A micromethod for measuring the molar concentration of polyadenylated RNA in the presence of ribosomal RNA

A quick and simple FISH protocol with hybridization-sensitive fluorescent linear oligodeoxynucleotide probes

Fluorescence in situ hybridization (FISH) is a powerful tool used in karyotyping, cytogenotyping, cancer diagnosis, species specification, and gene-expression analysis. Although widely used, conventional FISH protocols are cumbersome and time consuming. We have now developed a FISH method using exciton-controlled hybridization-sensitive fluorescent oligodeoxynucleotide (ECHO) probes. ECHO-FISH uses a 25-min protocol from fixation to mounting that includes no stringency washing steps. We use ECHO-FISH to detect both specific DNA and RNA sequences with multicolor probes. ECHO-FISH is highly reproducible, stringent, and compatible with other fluorescent cellular labeling techniques. The resolution allows detection of intranuclear speckles of poly(A) RNA in HeLa cells and dissociated hippocampal primary cultures, and mRNAs in the distal dendrites of hippocampal neurons. We also demonstrate detection of telomeric and centromeric DNA on metaphase mouse chromosomes. The simplicity of the ECHO-FISH method will likely accelerate cytogenetic and gene-expression analysis with high resolution.

Factors influencing the separation of metallothioneins by capillary zone electrophoresis

The factors influencing the separation of metallothioneins (MTs) by capillary zone electrophoresis (CZE) were studied using untreated fused-silica capillaries. A comparison was made between the various buffers of 20 mM Na2B4O7, 10 mM Na2B4O7-10 mM Na2HPO4 and 20 mM Na2B4O7-10 mM Tris for the separation of MTs in terms of migration time and UV-absorbance under the various applied voltages. The migration times for MT-I and MT-II decreased with increase in the applied voltage and column temperature. However, no significant change in UV absorbance was observed. When Na2B4O7-Tris buffer was chosen for the separation of MTs, the migration time, UV absorbance, theoretical plates and resolutions also increased with increasing buffer concentrations. The effect of buffer pH on migration time was relatively complicated. Under the optimal operating conditions the standard MTs were well separated. Determination of MTs in the real samples failed due to the adsorption of other proteins onto the capillary walls.

Reverse transcriptase from human immunodeficiency virus: a single template-primer binding site serves two physically separable catalytic functions

The binding of substrates to recombinant reverse transcriptase from human immunodeficiency virus (HIV) and the natural enzyme from avian myeloblastosis virus (AMV) has been examined by analyzing both the ribonuclease H and the RNA-dependent DNA polymerase activities. With 3'-end-labeled globin mRNA hybridized to (dT)15 as the substrate in the ribonuclease H reaction, the enzymes partially deadenylated the mRNA in a distributive manner. Under these conditions, there was a rapid initial burst followed by a prolonged, but much slower, steady-state rate. The biphasic reaction made possible determinations of kinetic constants as follows: values for Km, KD, and kcat were, respectively, 27 nM, 11 nM, and 5 x 10(-3) s-1 for the HIV enzyme and 30 nM, 9 nM, and 5 x 10(-3) s-1, respectively, for the avian enzyme. These constants were used to derive other parameters: The rate of association of the template-primer with reverse transcriptase was approximately 2 x 10(5) M-1 s-1, and the rate of dissociation was approximately 2 x 10(-3) s-1, regardless of the source of the enzyme. The rate of release of the product was essentially equivalent to the value of kcat indicated above for each of the enzymes. The polymerase reaction was evaluated under processive conditions of synthesis; values of Km and kcat of approximately 6 nM and approximately 2.5 s-1, respectively, for the human enzyme, and approximately 10 nM and approximately 2 s-1, respectively, for the avian enzyme were observed. The interaction of substrates with HIV reverse transcriptase was characterized further with the aid of ribonucleoside-vanadyl complexes. These complexes inhibited the polymerase and ribonuclease H activities of the enzyme competitively with respect to globin mRNA.(dT)15. Values of Ki ranging from 1 to 3 mM were obtained. With respect to deoxyribonucleoside triphosphate substrates in the polymerase reaction, mixed inhibition was observed. Deoxyribonucleoside triphosphates had no effect on kinetic parameters governing the ribonuclease H activity of the HIV enzyme but apparently facilitated the formation of active enzyme. These data fit a model in which one template-primer binding site serves both the polymerase and the ribonuclease H catalytic sites.

Combined use of oligo(dt) and 28S cDNA probes for the quantitation of total mRNA in polyribosomes: application to the castration-induced atrophy of the rat prostate

The castration-induced atrophy of the rat prostate was used as a model for the validation of a sensitive technique allowing the quantitation of total mRNA in polyribosomes. Electron micrographs of polyribosome samples showed a decrease in polyribosomes length 7 days after castration (GDX). Specificity of labeled oligo(dt) probe for poly(A) was demonstrated and the technique was successfully applied to demonstrate that GDX is associated with a decrease in poly(A) mRNA content of polyribosomes. Provided that normalization of the hybridization signal for mRNA is achieved with a rRNA cDNA probe, the assay therefore represents a suitable tool for further studies regarding the translational regulation of total and/or specific mRNAs.

Ribonuclease H activities associated with viral reverse transcriptases are endonucleases

A series of test substrates have been synthesized to establish the effect of termini on the putative exoribonuclease H activity of reverse transcriptase. Recombinant reverse transcriptase from human immunodeficiency virus, natural enzyme from avian myeloblastosis virus, and a known endonuclease, Escherichia coli ribonuclease H, cleaved relaxed, circular, covalently closed plasmids in which 770 consecutive residues of one strand were ribonucleotides. The avian enzyme also deadenylated capped globin mRNA with a covalently attached oligo(dT) tail at the 3' end. These results resolve a long-standing controversy--that the viral enzymes are obligatory exonucleases in vitro, based on their failure to cleave certain substrates for E. coli ribonuclease H, including circular poly(A).linear poly(T) and ribonucleotide-substituted supercoiled plasmids, but resemble endonucleases in vivo, based on their ability to degrade RNA in complex DNA.RNA hybrids. The data strongly suggest that the viral enzymes are endonucleases with exquisite sensitivity to the conformation of heteroduplexes. Inhibition of viral, but not cellular, ribonuclease H with ribonucleoside-vanadyl complexes further distinguishes these enzymes.

Direct mapping of rare messenger RNAs by means of oligomer-directed ribonuclease H cleavage

A method has been developed for characterizing rare messenger RNAs in the bulk population by using oligodeoxyribonucleotide: RNA hybrids as substrates for Escherichia coli ribonuclease H. Two 1.3-kb mRNAs in lymphocyte cytoplasm, interferon-gamma (0.002% of polyadenylated mRNA), and prothymosin-alpha, have been studied. Interferon-gamma mRNA was cut virtually completely into two fragments, each about 0.6 kb in length, by using an interferon-specific 24-mer to direct cleavage. Prothymosin-alpha mRNA in the same bulk population was unaffected by this treatment. When the 24-mer was replaced by a 12-mer, whose sequence was based on an incomplete cDNA clone for prothymosin-alpha, the products included two fragments of prothymosin-alpha mRNA. The sum of the fragment lengths equaled the length of the mRNA. Although the reaction directed by the smaller oligomer did not go to completion, the 12-mer, and hence the cDNA clone from which it was derived, could nevertheless be oriented with respect to prothymosin-alpha mRNA. With this technique, sequences in mRNA can be mapped without first isolating full-length cDNA clones.

Hybridization of oligo(dT) to RNA on nitrocellulose

Quantitation of mRNA immobilized on nitrocellulose filters is an essential aspect of some studies in molecular biology. Hybridization of oligo(dT)18 to the poly(A) tails of mRNA can be used to measure filter-bound mRNA and thus provides a basis for comparing abundance of specific mRNAs. Hybridization rate of 32P-labeled oligo(dT)18 in 0.75 M NaCl, 75 mM sodium citrate, pH 7 (5 x SSC) to immobilized RNA was maximal at 25 degrees C. Filters were fully hybridized under these conditions within 1 hr when the oligo(dT)18 concentration was 10 pmol/ml or higher. Salt dependence of the dissociation temperature (Td) of oligo(dT)18:RNA duplex on filters was described by the equation Td = 42 - 20log10[molar Na+] (degrees C). With stringent washing of the duplex (four 5-min washes in 2 x SSC at room temperature), oligo(dT)18 gave no signal with plasmid DNA, rRNA, or tRNA. We have found that oligo(dT)18 can be used to normalize signal strengths rapidly and conveniently from total or oligo(dT)-selected eukaryotic RNA.

Loss of brown adipose tissue uncoupling protein mRNA on deacclimation of cold-exposed rats

The effect of environmental temperature on the level of uncoupling protein mRNA from rat brown adipose tissue was examined using a cDNA probe. A 4.4 fold increase in the mRNA level was observed after 1 day exposure of rats to 6 degrees C, which was followed by a slow loss with longer times of exposure. When rats were returned to a thermoneutral environment, there was a dramatic loss of uncoupling protein mRNA within 1 day. Comparison wih poly(A)+ RNA levels suggest that the response to temperature is specific for uncoupling protein mRNA.