse transcriptase. Introduction of the modification at position 37 of the tRNA ASL modestly decreases the thermodynamic stability of the RNA hairpin as has been seen previously for the prokaryotic t6A nucleoside lacking the 2-methylthio substituent. 2D NOESY NMR spectra of the ms2t6A containing tRNA ASL indicate that the threonyl side chain adopts a conformation similar to that seen in the solution structure of the analogous t6A containing E. coli tRNA(Lys), despite the presence of the bulky methylthio group. This synthetic approach allows for site-specific incorporation of the hypermodified nucleoside and should facilitate future studies directed at understanding the roles of nucleoside modification in modulating the stability and specificity of biologically important RNA-RNA interactions. Our synthesis of the ms2t6A containing RNAs demonstrates that this methodology is suitable for obtaining quantities of RNA required for structural studies of the HIV primer tRNA.

Anticodon↗
PubMed2001

Chemical and enzymatic synthesis of tRNAs for high-throughput crystallization.

Preparation of large quantities of RNA molecules of a defined sequence is a prerequisite for biophysical analysis, and is particularly important to the determination of high-resolution structure by X-ray crystallography. We describe improved methods for the production of multimilligram quantities of homogeneous tRNAs, using a combination of chemical synthesis and enzymatic approaches. Transfer RNA half-molecules with a break in the anticodon loop were chemically synthesized on a preparative scale, ligated enzymatically, and cocrystallized with an aminoacyl-tRNA synthetase, yielding crystals diffracting to 2.4 A resolution. Multimilligram quantities of tRNAs with greatly reduced 3' heterogeneity were also produced via transcription by T7 RNA polymerase, utilizing chemically modified DNA half-molecule templates. This latter approach eliminates the need for large-scale plasmid preparations, and yields synthetase cocrystals diffracting to 2.3 A resolution at much lower RNA:protein stoichiometries than previously required. These two approaches developed for a tRNA-synthetase complex permit the detailed structural study of "atomic-group" mutants.

Amino Acyl-tRNA Synthetases↗
PubMed1977

Metabolism of arginine-specific messenger ribonucleic acid in Escherichia coli K-12.

Ribonucleic acid-deoxyribonucleic acid (RNA-DNA) hybridization was employed for the determination of the level of messenger RNA (mRNA) transcribed from seven of the nine genes of the arginine regulon of Escherichia coli K-12. The quantity of RNA complexing with each of the separated DNA strands of the argA, argF, argE, and argCBH operons carried on specialized transducing phages was measured. The derepressed:repressed ratio of mRNA formed in vivo was found to vary between about 3 and 4 when measured by hybridization to DNA isolated from specialized transducing phages carrying the argA, argE, argCBH, argF, and argI operons.

Arginine↗
PubMed2002

Development and validation of a method for using breast core needle biopsies for gene expression microarray analyses.

PURPOSE: Gene expression microarray technologies have the potential to define molecular profiles that may identify specific phenotypes(diagnosis), establish a patient's expected clinical outcome (prognosis), and indicate the likelihood of a beneficial effect of a specific therapy (prediction). We wished to develop optimal tissue acquisition, processing, and analysis procedures for exploring the gene expression profiles of breast core needle biopsies representing cancer and noncancer tissues. EXPERIMENTAL DESIGN: Human breast cancer xenografts were used to evaluate several processing methods for prospectively collecting adequate amounts of high-quality RNA for gene expression microarray studies. Samples were assessed for the preservation of tissue architecture and the quality and quantity of RNA recovered. An optimized protocol was applied to a small study of core needle breast biopsies from patients, in which we compared the molecular profiles from cancer with those from noncancer biopsies. Gene expression data were obtained using Research Genetics, Inc. Named Genes cDNA microarrays. Data were visualized using simple hierarchical clustering and a novel principal component analysis-based multidimensional scaling. Data dimensionality was reduced by simple statistical approaches. Predictive neural networks were built using a multilayer perceptron and evaluated in an independent data set from snap-frozen mastectomy specimens. RESULTS: Processing tissue through RNALater preserves tissue architecture when biopsies are washed for 5 min on ice with ice-cold PBS before histopathological analysis. Cell margins are clear, tissue folding and fragmentation are not observed, and integrity of the cores is maintained, allowing optimal pathological interpretation and preservation of important diagnostic information. Adequate concentrations of high-quality RNA are recovered; 51 of 55 biopsies produced a median of 1.34 microg of total RNA (range, 100 ng to 12.60 microg). Snap-freezing or the use of RNALater does not affect RNA recovery or the molecular profiles obtained from biopsies. The neural network predictors accurately discriminate between predominantly cancer and noncancer breast biopsies. CONCLUSIONS: The approaches generated in these studies provide a simple, safe, and effective method for prospectively acquiring and processing breast core needle biopsies for gene expression studies. Gene expression data from these studies can be used to build accurate predictive models that separate different molecular profiles. The data establish the use and effectiveness of these approaches for future prospective studies.

Animals↗
PubMed1978

Polyoma virus-specific RNA synthesis in an inducible line of polyoma virus-transformed rat cells.

Viral RNA present in the inducible LPT clone 1A of polyoma virus-transformed rat cells was characterized before and after mitomycin C induction by hybridization with 32P-labeled separated E and L strands of polyoma viral DNA restriction endonuclease fragments. In clone 1A cells maintained under normal growth conditions, the cytoplasm contained a transcript of the E-strand DNA from the "early" region similar to that previously identified in lytically infected cells, as well as minor quantities of RNA complementary to less than one-half of the L- and the E-strand DNA from the "late" region. Nuclei of normally growing cells contained the same species found in the cytoplasm, as well as an additional abundant RNA complementary to one-half of the L-strand DNA of the late region. No significant changes occurred in the cytoplasmic viral RNA after mitomycin C treatment before the onset of viral DNA replication, but the concentration of the nuclear L-strand DNA transcript diminished. After the onset of viral DNA replication after mitomycin C treatment, transcripts of virtually the entire L-strand DNA were found in the nuclei, and a 10-fold increase was observed in the abundance of RNA transcribed from the E strand of the early region. In the cytoplasm, the abundance of the early RNA increased about 25-fold and late RNA complementary to the L-strand DNA of the late region was found in a similar quantity. The synthesis of both the early and the late RNA species was inhibited if viral DNA replication was blocked with 5-fluorodeoxyuridine. We conclude that the induction of viral DNA replication in LPT cells is not determined at the level of mRNA synthesis.

Animals↗
PubMed1978

RNA content in human lymphocyte subpopulations.

Human peripheral blood lymphocytes are stained with the metachromatic dye acridine orange and the fluorescence of individual cells is measured by flow cytometry. The relative content of stainable RNA per cell is estimated by comparison with RNase-treated cells. Non-T and T lymphocytes have different mean quantities of RNA per cell, and these classes exhibit different distributions of RNA content. Non-T cells have a unimodal distribution with a sharp peak and exponential distribution towards higher RNA values. T cells have a bimodal distribution with two separate peaks. When T cells having receptors for IgG (Tgamma cells) and IgM (Tmu cells) are separated, each of these cell populations displays a unimodal distribution. Of these three lymphocyte subpopulations, Tgamma cells have the lowest content of RNA per cell. Non-T cells have slightly higher RNA content than Tgamma, and Tmu cells have twice as much RNA as Tgamma cells. The RNA content, which surely relates to the different functions of these lymphocyte subpopulations, may also be a useful marker for rapidly distinguishing the lymphocyte subpopulations.

Acridines↗
PubMed2005

A simple method for the detection of measles virus genome by loop-mediated isothermal amplification (LAMP).

Approximately 20,000-30,000 measles patients were reported in a surveillance of infectious diseases because of low vaccine coverage of 80% in Japan. Among them, some were thought to be secondary vaccine failure (SVF) with generally mild or non-typical measles illness and sometimes became a source of further transmission. We have developed a new, sensitive, and rapid method to detect the measles virus genome by reverse transcription loop-mediated isothermal amplification (RT-LAMP). We examined 50 nasopharyngeal secretion (NPS) samples that were obtained during the 1999 outbreak and stored at -70 degrees C and fresh NPS, lymphocytes and sera from 11 patients in 2003. Total RNA was extracted from the samples and subjected to reverse transcription-polymerase chain reaction (RT-PCR) and RT-LAMP. We detected the genomic RNA corresponding to at least 0.01-0.04 TCID50, 30-100 copies in samples by RT-LAMP within 60 min after extraction of RNA, and all four genotypes isolated in Japan were equally amplified. Specific DNA amplification was monitored spectrophotometrically by real time turbidimeter and the quantity of RNA was calculated. Measles virus genome was detected in 44 of 50 stored NPS by RT-PCR and in 49 by RT-LAMP. The vaccine strain was discriminated from wild strains after sequencing the LAMP products. RT-LAMP is a useful rapid diagnostic method for the detection of measles virus without any special apparatus, showing higher sensitivity than RT-PCR, and expected to be applied for hospital-based infection control and for laboratory-based measles surveillance.

Base Sequence↗
PubMed1987

[Effect of DNA and RNA in foods on serum uric acid concentration in the human].

Nutritional experiments with formula diets show, that DNA taken orally raises the serum uric acid concentration only half as much as does the same quantity of RNA. In evaluating the suitability of foods used in the diet of patients with gout, however, food is only judged by its total purine-N content. In commercially available raw food the total purine content was determined enzymatically as uric acid. In the same samples the content of RNA, DNA, nucleotides, nucleosides and bases was determined. Eight healthy persons took part in a nutritional experiment, which began with a diet low in purines. During the first phase of the experiment, the participants ate 150 g veal-liver in addition to the low purine diet; in the second phase, they ate 80 g pork-spleen. In both additional foods, subjects took in an equal amount of total purines, determined as uric acid, but RNA dominated in veal-liver, DNA in pork-spleen. There was no statistically significant difference in the effect on serum uric acid concentration and urinary uric acid excretion between eating liver and spleen, however.

Adult↗
PubMed2006

Real-time reverse transcriptase polymerase chain reaction: an improvement in detecting mRNA levels in mouse cranial tissue.

BACKGROUND: Quantitation of messenger RNA levels has traditionally been carried out by Northern blot analysis. While this is regarded as the standard method, it is time-consuming and requires large quantities of RNA. Reverse-transcriptase polymerase chain reaction is a semiquantitative method that has been used as a more rapid and sensitive alternative to Northern blotting. Real-time reverse-transcriptase polymerase chain reaction is a quantitative technique that is gaining widespread acceptance as a rapid and reliable way of quantifying mRNA. Since both techniques are currently being used to evaluate gene expression in the murine cranial suture model, the present study was performed to compare the sensitivity and variability of real-time to conventional reverse-transcriptase polymerase chain reaction in this model. METHODS: Mouse brain RNA was isolated and amplified using real-time and conventional methods. For the real-time method, a serial 10-fold dilution of RNA, ranging from 1 fg to 100 ng, was performed. For the conventional method, the minimum amount of RNA needed for consistent polymerase chain reaction amplification was determined. Transforming growth factor beta-1 and beta-actin RNA transcripts were measured using both techniques. RESULTS: One femtogram of RNA could be detected by the real-time method, although 10 fg were required to reliably detect differences; 500 ng of RNA was required for consistent polymerase chain reaction amplification using the conventional method. The variability of real-time reverse-transcriptase polymerase chain reaction when expressed as a coefficient of variation (SD as a percentage of the mean) ranged from 0.23 to 2.6 percent for all genes tested, as compared with 9 to 70 percent for conventional reverse-transcriptase polymerase chain reaction. CONCLUSIONS: Real-time reverse-transcriptase polymerase chain reaction was used successfully to detect mRNA from different mouse genes. The real-time method is much more sensitive in detecting small amounts of mRNA than both Northern blot analysis and conventional polymerase chain reaction. The variability of the real-time method is more than 10-fold lower compared with the conventional method performed in the authors' laboratory for all genes tested.

Actins↗
PubMed1986

Effect of non-lethal scalding on the amount of DNA and RNA in rat liver.

The quantities of DNA and RNA were measured in rat liver homogenate, supernatant and nuclei after scalding. Maximal increases of nuclear DNA and RNA were found 12 h after thermal injury. The RNA content in the rat liver supernatant and homogenate reached its maximum at 24 and 48 h, respectively. The results obtained in this study show that the thermal injury resulted in an activation of the genetic apparatus in rat liver cells. These findings correspond well with a significant role of the liver in post-traumatic metabolism.

Animals↗
PubMedDate not supplied

[Detection of RNA in vaccine " EnceVir" against tick-borne encephalitis virus].

Fractionation of RNA isolated from the inactivated purified concentrated vaccine "EnceVir" ("Virion", Tomsk, Russia) allowed the authors to reveal predominantly double-stranded RNA and trace quantities of single-stranded RNA sizing mainly less than 200 n. The fragments of tick-borne encephalitis virus (TBEV) were detected among the total RNA by the reverse transcription test, followed by nested polymerase chain reaction with the primers specific to the E gene of TBEV. The findings may suggest that immunity may be induced through activation of Th1 and Th2 after immunization with such an inactivated vaccine for effective elimination of intracellular infection and intracellular virions, respectively.

Base Sequence↗
PubMed1992

Regulation of transcription by translational components in coupled translation-transcription cell-free system.

A coupled translation-transcription cell-free system was established from eukaryotic cells. The biosynthetic activity of this coupled system closely resembles the synthetic behavior of cells in vivo, and exhibits regulatory phenomena similar to that of intact cells. The translational system consists of rabbit reticulocyte lysate, or its components fractionated by centrifugation. The transcriptional portion consists of cockerel liver nuclei. Incorporation of amino acids into protein by the coupled system is linear for hours. Similarly, transcription in the coupled system is continuous for hours and is proportional with time. More than 90% of the transcriptional products are secreted into the incubation medium. The components of the translational system influence and regulate transcriptional activities. In the presence of ribosomes the nuclei transcribe mostly poly(A)+ RNA with alpha-amanitin sensitivity consistent with activation of RNA polymerase II. Hybrid selection experiments demonstrate authentic preproalbumin mRNA among the transcriptional products. The putative mRNA secreted into the medium in the coupled system is found on polysomes, indicating translation of de novo synthesized message. Addition of excess reticulocyte mRNP to the medium of the coupled system results in transcription of primarily ribosomal RNA, 5S RNA, and tRNA, the products of RNA polymerases I and III. These activities closely imitate the behavior of liver in vivo under conditions of nutritional shifts or hormonal influences. The coupled system transcribes, processes, and transports substantial quantities of RNA, about 1.6 micrograms/10(6) nuclei/h. Thus, a coupled system has been established that lends itself to the exploration of regulatory interactions of cell components as it appears to closely resemble the in vivo situation.

Animals↗
PubMed2004

Assessment of gene expression in head and neck carcinoma using laser capture microdissection and real-time reverse transcription polymerase chain reaction.

OBJECTIVES: To quantify gene expression in tumor cells from human head and neck squamous cell carcinomas (HNSCC) using laser capture microdissection (LCM). STUDY DESIGN: Histopathologically identified HNSCC cells were microdissected from frozen sections, RNA was isolated, and vascular endothelial growth factor (VEGF) gene expression was measured by real-time reverse transcriptase polymerase chain reaction (RT-PCR). MATERIALS AND METHODS: Two human HNSCC tumor samples and matched normal mucosal biopsies and five human xenograft tumor specimens were harvested, embedded, and frozen in OCT. The frozen tumors were sectioned to 8 to 10 mum in thickness, and hematoxylin-eosin (H&E) staining was performed before LCM. An estimated 2,000 to 3,000 tumor cells were microdissected from frozen sections and processed for RNA isolation. mRNA for VEGF was analyzed by real time RT-PCR (TaqMan) with commercially available primers and probes. RESULTS: Two thousand to 3000 cells were necessary to obtain a suitable quantity of RNA for subsequent gene expression study by real-time RT-PCR. The gene expression of VEGF, a major tumor angiogenic factor, was tested in microdissected HNSCC and compared with uninvolved normal mucosal controls. A greater than seven-fold increase of VEGF expression in tumor specimens versus mucosal controls was observed. CONCLUSIONS: LCM is a novel sample conserving technique that allows the precise selection of tumor cells from a heterogeneous architecture. The combination of LCM and real-time RT-PCR appears particularly efficacious for studying HNSCC molecular pathogenesis and identifying tissue-specific biomarkers.

Biopsy, Needle↗
PubMedDate not supplied

[Effect of hyperoxia on RNA and protein concentration in cortical and spinal motor neurons and surrounding neuroglia].

Double-beam recording visible cytospectrophotometry showed that 30-minute convulsions due to 6 at. ga. hyperoxia result in a decrease in the RNA and protein content per cell in layer V neurons of the cerebral motor cortex and in the motoneurons of spinal cord anterior horn in albino rats. A decrease is also found in the glial cells, except for a spinal cord neuroglia. A decrease in the RNA content in the neurons as well as the protein content in the neurons and glia of the spinal cord is more pronounced than in similar structures of the cerebral motor cortex. The quantity of RNA and protein in the neurons and neuroglia of the cerebral cortex remins decreased for 24 h after hyperoxia cessation. In the spinal cord motoneurons the level of the RNA and protein becomes normal 3 h after hyperoxia, and 24 h later it exceeds the initial one.

Animals↗