Antisense properties of peptide nucleic acid

Peptide nucleic acid (PNA) is a nucleic acid mimic in which the deoxyribose phosphate backbone has been replaced by a pseudo-peptide polymer to which the nucleobases are linked. PNA-oligomers can be synthesized in relatively large amounts, are highly stable in biological environments, and bind complementary DNA and RNA targets with remarkably high affinity and specificity. Thus PNA possesses many of the properties desired for a good antisense agent. Until recently, limited uptake of PNA into cells has been the major obstacle for applying PNA as an antisense agent in cell cultures and in vivo. Here, the antisense properties of PNA in vitro and in vivo will be reviewed. In particular, we will focus on recent observations indicating that PNA equipped with or without various uptake moieties may function as an efficient and gene-specific inhibitor of translation in Escherichia coli and in certain mammalian cell types.

Nucleic acid duplex stability: influence of base composition on cation effects

The effects of counter ion on a nucleic acid duplex stability were investigated. Since a linear free energy relationship for the thermostability of oligonucleotide duplexes between those in 1 M and in 100 mM NaCl-phosphate buffer were observed regardless of whether they are DNA-DNA, RNA-RNA or RNA-DNA duplexes, simple prediction systems for [Delta] G degrees 37as well as T mvalues in 100 mM NaCl-phosphate buffer were established. These predictions were successful with an average error of only 2.4 degrees C for T mand 5. 7% for G degrees 37values. The number of Na+newly bound to a duplex when the duplex forms (-[Delta] n) was significantly influenced by the base composition, and -[Delta] n for d(GCCAGTTAA)/d(TTAACTGGC) was different for MgCl2, CaCl2, BaCl2and MnCl2(from 0.70 to 0.76 with the same order of the duplex stability). Almost no additive effects on the duplex stability was observed for NaCl and MgCl2, suggesting a competitive binding for these cations. The sequence-dependent manner of [Delta] n suggests the presence of preferential base pairs or nearest-neighbor base pairs for the cation binding, which would affect nearest-neighbor parameters.

Differential effects of cyclopolyamines on the stability and conformation of triplex DNA

Linear polyamines are excellent promoters of triplex DNA formation. The effects of structural rigidization of polyamines on triplex DNA stability are not known at present. We wished to develop a series of polyamine analogs as secondary ligands for triplex DNA stabilization for antigene applications. To accomplish this goal, we synthesized cyclopolyamines by interconnecting the two amino or imino groups of linear polyamines with a --(CH2)n-bridge (n=3,4,5). Melting temperature (Tm) data showed that [4,3]-spermine and [4,4]-spermine stabilized poly(dA) x 2poly(dT) triplex at >25 microM concentrations (Tm = 71 degrees C at 100 microM). The dTm/dlog [polyamine] values for these compounds were 26 and 40, respectively. [4,3]-Spermine and [4,4]-spermine also stabilized triplex DNA formed by a purine-motif triplex-forming oligonucleotide, TG3TG4TG4TG3T with its target duplex, as determined by Tm, circular dichroism (CD) spectroscopy, and electrophoretic mobility shift assay (EMSA). In contrast, [4,4]-putrescine and [4,5]-putrescine as well as [4,5]-spermine had no triplex DNA stabilizing effect. CD spectra also showed triplex DNA aggregation and psi-DNA formation at >100 microM [4,3]-spermine. These data demonstrate that structural rigidization of linear polyamines has a profound effect on their ability to stabilize triplex DNA and provoke conformational transitions.

Anomeric inversion (from beta to alpha) in methylphosphonate oligonucleosides enhances their affinity for DNA and RNA

Here we report that the poor binding of methylphosphonate oligodeoxynucleosides (MP-ODNs) to their nucleic acid targets can be improved by additional inversion of the anomeric configuration (from beta to alpha) in the sugar moieties to give a new class of analogs, MP alpha-oligonucleosides. MP alpha-dT12and MP 5' alpha-d(TCTTAACCCACA) 3' were synthesized and their ability to form hybrids with complementary single stranded (ss)DNA and ssRNA, as well as with double stranded (ds)DNA, was evaluated. The thermal stability of hybrids formed with MP alpha-analogs was compared with the affinity of phosphodiester (PO) and phosphorothioate (PS) beta- and alpha-oligomers for their targets. Non-ionic MP alpha-oligonucleosides bound to their complementary DNA and RNA strands more tightly than their homologues with natural beta-anomeric configuration did. With DNA target, MP alpha-oligomers formed duplexes more stable than the corresponding natural PO beta-oligomer did. MP alpha-heteropolymer hybridized to RNA target better than PS beta-oligonucleotide did but the hybrid was less stable (DeltaTm-0.5 degrees C per mod.) than the hybrid formed with the natural PO beta-oligomer. Only MP alpha-dT12 bound to dsDNA target at low salt concentration (0.1 M NaCl).

Modulation of Cm/T, G/A, and G/T triplex stability by conjugate groups in the presence and absence of KCl

Apparent equilibrium association constants were determined by gel mobility shift analysis for triple strand formation between a duplex target containing a 21 base long A-rich homopurine run and several end-modified C(m)/T (pyrimidine motif; C(m) = 5-methylcytosine), G/A (purine motif), and G/T (purine-pyrimidine motif) triplex-forming oligonucleotides (TFOs). Incubations were carried out for 24 h at 37 degrees C in 20 mM HEPES, pH 7.2, 10 mM MgCl2, and 1 mM spermine. The purine motif triplex was the most stable (Ka = 6.2 x 10(8) M-1) even though the TFO self-associated as a linear duplex. Conjugation of a terminal hexanol or cholesterol group to the G/A-containing TFO reduced triplex stability by 1.6- or 13-fold, whereas an aminohexyl group or intercalating agent (acridine or psoralen) increased triplex stability by 1.3- or 13-fold. These end groups produced similar effects in C(m)/T and G/T triplexes, although the magnitude of the effect sometimes differed. Addition of 140 mM KCl to mimic physiological conditions decreased stability of the G/A triplex by 1900-fold, making it less stable than the C(m)/T triplex. The inhibitory effect of KCl on G/A triplex formation could be partially compensated for by conjugating the TFO to an intercalating agent (30-350-fold stabilization) or by adding the triplex selective intercalator coralyne (1000-fold stabilization). Although the G/T triplex responded similarly to these agents, the stability of the C(m)/T triplex was unaffected by the presence of coralyne and was only enhanced 1.4-2.8-fold when the TFO was linked to an intercalating agent. In physiological buffer supplemented with 40 microM coralyne, the G/A triplex (Ka = 3.0 x 10(8) M-1) was more stable than the C(m)/T and G/T triplexes by factors of 300 and 12, respectively.

Modulation of nucleic acid structure by ligand binding: induction of a DNA.RNA.DNA hybrid triplex by DAPI intercalation

The aromatic diamidine, DAPI (4',6-diamidino-2-phenylindole), is used as an important biological and cytological tool since it forms highly fluorescent complexes with nucleic acid duplexes via minor groove-directed/intercalative modes of interaction. In this study, we find that DAPI binding can induce the formation of an RNA-DNA hybrid triplex that would not otherwise form. More specifically, through application of a broad range of spectroscopic, viscometric, and molecular modeling techniques, we demonstrate that DAPI intercalation induces the formation of the poly(dT).poly(rA).poly(dT) hybrid triple helix, a structure which does not form in the absence of the ligand. Using UV mixing studies, we demonstrate that, in the presence of DAPI, the poly(rA).poly(dT) duplex and the poly(dT) single strand form a 1:1 complex (a triplex) that does not form in the absence of DAPI. Through temperature-dependent absorbance measurements, we show that the poly(dT).poly(rA).poly(dT) triplex melts via two distinct transitions: initial conversion of the triplex to the duplex state, with the DAPI remaining bound, followed by denaturation of the duplex-DAPI complex to its component single strands and free DAPI. Using optical melting profiles, we show that DAPI binding enhances the thermal stability of the poly(dT).poly(rA).poly(dT) triplex, an observation consistent with the preferential binding of the ligand to the triplex versus the duplex and single-stranded states. Our differential scanning calorimetric measurements reveal melting of the DAPI-saturated poly(dT).poly(rA).poly(dT) triplex to be associated with a lower enthalpy but greater cooperativity than melting of the corresponding DAPI-saturated poly(rA).poly(dT) duplex. Our flow linear dichroism and viscometric data are consistent with an intercalative mode of binding when DAPI interacts with both the poly(dT).poly(rA).poly(dT) triplex and the poly(rA).poly(dT) duplex. Finally, computer modeling studies suggest that a combination of both stacking and electrostatic interactions between the intercalated ligand and the host nucleic acid play important roles in the DAPI-induced stabilization of the poly(dT).poly(rA).poly(dT) triplex. In the aggregate, our results demonstrate that ligand binding can be used to induce the formation of triplex structures that do not form in the absence of the ligand. This triplex-inducing capacity has potentially important implications in the design of novel antisense, antigene, antiviral, and diagnostic strategies.

Promoter proximal sequences modulate RNA polymerase II elongation by a novel mechanism

The adenovirus major late arrest site blocks transcription by mammalian RNA polymerase II in vitro downstream of the major late promoter but not the mouse beta-globin promoter. We localized the sequences responsible for anti-arrest to the 5' end of the beta-globin transcript and demonstrated that anti-arrest required that this region of RNA form base pairs with the nascent transcript upstream of the arrest site. Small antisense RNA or DNA oligonucleotides hybridizing upstream of the arrest site also prevented arrest when added in trans. Our results suggest that arrest is accompanied by retraction of the nascent transcript into the interior of the polymerase and that hybridization of the transcript prevents this movement, thereby allowing the polymerase to continue elongation.

Restriction endonuclease recognition and southern hybridization of bromodeoxyuridine-substituted genomic DNA

Human glioma cell lines exposed to various concentrations of bromodeoxyuridine (BrdUrd) were studied to determine the effect of BrdUrd substitution on restriction endonuclease recognition and Southern hybridization of genomic DNA. BrdUrd substitution had no effect on the recognition of restriction endonucleases. When the exposure to BrdUrd was 2h or less and the BrdUrd substitution rate was less than 40%, there was no difference in the density of hybridized bands after Southern hybridization using human non-recombinant complementary DNA as a probe. Hybridization was suppressed significantly by exposures longer than 24 h or BrdUrd substitution rates greater than 40%. These results suggest that the BrdUrd substitution rate and the exposure time to BrdUrd influence the hybridization reaction by a DNA probe. Brief exposure (up to 2 h) to BrdUrd does not influence restriction endonuclease recognition or Southern hybridization of genomic DNA.

Regulation of Hepatic Lipogenic Enzyme Gene Expression by Diet Quantity in Rats Fed a Fat-Free, High Carbohydrate Diet

This investigation concerns the effects of the level of intake of a high carbohydrate diet on transcriptional rate, mRNA concentration and enzyme induction for lipogenic enzymes in rat liver. Six hours after refeeding fasted rats, the transcriptional rates in livers reached low maximum levels with small quantities of diet, but the mRNA concentrations continued to increase as diet intake increased. Greater diet intake primarily increased transcriptional rates and mRNA concentrations of lipogenic enzymes. After refeeding for 16 h, the mRNA concentrations were sigmoidly increased relative to the diet quantity and reached maximum levels of 20-, 110-, 22- and 16-fold above each fasted level for acetyl-CoA carboxylase, fatty acid synthase, malic enzyme and glucose-6-phosphate dehydrogenase, respectively. After 3 d of refeeding (in a steady state of lipogenic enzyme activities), however, the transcriptional rates, mRNA concentrations and activity inductions of all the enzymes were sigmoidly increased relative to diet quantity, but were not different among the enzymes. Consequently, fatty acid synthesis and triglyceride levels in the liver were not increased by feeding less than 70% of ad libitum intake but were greatly increased by feeding greater than 70% of ad libitum intake.

[Study of the structure of amplifying sequence of Streptomyces antibioticus]

A low productive laboratory strain of S. antibioticus and a strain with an increased productivity of oleandomycin derived from it were studied comparatively with using restriction analysis and blotting hybridization. Amplification, site specific integration and segregation of the DNA sequence 32.0 kb in size were detected in the strains. The chromosomes of the laboratory strain contained one copy of the amplifying sequence AUD. After uniting of the end sequences AUD appeared to be capable of segregating from the chromosomes and its one copy per five genomes was present in the form of an extrachromosomal genetic element eSA1. The genome of the strain with increased productivity of oleandomycin contained in its chromosomes sequence ADS-Sa1 amplified to 150 copies and the eSA1 extrachromosomal genetic element in the form of mono-, di- and trimeric structures in the quantity of approximately one copy per genome. The BamHIB fragment of the eSA1 DNA 4 kb in size was identified. The fragment was able to participate in segregation or integration of eSA1 from or into the chromosomes since its subfragments were flanking AUD and ADS-SA1 in the chromosomes. The BamHIB fragment was hybridizing with a number of fragments of the chromosomal DNA of S. antibioticus, S. erythraeus. S. lividans and other strains of streptomycetes. It probably contained an IS-like element or a dispersed genetic element of another class. The DNA sequence of the eSA1 genetic element contained regions homologous to the sequence of the Erm E gene in S. erythraeus NRRL 2338.

Phylogenetic relationships among Tetrahymena species determined using the polymerase chain reaction

The species of the Tetrahymena pyriformis complex present a conundrum with regard to their highly conservative morphology and widely divergent molecular characteristics. We have investigated the phylogenetic relationships among these species using the nucleotide sequences from the histone H3II/H4II region of the genome. This region includes portions of the two histone coding sequences, as well as the intergenic region. The DNA sequences of these regions were amplified by the polymerase chain reaction (PCR) and the sequence of each was determined. Nucleotide substitutions and insertions/deletions within this set of sequences were compared to determine the phylogenetic relationships among the species of the complex. These data yield phylogenetic trees with identical topologies when different tree-building routines are used, indicating that the data are very robust. Glaucoma chattoni was used as an outgroup to root the trees for this analysis. The genome organization of G. chattoni and the divergence of its histone H3II/H4II region sequence relative to those of the complex clearly indicate that this species has diverged considerably from the complex. These results show that PCR amplification analysis is feasible over considerable evolutionary distances. However, DNA-DNA hybridization may be more useful than sequence analysis in resolving the relationships among the closely related species in the complex.

Suppression of c-myc mRNA expression by steroid hormones in HTLV-I-infected T-cell line, KH-2

The effects of 1,25(OH)2D3 and dexamethasone on cellular proliferation and gene expression of the HTLV-I-infected T-cell line, KH-2, established from a patient with adult T-cell leukemia, endemic in the south-west Japanese islands and the Caribbean, were examined. KH-2 cells are integrated by HTLV-I proviral DNA and expressed mRNA for c-myc, IL-2 receptor alpha-chain (IL-2R alpha), and T-cell receptor beta-chain (TCR beta) while it did not express IL-2 mRNA. 1,25(OH)2D3 and dexamethasone did not suppress the mRNA levels of HTLV-I, IL-2R alpha or TCR beta but reduced the c-myc mRNA level. The reduction of c-myc mRNA level was marked in 1,25(OH)2D3-treated cells but relatively weak in dexamethasone-treated cells. This inhibitory effect of the steroid hormones correlated with the inhibition of KH-2 cell proliferation.

[The time-dependent stimulating action of hydrocortisone on mitochondrial RNA biosynthesis in the rat liver]

Mitochondrial RNA biosynthesis was studied at different time after hydrocortisone administration. Hydrocortisone induced liver mitochondrial RNA biosynthesis in vivo and in isolated organellae 15 min., 1.5 and 4 h after hormone injection. As shown by means of molecular hybridization of RNA-DNA, an increase in liver mitochondrial RNA biosynthesis induced by hydrocortisone administration was due to an increase in the expression of all mitochondrial genes simultaneously rather than to selective enhancement of individual gene transcription. Hydrocortisone changed the biosynthesis and transport of cytoplasmic RNA in the liver of intact rats. The incorporation of 3H-UTP into RNA by isolated liver mitochondria of control and hydrocortisone-treated rats was inhibited by ethidium bromide. RNA biosynthesis in isolated rat liver mitochondria was unchanged in 15-300 min. of 0.9% NaCl administration.

Evidence for the participation of topoisomerases I and II in cadmium-induced metallothionein expression in Chinese hamster ovary cells

CHO-Cdr20 cells are 10-20 times more resistant to killing by cadmium than the parental CHO cells. Resistance has been linked to amplification of the metallothionein genes MT-I and MT-II and their coordinate induction by cadmium and other toxic metals. We studied the roles of the nuclear enzymes topoisomerase I and topoisomerase II in Cd-induced expression of MT-II. Camptothecin-induced DNA strand breakage, mediated by topoisomerase I in cells, increased by approximately 20% when the resistant cells were incubated first with 50 microM Cd and then with camptothecin. Short DNA fragments were enriched in MT-II-hybridizing sequences, indicating that topoisomerase I-associated breakage was directed in part toward the location of induced gene activity. Ten microM camptothecin inhibited Cd-induced accumulation of MT-II mRNA as well as induced and uninduced RNA synthesis in the resistant cells. These data are consistent with the notion that topoisomerase I participates in most or all forms of RNA synthesis. Topoisomerase II inhibitors which trap cleavable complexes (amsacrine, VM-26, VP-16) increased DNA strand breakage at very high concentrations (50-100 microM); the increased breakage appeared to be concentrated near the MT-II gene. This class of inhibitor did not block the accumulation of MT-II message. Novobiocin, a second type of topoisomerase II inhibitor blocked transcription at 300 microM. Merbarone, a novel, third type of topoisomerase II inhibitor, blocked MT-II transcription at 50-100 microM. The latter two inhibited total RNA synthesis in induced, but not uninduced cells. Thus, it is possible that topoisomerase II plays more than one role in transcription and that more than one form of this enzyme is involved.

Induction of Epstein-Barr virus in B-lymphoblastoid cells by human immunodeficiency virus type 1

Individuals infected with the human immunodeficiency virus (HIV), the etiologic agent of acquired immunodeficiency syndrome (AIDS), often show symptoms associated with reactivation of Epstein-Barr virus (EBV). In this study, we show that exposure of EBV-positive B lymphocytes to HIV-1 in vitro induced the EBV replicative cycle in these cells, as evidenced by an increased proportion of cells expressing EBV early antigens (EA) and capsid antigens (VCA). Reactivation of EBV by HIV-1 appeared to be virus-dose-dependent and required virus penetration and expression in B cells. Although HIV-1 RNA was detected by in situ hybridization in the majority of HIV-1-infected B lymphocytes, induction of EA and VCA was transient and limited to less than 20% of the cell population. The tumor-promoting phorbol ester 12-O-tetradecanoyl-phorbol-13-acetate (TPA) and HIV-1 acted synergistically and had similar kinetics in inducing the expression of EBV. Direct reactivation of EBV by HIV-1 may contribute to the role of EBV as a factor in the genesis of AIDS-related conditions.

Quantitation of hepatitis B viral DNA by solution hybridization: comparison with DNA polymerase and hepatitis B e antigen during antiviral therapy

Serological markers of hepatitis B virus (HBV) replication were assessed in a randomized, controlled trial of prednisone withdrawal followed by alpha-interferon in the treatment of chronic hepatitis B. HBV DNA levels in more than 700 serial serum samples from 41 patients were determined by a sensitive and quantitative solution hybridization assay. Results were compared with HBV DNA polymerase (DNAp) activity and hepatitis B e antigen (HBeAg) in 21 untreated controls and 20 treated patients. Among treated patients, the mean pretherapy HBV DNA values were higher in nonresponders than in responders. During prednisone treatment, DNA levels increased an average of 2.1-fold in responders and 1.4-fold in nonresponders. During the 2-week rest interval between prednisone and interferon, DNA values fell an average of 57% in responders. In contrast, the mean DNA values in nonresponders did not change during the same interval. This early distinction between responders and nonresponders was not apparent from DNAp or HBeAg results. During interferon treatment, HBV DNA became undetectable in responders and remained negative during a 1-year follow-up. DNA in nonresponders declined to 14% of baseline during interferon treatment but increased to pretherapy levels after treatment. DNAp values generally paralleled HBV DNA values, but DNAp activity showed more variability and lower sensitivity than did the hybridization assay results. HBeAg values varied independently of HBV DNA and DNAp with a much delayed decline in responders. These results indicate that HBV DNA, when measured quantitatively by a sensitive solution hybridization assay, is an early predictor of the effects of antiviral agents on replication.

Interleukin-2-induced tumor necrosis factor-alpha (TNF-alpha) gene expression in human alveolar macrophages and blood monocytes

Recent investigations have demonstrated interleukin-2 receptor (IL-2R) expression on both human alveolar macrophages (AM phi) and blood monocytes (PBM), but the function of these receptors has not been fully elucidated. In this study, we demonstrate that human AM phi, as well as PBM, can be induced to express biologically active TNF-alpha after challenge with interleukin-2 (IL-2). Furthermore, we examined the expression of TNF-alpha at the mRNA level via Northern blot and in situ hybridization analysis. Normal AM phi, obtained by bronchoalveolar lavage, and PBM were stimulated with either IL-2 (2,000 U/ml) or lipopolysaccharide (LPS) (10 micrograms/ml) for 18 h. Specificity was demonstrated by neutralizing TNF-alpha activity with a polyclonal rabbit anti-human TNF-alpha antibody. PBM TNF-alpha biologic activity from 11 subjects challenged with either IL-2 or LPS was 19 +/- 6 and 85 +/- 15 U/ml/10(6) cells, respectively, which represented 5-fold and 21-fold increases over control values. AM phi TNF-alpha biologic activity from nine subjects was 110 +/- 28 (IL-2-mediated) and 304 +/- 69 (LPS-mediated) U/ml/10(6) cells, which represented 2- and 6-fold increases over controls. AM phi exhibited statistically greater (p less than 0.05) TNF production in response to both IL-2 and LPS as compared to PBM. IL-2 challenge resulted in an induction of TNF-alpha mRNA accumulation, as demonstrated by Northern blot and in situ hybridization analyses. TNF-alpha mRNA was quantitated by laser densitometry for Northern blots or by counting the number of silver grains/mononuclear phagocytic cell in the in situ hybridization analysis.(ABSTRACT TRUNCATED AT 250 WORDS)

Effects of 5-fluorouracil on cytotoxicity and RNA metabolism in human colonic carcinoma cells

The cytotoxicity of 5-fluorouracil (5-FU) is due in part to the incorporation of the base into RNA molecules. We assessed the cytotoxicity of 5-FU in human colonic carcinoma HT-29 cells and examined mRNA activity (measured by protein biosynthesis in vivo and in vitro) and the maturation of rRNA precursors as two possible modes of action of 5-FU. The rRNA processing pathways were studied using rDNA sequences as probes in blot hybridisation protocols and were specific for both the precursors and mature rRNA species of the maturation pathways. The conclusion from the studies was that although differences in mRNA activity were detected in vivo and in vitro, the significance of these changes are as yet unknown. In contrast, the effects on the pre-rRNA processing pathways proved to be highly significant cytotoxic consequences of 5-FU administration. We discuss the implications of this finding for an understanding of the mode of action of the drug and for the future monitoring of tumour sensitivity to 5-FU.

In situ cellular analysis of alpha-fetoprotein gene expression in regenerating rat liver after partial hepatectomy

Cellular analysis of hepatic alpha-fetoprotein gene expression in normal adult rat and during regeneration induced by partial hepatectomy was performed at the cellular level by in situ hybridization using 35S-labeled complementary DNA probes and immunoperoxidase techniques. In normal adult rat liver sections, a few alpha-fetoprotein mRNA-cDNA hybrids are detected over all hepatocytes. No protein is detected with routine immunoperoxidase methods. However, after in vivo colchicine blockade of alpha-fetoprotein secretion, 10 to 20% alpha-fetoprotein-positive hepatocytes are observed. In regenerating livers, at 2,6 and 24 hr (before and at the time of the peak of DNA synthesis in the periportal zones), a rise of the nuclear signal level is observed selectively in periportal hepatocytes, without modification of the cytoplasmic signal. At 48 hr (when most hepatocytes have completed at least one replicative cycle), almost all hepatocytes throughout the liver lobule display a rise of the nuclear (2- to 3-fold) and cytoplasmic (1.5- to 2-fold) signal level compared to nonoperated rats. These data show that all hepatocytes in the adult liver express a small number of alpha-fetoprotein mRNA sequences; they appear to be translated in protein whose secretion can be blocked by colchicine. The moderate increase in alpha-fetoprotein gene expression induced by liver regeneration takes place in all hepatocytes, in apparently two distinct steps: a very early nuclear accumulation of alpha-fetoprotein mRNA sequences and a late cytoplasmic accumulation of alpha-fetoprotein mRNA molecules.

Transcript mapping using [35S]DNA probes, trichloroacetate solvent and dideoxy sequencing ladders: a rapid method for identification of transcriptional start points

A simple method for RNA transcript mapping has been developed that combines the use of 35S-labeled M13 DNA probes and the presence of high concentrations of sodium trichloroacetate in the hybridization buffer. These hybridization conditions permit the use of M13 probes without purification from the template. The dideoxy sequencing ladders used for sizing the protected DNA fragments are obtained from the same M13 templates utilized to synthesize the DNA probes. The method was tested by analyzing the transcripts controlled by lac, ptr and trxA promoters. Comparison of the results with previously published data obtained with the conventional S1 nuclease mapping technique indicated that the present method is just as precise and at least 50 times more sensitive. Clones constructed for sequencing a gene of interest can be used directly to identify transcriptional start points.

Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology

To address the long-standing need for more precise descriptions of natural microbial ecosystems, 16S rRNAs were used to track certain species and phylogenetically coherent groups of microorganisms in their natural setting without culturing. Species- and group-specific 16S rRNA-targeted oligonucleotide hybridization probes were developed to enumerate various strains of Bacteroides succinogenes and Lachnospira multiparus-like organisms in the bovine rumen before, during, and after perturbation of that ecosystem by the addition of the ionophore antibiotic monensin. Based on probe hybridization, relative numbers of L. multiparus-like organisms were depressed about 2-fold during monensin addition and demonstrated a transient 5- to 10-fold increase immediately after removal of the antibiotic from the diet. The most pronounced population changes were observed among different strains of B. succinogenes, as evaluated by three hybridization probes. One probe hybridized to all strains, whereas the other two identified genetically distinct groups represented by strains isolated from the rumen and from the ceca of nonruminants. The rumen-type strains predominated on most days (ca. 0.2 to 0.8% of total ribosome numbers). Their proportion transiently increased about fivefold immediately after the addition of monensin to the feed and then transiently fell below the average premonensin level. During this time (ca. 2 weeks after monensin addition) the cecal type predominated (ca. 0.1 to 0.2%). Cultural enumeration of B. succinogenes on nonselective agar and by observing clearings in cellulose agar media were largely unsuccessful due to the low number of organisms present and the predominance of other cellulolytic species.(ABSTRACT TRUNCATED AT 250 WORDS)

Deoxycytidine methylation does not affect DNA.RNA hybrid formation or B-A transitions of (dG)n.(dC)n sequences

Optical thermal denaturation and circular dichroism (CD) experiments were performed with the following non-selfcomplementary duplex DNA, RNA and DNA.RNA hybrids: (I) dGAG3C3G3CTC.dGAGC3G3C3TC, (II) dGAG3m5C3G3m5CTC.dGAGm5C3G3m5C3TC, (III) rGAG3C3G3CUC.rGAGC3G3C3UC, (IV) dGAG3C3G3CTC.rGAGC3G3C3UC, (V) rGAG3C3G3CUC.dGAGC3G3C3TC, (VI) dGAG3m5C3G3m5CTC.rGAGC3G3C3UC, (VII) rGAG3C3G3CUC.dGAGm5C3G3m5C3TC. Duplex stabilities (delta G degrees at 60 degrees C) increase in the order: I less than IV less than II = V = VI less than VII less than III. Large enthalpic stabilization is associated with intrastrand stacking of guanosine (rG) residues. CD spectroscopy indicates B-form conformations for the unmethylated and methylated DNA (I,II), A-form geometry for the RNA (III), and DNA.RNA hybrid (IV - VII) conformations resembling but not identical to A-RNA. C5-methyldeoxycytidine does not significantly influence DNA conformation, DNA.RNA hybrid formation, or the ability of DNA to adopt an A-type conformation in trifluoroethanol solutions.

Dexamethasone inhibits corticotropin-releasing factor gene expression in the rat paraventricular nucleus

The effect of glucocorticoids on corticotropin-releasing factor (CRF) gene expression was studied by combination of in situ hybridization histochemistry and steroid implantation. Dexamethasone micropellets, implanted around the hypothalamic paraventricular nucleus (PVN), caused total inhibition of the hybridizable CRF mRNA signal above the parvocellular neurons of the PVN. Unilateral implantation of dexamethasone around the PVN resulted in a decrease of hybridizable CRF mRNA at the dexamethasone-implanted side. Dexamethasone implants into the cerebral cortex, dorsal hippocampus, ventral subiculum, lateral septum or amygdala were without any effect on the CRF expression in the PVN. Corticosterone did not result in any significant change in CRF mRNA, when implanted into the paraventricular region, dorsal hippocampus or ventral subiculum. When it was placed into the amygdala however, in a few cases it slightly inhibited the CRF mRNA levels in the ipsilateral PVN.