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A general study has been carried out to determine how well hammerhead ribozymes might reduce levels of specific protein synthesis in living cells, compared with RNA hairpin loops as stable but noncleaving controls. Four different experiments are described. First, a wide variety of hammerhead ribozymes, as well as hairpin loops, was cloned into a gene-expression cassette for beta-galactosidase, upstream of the coding sequences for that reporter gene, and expressed from plasmids in several strains of Escherichia coli. The results show that ribozymes, when acting intramolecularly in E. coli, do not significantly reduce the amount of protein synthesized from any construct. As a control, long RNA hairpin loops do greatly reduce the amount of protein made. Secondly, we studied the transcription-translation of these same plasmids in a cell extract from E. coli. Once again, hammerhead ribozymes show no effect on levels of beta-galactosidase, whereas long RNA hairpin loops produce a strong reduction, by apparent attentuation at the level of translation. Thirdly, we added an SV40 promoter to each plasmid, in order to study the effects of these gene-regulators on protein synthesis in Chinese hamster ovary cells. Here active intramolecular ribozymes produce a slight reduction in beta-galactosidase, whereas long RNA hairpin loops produce an even stronger reduction than before. Those hairpin loops apparently induce degradation of their own mRNA in Chinese hamster ovary cells, by a mechanism not seen in E. coli. Finally, analyses of total RNA by S1-trimming show that hammerhead ribozymes will self-cleave a mRNA by a total of no more than 45-50% in E. coli, compared with 70-80% in vitro. Other analyses using Northern blotting were unable to detect any ribozyme cleavage in E. coli or Chinese hamster ovary cells. In summary, the ability of hammerhead ribozymes to reduce protein synthesis appears weak or nonexistent in all the cellular systems tested. By comparison, long RNA hairpin loops reduce protein synthesis strongly: by an apparent attentuation mechanism in E. coli or by a novel degradation of their own mRNA in Chinese hamster ovary cells.

The family of cationic lipid transfection reagents described here demonstrates a modular design that offers potential for the ready synthesis of a wide variety of molecular variants. The key feature of these new molecules is the use of Tris as a linker for joining the hydrophobic domain to a cationic head group. The molecular design offers the opportunity to conveniently synthesise compounds differing in charge, the number and nature of hydrophobic groups in the hydrophobic domain and the characteristics of the spacer between the cationic and hydrophobic moieties. We show that prototype reagents of this design can deliver reporter genes into cultured cells with efficiencies rivaling those of established cationic lipid transfection reagents. A feature of these reagents is that they are not dependent on formulation with a neutral lipid for activity.

A crucial step in cell migration involves changes in the actin cytoskeleton in response to extracellular signals. We have previously shown that beta-actin transcripts are associated with mobile regions of mouse 3T3 fibroblasts when grown in the presence of serum. In the current study we used in situ hybridization and laser scanning confocal microscopy to show that cultured rat smooth muscle cells also localize beta-actin mRNA to the cell periphery and that this peripheral pool of beta-actin mRNA is dependent on the presence of growth factors in the culture medium. We also show that antisense phosphorothioated oligonucleotides directed against sequences in the 3' untranslated region of rat beta-actin mRNA block peripheral localization of beta-actin mRNA while the corresponding control oligonucleotides have no effect. Time-lapse video analysis demonstrates that the antisense oligonucleotides inhibit rat smooth muscle cell migration in culture and analysis of beta-actin mRNA confirms this is not due to changes in beta-actin gene expression or instability of the message. Our results suggest that depletion of beta-actin transcripts from the cell periphery is associated with suppression of SMC migration.

A "minizyme" is a smaller version of the hammerhead ribozyme, in which stem-loop II has been replaced by a short linker. Here, we have synthesised a DNA-containing minizyme and a ribozyme, which are designed to cut within a 15-nucleotide sequence in human interleukin-2 mRNA, and have tested for their activity in vitro and in cells. In vitro at 37 degrees C, a minizyme with linker of sequence d(GTTTT) cleaves a 15-ribonucleotide synthetic substrate 5-fold slower than does the full-sized ribozyme. In human cells, the minizyme inhibits the production of interleukin-2 protein to a similar extent as does the ribozyme. Also, the minizyme and the ribozyme are more effective in cells than any of three controls: an inactive minizyme, a 15-nucleotide antisense DNA, or DNA of random sequence. The positive effect observed in cells indicates that minizymes may be useful as pharmaceuticals.

The rate of cleavage of a 13-mer substrate by an all-RNA ribozyme with 2 10-mer hybridising arms (TAT RA), appears to be limited by a conformational change involving the longer than necessary arms. The same limitation does not apply to a similar ribozyme with DNA arms (TAT RB) or to an all-RNA ribozyme with only 6 hybridising bases on each arm (TAT RA 6x2). The limitation does not arise in the hybridisation step nor in the dissociation of products. An extra step involving a conformational change of the pre-formed ribozyme-substrate prior to cleavage is introduced to explain the observed kinetics.

We describe a new vector for the P-element-mediated introduction of gene constructs into the germ line of Drosophila melanogaster. The P-element vector carries 6.8 kb of genomic DNA containing the rough gene (ro) from D. melanogaster and a polylinker (MCS) containing ten unique cloning sites. To demonstrate its utility, we have cloned into the MCS of this vector, the firefly luciferase (Luc)-encoding gene (luc) under the control of the D. melanogaster hsp70 promoter and have transformed flies with the resultant P-element. Single insertions of this element, whether in the hemizygous or homozygous condition, completely rescued the ro- mutation and directed heat-inducible synthesis of Luc mRNA and enzyme.

A method for the efficient preparation of high quality bacteriophage lambda DNA from cleared lysates is described. Advantages of the method include high DNA yields (typically around 0.8 micrograms of DNA/1 ml of cleared lysate), speed of processing (approximately 2 h from lysate to DNA), economy, and the absence of any requirement for phenol or chloroform extractions. The technique involves the concentration of phage particles by standard polyethylene glycol precipitation followed by enzymatic treatment to remove contaminating RNA and DNA. Phage particles are then lysed with sodium dodecyl sulfate (SDS) at elevated pH and temperature. Contaminating protein/SDS complexes are rendered insoluble by the addition of potassium acetate and removed by centrifugation. The quality of the resultant DNA is comparable to that prepared by cesium chloride banding for all standard molecular biological purposes providing that spermidine is included in all restriction endonucleases digestions.

DNA competition studies have been used to investigate the presence of a repressor of viral enhancer function in F9 mouse embryonal carcinoma cells. The complete polyoma virus enhancer region, cotransfected into F9 cells with the SV40 promoter/enhancer attached to a chloramphenicol acetyl transferase marker gene, induced a small increase in pSV2CAT expression. This can be explained by preferential but weak binding by polyoma sequences of a molecule repressing pSV2CAT transcription. Repressor activity substantially disappeared when the cells were induced to differentiate by retinoic acid. Repressor binding was localised to one half of the polyoma enhancer, but was lost on further fragmentation of this region. It appears that multiple sequence elements may be required for repressor binding and that these are at least partially separable from the complement of elements binding enhancer activating molecules.

The transient expression vector pSV2CAT, which carries the bacterial chloramphenicol acetyl transferase (CAT) gene under the control of the SV40 early promoter, was used to transfect the murine embryonal carcinoma cell line F9 at various times during the retinoic acid-induced differentiation of these cells. Expression of the CAT gene under SV40 promoter control was found to increase markedly on F9 cell differentiation, measured relative to expression from the thymidine kinase promoter in the same cells. A series of constructs was prepared to identify the features of the SV40 early promoter required for transcription in differentiated and undifferentiated cells, as well as the factors limiting transcription in each case. The increased transcription seen on F9 cell differentiation was not observed when cells were transfected with molecules lacking a functional enhancer. It appears that as embryonal carcinoma cells differentiate, increased SV40 transcription results from enhancer sequence activation. In both differentiated and undifferentiated cell types the level of transcription was found to be limited by the availability and/or activity of cellular factors necessary for enhancer function.

Differentiation of F9 mouse embryonal carcinoma cells in culture is accompanied by a decrease in growth rate and loss of tumorigenicity. Cells differentiating in monolayer culture (to parietal endoderm-type cells) or in aggregates (to visceral endoderm-type cells) show qualitatively similar changes in transcript levels from several c-oncogenes. In contrast with other studies with F9 cells, we find an early decrease in c-myb RNA but not in c-myc RNA. This and a later increase in c-src RNA may be associated with decreasing cell growth rate. Before differentiation, induction and maintenance of elevated c-abl RNA levels depend on the presence of retinoic acid in the medium. After differentiation c-abl RNA levels decline only partially when retinoic acid is removed. Increased RNA from c-fos is seen late in differentiation in monolayer cultures only, a change also seen with appearance of similar endoderm cell types in the developing mouse embryo.

Homoeo-box genes play a central role in the regulation of embryogenesis in Drosophila melanogaster. Their widespread phylogenetic distribution, and the tissue and stage specificity of their expression in other organisms, argue that they play a general and significant role in animal development. In D. melanogaster, all homoeo-box genes characterized to date are involved in major aspects of embryogenesis. We report here the molecular characterization of a Drosophila homoeo-box gene that has no apparent involvement in early embryogenesis. The gene appears to be rough, a gene implicated in pattern formation in the developing eye. It is expressed in cells within, and posterior to, the morphogenetic furrow, the site of the primary pattern forming events in the developing retina, and also in a region of the brain of the third instar larva. We have found no genetic or molecular evidence of a role for this gene in other aspects of fly development.

The Notch locus appears to correspond to a 37 kb transcription unit. Homologous poly(A)+ RNA is about 11.7 kb. Nine RNA coding regions have been detected and localized within the transcription unit by S1 nuclease analyses. These range in size from 130 to 7250 bp. Sequences within the 3' coding region are variably used. Twenty-four Notch locus "point" mutations have been examined. Seven are associated with DNA insertions. Four insertions are associated with dominant mutations and are located within or very near RNA coding sequences of the 37 kb transcription unit. Three insertions are associated with recessive mutations and fall within intervening sequences. The positions of all insertions agree with the genetic map. It is estimated that, in the Notch region, one map unit corresponds to approximately 275 kb. On this basis, most of the 17 mutations that were not associated with DNA insertions can be placed within coding sequences of the 37 kb transcription unit.

The enzyme alcohol dehydrogenase of Drosophila melanogaster is encoded by a single structural gene (Adh) with two promoters, distal and proximal (PD and PP). During development these two promoters are used differently: the major Adh transcript of larvae is from PP, the major transcript of adult flies is from PD. At a few discrete times in development transcription occurs simultaneously from both promoters. In situ hybridization has been used to investigate the spatial and temporal aspects of promoter activity at these stages of development. Maternally inherited Adh transcripts are not localized in the embryo; they decay very rapidly after fertilization. Zygotic expression of Adh RNA begins after germ-band retraction, 10.5 hr after fertilization. Expression is confined to the fat body, but occurs from both distal and proximal promoters. By 15 hr expression is first seen in the gut, from PP. By the same time fat body expression from PD has ceased, and transcription in this tissue is exclusively from PP for the next 4 days. The steady-state level of Adh transcript begins to decline at the end of larval development. There is then the transient accumulation of transcripts from PD, but predominantly in the larval fat body, rather than in the gut. These data illustrate a surprising complexity in the tissue and temporal regulation of Adh expression in D. melanogaster. Moreover, they show that transcripts from two different promoters of the same gene can, at certain well-defined stages of development, accumulate in the same cells.