Enhanced expression of the bacterial chloramphenicol acetyltransferase gene in mouse cells cotransfected with synthetic polynucleotides able to form Z-DNA

Bias of purine stretches in sequenced chromosomes

We examined more than 700 DNA sequences (full length chromosomes and plasmids) for stretches of purines (R) or pyrimidines (Y) and alternating YR stretches; such regions will likely adopt structures which are different from the canonical B-form. Since one turn of the DNA helix is roughly 10 bp, we measured the fraction of each genome which contains purine (or pyrimidine) tracts of lengths of 10 bp or longer (hereafter referred to as 'purine tracts'), as well as stretches of alternating pyrimidines/purine (pyr/pur tracts') of the same length. Using this criteria, a random sequence would be expected to contain 1.0% of purine tracts and also 1.0% of the alternating pyr/pur tracts. In the vast majority of cases, there are more purine tracts than would be expected from a random sequence, with an average of 3.5%, significantly larger than the expectation value. The fraction of the chromosomes containing pyr/pur tracts was slightly less than expected, with an average of 0.8%. One of the most surprising findings is a clear difference in the length distributions of the regions studied between prokaryotes and eukaryotes. Whereas short-range correlations can explain the length distributions in prokaryotes, in eukaryotes there is an abundance of long stretches of purines or alternating purine/pyrimidine tracts, which cannot be explained in this way; these sequences are likely to play an important role in eukaryotic chromosome organisation.

Sequencing and characterization of the human thiazide-sensitive Na-Cl cotransporter (SLC12A3) gene promoter

The thiazide-sensitive Na-Cl cotransporter SLC12A3 displays expression restricted to distal convoluted tubule cells where it catalyzes the uptake of sodium and chloride through the apical membrane. We sequenced 1959 bp of the 5' flanking region of human SLC12A3, located the area of transcription initiation, and used deletion constructs of the flanking region to determine areas that affect reporter gene expression in two cell lines, MDCT and CHO. Amplification of the 5' end of SLC12A3 cDNA from an adapter-ligated human kidney cDNA library demonstrated that transcription initiation is confined to an area from -18 to -6 bp upstream of the translation start codon. Maximum promoter activity (9.815 +/- 0.864 times control) was observed in MDCT cells using a promoter containing 1019 bp of the 5' flanking region. A promoter containing only 134 bp of the 5' flanking region upstream of the translation initiation codon maintained reporter gene expression at levels equal to 75% of that maximally observed (7.375 +/- 0.533 times control). Sequence analysis of this minimal promoter responsible for most of the SLC12A3 promoter activity revealed a TATA element, two Sp binding sites, a potential E box, and a potential binding site for NF-1/CTF or NY-I/CP-I. This promoter, and all other promoter constructs from SLC12A3, displayed repressor activity in CHO cells. A construct containing sequence 94 bp upstream of the initiation codon with two potential Sp binding sites was required for this repression. Protein-DNA interactions between the 182 bp region immediately upstream of the start codon and the nuclear proteins from rat kidney cortex and HeLa cells were examined to further clarify the role of the putative binding sites for SLC12A3 expression. Physiological studies investigating the effects of osmolarity, pH, and mineralocorticoid steroid on promoter activity demonstrated that the promoter activity was repressed by acidification, whereas no effects of increased osmolarity or deoxycorticosterone acetate addition were observed.

A potential Z-DNA-forming sequence is located between two transcription units alternatively expressed during development of Drosophila hydei

Recent studies have demonstrated that Z-DNA exists in vivo in Escherichia coli as well as in Drosophila and mammalian cells. In the present paper, we show the existence in vivo of Z-DNA epitopes in the developmentally regulated subregion 4-75C of polytene chromosomes in Drosophila hydei. The Z-DNA epitopes were detected in subdivision C2 only during late third instar when the transcriptional activity of the locus was high. Accumulation of nonhistone chromosomal proteins in that locus was also detected during late third instar only at the time of the Z-DNA formation. Northern blot data and nucleotide sequence analysis indicated that the Z-DNA-forming sequence is located between two transcription units whose expression is regulated during the third instar. Our results suggest that in subdivision 4-75C2 a B- to Z-DNA flux occurs at a specific time during late third instar and that this flux may play a negative as well as a positive role in gene expression.

Molecular cloning of a Drosophila potential Z-DNA forming sequence hybridizing in situ to a developmentally regulated subdivision of the polytene chromosomes

We describe the selection of a group of plasmids with potential to form Z-DNA, from libraries of Drosophila hydei nuclear DNA using anti Z-DNA monoclonal (22) or polyclonal (10c) antibodies. The supercoiled closed circular forms of most of the selected recombinant plasmids from the 10c Z-DNA library show affinity to the polyclonal 10c antibody as indicated by DNA binding assays. One of these plasmids, pF17, was selected for further study. The insert in this plasmid adopts the Z conformation at bacterial supercoiled density. Analysis of deletion plasmids indicates that a Z-epitope is located within a short fragment of the insert in which 3 GC repetitions are found. The Drosophila DNA insert in pF17 hybridizes in situ with locus 4-75C1-2 of the polytene chromosomes, a locus whose transcriptional activity is developmentally regulated during the third instar.

Identification of protein-binding sites in the hepatitis B virus enhancer and core promoter domains

We have investigated the role of liver-specific trans-acting factor(s) in the regulation of hepatitis B virus (HBV) gene expression. A recorder plasmid (pEcoAluCAT; HBV nucleotides 1 through 1878) was constructed containing the HBV enhancer and the promoter region of the pregenomic RNA, which was ligated to the bacterial chloramphenicol acetyltransferase (CAT) gene. Upon transfecting this plasmid into various cell lines, the CAT gene was expressed only in cells of liver origin. Moreover, competition cotransfections with pEcoAluCAT and plasmids containing HBV enhancer sequences in human hepatoblastoma-derived HepG2 cells indicated the presence of titratable trans-acting factor(s) in these cells. Gel mobility shift assays using HBV enhancer and core promoter domains confirmed the existence of sequence-specific DNA-binding proteins in liver cell nuclear extract which bound to these regions. These binding sites encompass 17- and 12-nucleotide palindromes in the HBV enhancer and core promoter domains, respectively, when mapped by the methylation interference assay.

Identification of protein-binding sites in the hepatitis B virus enhancer and core promoter domains

We have investigated the role of liver-specific trans-acting factor(s) in the regulation of hepatitis B virus (HBV) gene expression. A recorder plasmid (pEcoAluCAT; HBV nucleotides 1 through 1878) was constructed containing the HBV enhancer and the promoter region of the pregenomic RNA, which was ligated to the bacterial chloramphenicol acetyltransferase (CAT) gene. Upon transfecting this plasmid into various cell lines, the CAT gene was expressed only in cells of liver origin. Moreover, competition cotransfections with pEcoAluCAT and plasmids containing HBV enhancer sequences in human hepatoblastoma-derived HepG2 cells indicated the presence of titratable trans-acting factor(s) in these cells. Gel mobility shift assays using HBV enhancer and core promoter domains confirmed the existence of sequence-specific DNA-binding proteins in liver cell nuclear extract which bound to these regions. These binding sites encompass 17- and 12-nucleotide palindromes in the HBV enhancer and core promoter domains, respectively, when mapped by the methylation interference assay.

Biocatalysis made to order

Recombinant DNA technology is now being explored to engineer enzyme molecules. It has many far-reaching applications in biocatalytic processes of enzyme engineering. The facts have pursued certain important industrial, biomedical, and environmental problems. These current excitements are mainly focused on the basis of gene cloning and in vitro mutagenesis for overproduction and redesigning of enzymes, as well as their probable implications in industry, antibiotic research, and waste degradation.