Chemical DNA synthesis and recombinant DNA studies.

Chemically synthesized DNA has been used in many recombinant DNA studies. These uses have included the total synthesis and cloning of functional genes, the cloning and expression of natural genes, and editing of changing genes by directed mutation.

DNA conformation, dynamics, and interactions in solution.

The conformation and dynamics of the d(CGCGAATTCGCG) duplex, its analogs containing mismatched base pairs and helix interruptions, and its complexes with actinomycin and Netropsin, bound separately and simultaneously, have been investigated by nuclear magnetic resonance spectroscopy in aqueous solution. Structural information has been deduced from chemical shift and nuclear Overhauser effect parameters, while the kinetics have been probed from line width and saturation recovery experiments on proton and phosphorus markers at the individual base pair level. These studies lead to an improved understanding of the role of nucleic acid sequence on the structure, flexibility, and conformational interconversions in the duplex state. The nuclear magnetic resonance measurements readily identify helix modification and antibiotic binding sites on the nucleic acid and estimate the extent to which the observed conformational and dynamic perturbations are transmitted to adjacent base pair regions.

Requirement for signal peptide cleavage of Escherichia coli prolipoprotein.

Oligonucleotide-directed site-specific mutagenesis was applied to alter the cleavage site in the signal peptide of the major outer membrane lipoprotein of Escherichia coli. Replacing the glycine residue at the cleavage site with an alanine residue did not affect the processing of the signal peptide. However, when the same cleavage site was constructed by the deletion of the glycine residue, the signal peptide was no longer cleaved. These results indicate that stringent structural integrity at the cleavage site in the lipoprotein signal sequence is required for correct processing of prolipoprotein.

Directed deletion of a yeast transfer RNA intervening sequence.

Many eukaryotic genes contain intevening sequences, segments of DNA that interrupt the continuity of the gene. They are removed from RNA transcripts of the gene by a process known as splicing. The intervening sequence in a yeast tyrosine transfer RNA (tRNA Tyr) suppressor gene was deleted in order to test its role in the expression of the gene. The altered gene and its parent were introduced into yeast by transformation. Both genes exhibited suppressor function, showing that the intervening sequence is not absolutely essential for the expression of this gene.

Chemical synthesis of restriction enzyme recognition sites useful for cloning.

By a triester chemical synthesis method, three decameric DNA's have been made; these act as substrates for several restriction endonucleases, including Eco RI, Bam I, and Hind III. These homogenous decamers form duplexes that can be efficiently blunt-end ligated to themselves or to other DNA molecules by the action of T4 DNA ligase and thus are useful tools for molecular cloning experiments.

Location of the second gene required for expression of the leukemia-associated mouse antigens G IX .

Some mouse strains express G(IX) antigen on their thymocytes; others do not. Expression depends on two genes, Gv-1 and Gv-2, in linkage groups IX and I, respectively. Cells producing leukemia virus, however, express G(IX) antigen regardless of their inherited Gv-1 and Gv-2 genotype.

Expression in Escherichia coli of a chemically synthesized gene for the hormone somatostatin.

A gene for somatostatin, a mammalian peptide (14 amino acid residues) hormone, was synthesized by chemical methods. This gene was fused to the Escherichia coli beta-galactosidase gene on the plasmid pBR322. Transformation of E. coli with the chimeric plasmid DNA led to the synthesis of a polypeptide including the sequence of amino acids corresponding to somatostatin. In vitro, active somatostatin was specifically cleaved from the large chimeric protein by treatment with cyanogen bromide. This represents the first synthesis of a functional polypeptide product from a gene of chemically synthesized origin.

A bipartite suppressor: conjunction of two distinct factor-binding sites is essential for down-regulation in rat epoxide hydrolase gene expression.

We describe a novel transcriptional suppressor element found in the control region of the gene that encodes rat microsomal epoxide hydrolase (mEH), an inducible xenobiotic metabolizing enzyme. This element consists of the juxtaposition of two distinct factor-binding regions. The first region is composed of a series of five tandemly repeated factor-binding sequences, and the second region is an unique AT-rich factor-binding sequence. Although each region binds its cognate factor(s) in vitro, a single region does not function as a suppressor independently of the other. Transcriptional suppression was observed only when the two regions were combined. Thus, we propose that this regulatory element is a bipartite suppressor, requiring two distinct factor-binding regions for its function. The element displayed position-independent but orientation-dependent suppressor activity. The level of suppressor activity was proportional to the number of repetitive sites in region 1. We speculate that this region could mediate the dose-response behavior of mEH gene expression induced by chemical carcinogens in vivo. A qualitative difference in the region 2 binding factor(s) was observed between normal liver cells and a hepatoma cell line or carcinogen-treated liver cells. The possible relationship between this observation and the deregulation of mEH gene expression during the course of hepatocarcinogenesis is discussed.

Human monoclonal antibody identified an immunoreactive tetrapeptide sequence (Lys-Tyr-Gln-Ile) in M(r) 43,000 protein of human melanoma.

The human monoclonal antibody (HuMAb) L92 reacts to an M(r) 43,000 protein associated with human melanoma. To identify the gene encoding its antigenic epitope, a complementary DNA expression library constructed from the human melanoma cell line UCLASO M14 was screened with HuMAb L92. DNA sequence analysis of the isolated clone revealed that the immunoreactive peptide was composed of 10 amino acids (QDLT-MKYQIF). The peptide was expressed in Escherichia coli with beta-galactosidase as a fused protein. There is no homology between the cloned sequence and other reported DNA sequences. Western blot analysis showed that the fused protein had specific binding to HuMAb L92. An antigen-encoding peptide with 10 amino acids was synthesized and tested for its immunoreactivity in vitro. HuMAb L92 reacted specifically to the 10-amino acid peptide in both an antibody-binding inhibition to the M(r) 43,000 protein and a solid-phase enzyme-linked immunosorbent assay. Using several truncated fusion proteins, we found the minimum number of amino acids required for the antibody binding to be 4 (KYQI). These results suggest that the identified peptide sequence encodes the antigenic epitope of the M(r) 43,000 protein.

Induction of heat shock gene expression without heat shock by hepatocarcinogens and during hepatic regeneration in rat liver.

We investigated the expression of the rat hepatic heat-shock protein (hsp) genes under the influence of hepatocarcinogens and during hepatic regeneration. This was undertaken because of the inducibility of the heat-shock response in rat liver and because heat-shock genes can be expressed with or without heat shock in various cell states in a developmentally regulated manner. We found that acute administration of hepatocarcinogens to rats induced an increased hsp gene transcription in a time- and dose-dependent manner. Chronic exposure of rats to complete hepatocarcinogens induced increased levels of mainly Mr 83,000 heat-shock protein gene transcription and, to a lesser extent, Mr 70,000 heat-shock protein. However, the tumor promoter phenobarbital did not induce increased hsp gene expression. Increased levels of both Mr 83,000 heat-shock protein and Mr 70,000 heat-shock protein gene transcription were found during hepatic regeneration. Thus, increased hsp gene transcription, which correlated with increased heat-shock protein synthesis, was observed under the acute and chronic influence of hepatocarcinogens and during normal hepatic proliferation. These results are similar to those observed for c-H-ras and c-myc expression in rat liver, and they suggest that a coordinate expression of these three genes may occur in hepatic regeneration and in the early stages of experimental chemical hepatocarcinogenesis.

Expression of rat microsomal epoxide hydrolase gene during liver chemical carcinogenesis.

A complementary DNA library was constructed from mRNA of rat liver induced by an initiating dose of a chemical carcinogen, diethylnitrosamine. Using a differential hybridization technique, a complementary DNA clone which is induced more than 10-fold by an acute single dose of diethylnitrosamine was identified. The DNA sequence of this clone was matched with rat microsomal epoxide hydrolase. This gene may be of great interest, since it was found to be highly expressed in neoplastic nodules and primary hepatocellular carcinomas induced by different carcinogenic regimes. The inducible high level expression of this gene becomes constitutive during the process of hepatocarcinogenesis. The gene was also found to be inducibly expressed during partial hepatectomy in a similar manner as a multidrug-resistant gene (mdr-I). No change in the transcriptional initiation site was observed in the gene expression between induced and uninduced rat livers. The 5' upstream region of the gene was characterized and some potential controlling elements for gene regulation, such as Sp-1, AP-2, and Hepatitis B virus enhancer, were found. Based on our own and published results, we hypothesize that the altered expression of this xenobiotic enzyme in nodules and cancer cells could be a result of constitutive internal stimuli which might be associated with cell growth.

MAZ, a Myc-associated zinc finger protein, is essential for the ME1a1-mediated expression of the c-myc gene during neuroectodermal differentiation of P19 cells.

To investigate whether MAZ (Myc-associated zinc finger protein) affects the expression of the c-myc gene during the retinoic acid-induced (RA-induced) neuroectodermal differentiation of P19 embryonal carcinoma (EC) cells, we introduced a CAT reporter construct, human c-myc promoter/CAT (pMyc2CAT), and a mutant CAT derivative that lacked an ME1a1 site (pMyc1CAT) into P19EC cells to monitor the promoter activity of the c-myc gene. The expression of CAT in pMyc2CAT-transformed cells declined fivefold after 24 h in the presence of RA, returned to the normal level within 48 h, and decreased again to below 20% of the normal level after 96 h. By contrast, the expression of CAT in pMyc1CAT-transformed cells did not return to the normal level after 48 h in the presence of RA. In addition, an electrophoretic mobility shift assay (EMSA) with ME1a1 DNA as probe demonstrated that the kinetics of the DNA-binding activity of MAZ were closely correlated with the changes in the expression of CAT from the c-myc promoter/CAT gene during the differentiation of P19EC cells. Taken together, these results suggest that MAZ plays a key role in the transient increase in the expression of the c-myc gene after 48 h of exposure to RA during the neuroectodermal differentiation of P19EC cells.

Saccharomyces cerevisiae actin--Escherichia coli lacZ gene fusions: synthetic-oligonucleotide-mediated deletion of the 309 base pair intervening sequence in the actin gene.

Plasmids carrying gene fusions between the yeast (Saccharomyces cerevisiae) actin gene and an initiation-defective Escherichia coli lacZ (beta-galactosidase) gene have been constructed. Expression of beta-galactosidase in such fusion plasmids depends on transcription of the actin gene, and is possible only after the RNA-splicing machinery has removed from the primary RNA transcript the 309-bp intervening sequence (IVS) interrupting the actin coding region. Mutants deleting the actin IVS were constructed via synthetic oligonucleotide-mediated in vitro mutagenesis of the actin-beta-galactosidase fusion plasmid. A 17-base synthetic oligonucleotide was used to generate a 309-bp deletion which precisely removed the actin IVS. A partial deletion mutant was also constructed in which 272-bp, starting at the 5' end of the actin IVS, and including the 5' splice junction signal, were deleted. Both the complete and partial IVS-deletion mutants were transformed into yeast hosts. However, the partial deletion resulted in a greater than 98% reduction in beta-galactosidase activity. The precise deletion of the actin IVS did not reduce the levels of beta-galactosidase activity as compared with the parental fusion plasmid containing the intact IVS.

The use of synthetic oligodeoxyribonucleotides to produce specific deletions in the araBAD promoter of Escherichia coli B/r.

Two oligodeoxyribonucleotides were chemically synthesized and used to specifically mutate the regulatory region of the araBAD operon in Escherichia coli B/r. One oligodeoxyribonucleotide introduced a 3-bp deletion in the araC activator binding site, the other a 3-bp deletion in the CRP-cAMP binding site. The mutations were introduced onto an ara insert cloned in an M13 vector using the synthetic oligodeoxyribonucleotides as primers and the (+) strand of an M13 mp2::ara hybrid phage as a template in an in vitro polymerization reaction. Hybridizations using the original synthetic oligodeoxyribonucleotide as a radioactive probe identified phage containing the desired deletion. The mutant ara inserts were subcloned into a stable plasmid for functional analysis. Transcription studies performed on strains containing the mutant ara plasmids demonstrated that both mutations reduced the amount of araBA mRNA synthesized in the presence of L-arabinose.

A set of synthetic oligodeoxyribonucleotide primers for DNA sequencing in the plasmid vector pBR322.

Seven oligonucleotide primers complementary to the plasmid vector pBR322 at positions adjacent to five of the unique restriction endonuclease cleavage sites (EcoRI, HindIII, BamHI, SalI and PstI) have been chemically synthesized. The polarity of the primers is such that any DNA inserted at one or a combination of two of the above restriction sites may be sequenced by the chain termination method using one of the synthetic DNA primers. One of the primers for sequencing inserts at the PstI site of pBR322 is also complementary to the M13 phage vector designated bla6. This set of universal primers is useful for rapid sequence determination of DNA cloned into pBR322 or M13bla6.

Expression in Escherichia coli of a chemically synthesized gene for a "mini-C" analog of human proinsulin.

A gene has been constructed which codes for an analog of human proinsulin in which the normal 35-amino acid connecting peptide is replaced by a "mini-C" peptide of six amino acids (Arg-Arg-Gly-Ser-Lys-Arg). The gene, composed of oligonucleotide fragments synthesized by the triester method, was cloned and expressed as a beta-galactosidase hybrid protein. The proinsulin analog was separated from beta-galactosidase by cyanogen bromide cleavage and purified. Controlled disulfide exchange in the S-sulfonate of the analog generated a molecule having high-pressure liquid chromatography (HPLC) and radioimmunoassay (RIA) behavior consistent with a proinsulin-like structure.

Detection of lipofuscin-like fluorophore in oxidized human low-density lipoprotein. 4-hydroxy-2-nonenal as a potential source of fluorescent chromophore.

It has recently been shown that the lipid peroxidation product 4-hydroxy-2-nonenal (HNE) forms a fluorescent hydroxyiminodihydropyrrole derivative with the epsilon-amino group of lysine residue. In this study, we raised a monoclonal antibody (mAb2C12) directed to the fluorophore-protein conjugate and found that the antibody was specific to the chromophore structure of the compound. Immunohistochemical analysis of atherosclerotic lesions from the human aorta showed that the fluorophore was indeed present in the lesions, in which intense positivity was primarily associated with macrophage-derived foam cells and thickening of the neointima of the arterial walls. Antigenic materials were also detected in the oxidatively modified low-density lipoprotein (LDL) with Cu(2+) and in the oxidatively modified bovine serum albumin with an iron/linoleic acid autoxidation system, indicating that the HNE, which originated from the peroxidation of polyunsaturated fatty acids, could be a potential source of the fluorescent chromophore in oxidized LDL.

HLA-linked susceptibility gene of Takayasu Disease.

The HLA-A, B, DR and MB antigens were investigated in patients suffering from Takayasu disease (Aortitis syndrome). Out of twenty-one HLA-A and B antigens tested, only HLA-Bw52 was significantly deviated (30147, PF = 63.8%, RR = 7.8) from the controls (14/76, PF = 18.4%). Since in the Japanese, HLA-Bw52 is in positive linkage disequilibria with HLA-DR2 and MB1, the association of the DR2 and MB1 antigens with Takayasu disease was studied. The HLA-DR2 antigen was significantly increased (23/30, PF = 76.7%,, RR = 6.0) in patients compared with the control (18/51, PF = 35.3%). Moreover, an almost perfect association of MBI (29/30, PF = 96.7%, RR = 12.6) with Takayasu disease was demonstrated. This finding supports the hypothesis that the genes in the HLA-D region play a major role in determining the susceptibility to Takayasu disease.

Association of B cell alloantigen with juvenile onset diabetes mellitus in the Japanese.

Sixty-four Japanese insulin dependent juvenile onset diabetes mellitus (JOD) were studied in relation to HLA-A, B, and DR. Significant deviations were observed. HLA-Bw54 was increased (PF = 49.2%, RR = 6.4) and HLA-B5 was decreased (PF = 7.9%, RR = 0.19). Using radioimmunoassay, two HLA-DR antigens were investigated. Hon 7 antigen, so-called MT3 (WIA4x7), which has linkage disequilibrium between HLA-BW54, is highly associated (PF = 96.9%, RR = 27.8) with JOD found in the Japanese.

Application of synthetic oligonucleotides to detect DQ beta genes transmission within insulin-dependent diabetes families.

Class II antigen genes encoded by the major histocompatibility complex region (HLA-D region) in man play an important role in susceptibility to insulin dependent diabetes mellitus (IDDM). Evidence suggests that the DQ subregion within the HLA-D region is more directly responsible for susceptibility to IDDM. Therefore, we designed a synthetic oligonucleotide specific for the DQ beta gene to further the understanding of the disease association with HLA-D region genes at the molecular level. Restriction fragment length polymorphism (RFLP) analysis was carried out using DNA isolated from nine families, each including at least two affected siblings (a total of 37 siblings). The segregation pattern of hybridizing fragments showed that: (1) for each of the DR2, DR3, and DR4 specificities, two different alleles can be identified by the DQ beta probe; (2) a 1.9 kb-Taq 1 fragment with the DR4 specificity and a 6.0 kb-Taq-1 fragment within the DR2 specificity tend to cosegregate with IDDM; (3) there was no preferential segregation of the two alleles detected within the DR3 specificity (one allele identified by a 4.7 kb-Taq 1 fragment is quite common among individuals with the DR3 specificity). The results from this study add to the evidence that certain DQ alleles appear to be more directly associated with the diabetogenic gene (or genes) in certain DR specificities.