Polymerase-chain reaction as a tool for investigations on sequence-selectivity of DNA-drugs interactions

Sequence-selectivity of DNA-binding drugs was recently reported in a number of studies employing footprinting and gel retardation approaches. In this paper we performed polymerase-chain reaction (PCR) experiments to study the in vitro effects of distamycin, daunomycin, chromomycin and mithramycin. As model systems we employed the human estrogen receptor (ER) gene and the Harvey-ras (Ha-ras) oncogene, in order to obtain PCR products significantly differing for the A + T/G + C frequency ratio. Distamycin, daunomycin, chromomycin and mithramycin are indeed known to differentially bind to different DNA regions depending upon the DNA sequences recognized. The main conclusion of our experiments is that distamycin, daunomycin, chromomycin and mithramycin inhibit polymerase-chain reaction in a sequence-dependent manner. Distamycin inhibits indeed PCR mediated amplification of AT-rich regions of the human estrogen receptor gene, displaying no inhibitory effects on PCR-mediated amplification of GC-rich sequences of Ha-ras oncogene. By contrast daunomycin, chromomycin and mithramycin were found to inhibit PCR-mediated amplification of the Ha-ras GC-rich oncogene sequences. We propose that polymerase-chain reaction technique could be applied to study the in vivo interactions of DNA-binding drugs to specific genes in intact cells.

Distamycin analogues with improved sequence-specific DNA binding activities

In the present study we have investigated the effect of unprecedented chemical modifications introduced in the distamycin molecule, with the aim of assessing their ability to interfere with sequence-specific DNA-protein interactions in vitro. By using an electrophoretic mobility shift assay, we have been able to identify novel distamycin analogues with improved displacing abilities on the binding of octamer nuclear factors to their target DNA sequence. While variations in the number of pyrrole rings and/or reversion of an internal amide bond result in distamycin-like compounds with identical or very similar properties, the reversion of the formamido into a carboxyamido group or its replacement with the charged formimidoyl moiety significantly improves the ability of the resulting novel distamycin derivatives to compete with OCT-1 (octamer 1 nuclear factor) for its target DNA sequence. Tissue-specific octamer-dependent in vitro transcription is similarly affected by these chemical modifications, suggesting that the ability of distamycins to bind octamer sequences has a direct influence on the functional state of octamer-containing promoters. These data represent an initial, successful attempt to rationalize the design of DNA binding drugs, using distamycins as a model.

Differential inhibition of DNA/protein interactions by aromatic amidines with 2, 3 and 4 benzamidine residues

We have recently reported that aromatic polyamidines are powerful inhibitors of in vitro proliferation of tumour cell lines and in vivo tumorigenicity of melanoma cells xenografted into nude mice. Interestingly, we have found that tetrabenzamidines are able to bind DNA, and to inhibit the interaction between transacting factors and specific target DNA sequences. In order to obtain more detailed information on structure-activity relationships, we have analysed the effects of different aromatic polyamidines on the binding of a recombinant protein, the Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA-1), to the target sequence of EBV DNA, containing the 12 bp palindromic consensus TAGCATATGCTA. The results obtained suggest that aromatic polyamidines inhibit the interactions between DNA-binding proteins and target DNA sequences with different efficiency, depending (i) on the number of amidine residues and (ii) on the presence of halogen substitutions (Cl, Br or I) on the benzene rings of tetra-benzamidine molecules.

A set of Alu-free frequent decamers from mammalian genomes enriched in transcription factor signals

We have recently reported that the statistical analysis of the frequency distribution of short oligonucleotides within mammalian and viral genomes allows the production of sets of DNA sequences enriched in signals for transcription factors. Such statistical approaches could facilitate the identification of new promoter regions playing a role in the transcriptional regulation of gene expression. In the case of mammalian oligonucleotides, we found that the published set of frequent decamers enriched in transcriptional motifs is not suitable for studies on genes of Homo sapiens and evolutionarily related genomes, because it contains decameric sequences belonging to genomic repeats. We report here that most of the decameric sequences of DNA repeats belong to Alu repeats. Accordingly, we produced a subset of Alu-free frequent decamers. In addition, we eliminated from the subset of Alu-free frequent decamers those that are frequently present within other common human repeats, including (GT)n, (AT)n, (CA)n, (ATT)n, (CAA)n and (GTT)n. The Alu-free (repeats-free) subset of frequent mammalian decamers is enriched in signals for transcription factors and allows the identification of putative signals in genes, such as those coding for plasminogen activator, adenosine deaminase and p53, that contain a large number of Alu-like repeats interspersed within our genomic sequences. The newly generated compilation of frequent decamers described here might be used to locate genomic regions playing functional roles in the expression of genes of Homo sapiens and related primates.

Kinetics of bromocriptine release from microspheres: comparative analysis between different in vitro models

This paper describes how the use of different in vitro experimental systems can influence the determination of (a) the drug release profile from microparticles and (b) the interpretation of the release mechanism(s). We employed, as model dosage form, the Parlodel LA, a recently marketed microsphere system especially designed for bromocriptine-controlled delivery. The release kinetics of bromocriptine from microspheres were determined by using two different experimental approaches: a dialysis method and a flow-through cell method. From the comparison of the obtained data it clearly appears that different in vitro experimental models lead to distinct results in terms of drug availability. On the contrary both series of data can be convincingly fitted with the same mathematical equation, giving almost identical results in terms of postulated release mechanism. Taken together these results indicate that different experimental approaches should always be employed to determine drug release kinetics from microparticles in order to obtain more reliable information on the therapeutic dose (bioavailable drug, for in vivo experiments) and on the uniformity of different batches of microspheres.

Capillary electrophoresis: detection of hybridization between synthetic oligonucleotides and HIV-1 genomic DNA amplified by polymerase-chain reaction

The polymerase chain reaction (PCR) is one of the most efficient techniques for measuring the viral load of HIV-infected samples. Determination of the specificity of PCR products is usually based on Southern blotting and hybridization of the amplified DNA to radioactive oligonucleotide probes specific for sequences comprised between the PCR primers. The recent introduction of capillary electrophoresis (CE) for identification of HIV-1 and HTLV-I PCR products appears interesting in light of its reproducibility, sensitivity and because it is fast and suitable for detection of DNA/DNA and DNA/RNA hybrids. We demonstrate that specific hybridization of a HIV-1 oligonucleotide probe to single-stranded DNA obtained by unbalanced PCR is detectable by capillary electrophoresis. This enabled us the application of a one-step, non-radioactive protocol to demonstrate the specificity of amplification of HIV-1 genomic sequences by PCR. This procedure is simple, reproducible and is suggested as an integral part of automated diagnostic systems based on the use of laboratory work stations for DNA isolation, preparation of PCR reactions and analysis of PCR products.

Production and in vitro evaluation of gelatin microspheres containing an antitumour tetra-amidine

The preparation and characterization of gelatin microspheres (GMs) containing the antitumour aromatic tetra-amidine TAPP-Br and its release characteristics from microspheres are described. Spherical gelatin microspheres, showing a high percentage of drug encapsulation (over 95 per cent) and an average diameter of 16 microns were obtained by a coacervation method. In addition, the effects of various reaction parameters on the production and chemical hardening of GMs have been investigated. In order to compare the TAPP-Br release profiles from GMs prepared with different procedures, in vitro studies were carried out. The biological effect of TAPP-Br released from gelatin microspheres was determined on 'in vitro' cultured tumour cell lines, showing that, after encapsulation, TAPP-Br still retains antiproliferative activity comparable with that exhibited by the free drug. Taken together, the results obtained suggest that gelatin-based microspheres offer excellent potential as carriers for the controlled release of polyamidines in anticancer chemotherapy.

Binding of Epstein-Barr virus nuclear antigen 1 to DNA: inhibition by distamycin and two novel distamycin analogues

Modulation of the interaction between cellular or viral transcription factors and target DNA sequences may represent a potential experimental strategy to control proliferation of neoplastic cells as well as virus DNA replication. Distamycin represents a likely candidate to mediate such modulation by pharmacological means. In order to obtain more detailed information on structure-activity relationships of these compounds, we have analysed the effects of distamycin and two distamycin analogues on the binding of a recombinant protein, the Epstein-Barr virus nuclear antigen 1 (EBNA-1) to its target sequence of Epstein-Barr virus, containing the 12 bp palindromic consensus TAGCATATGCTA. The sequence selectivity in the binding of distamycin to DNA was evaluated by footprinting experiments, while the effects of distamycins on DNA-protein interactions was analysed by means of electrophoretic mobility shift assay. The data presented in this paper suggest that distamycin and its analogues differentially inhibit the interaction between DNA-binding proteins and target DNA sequences.

Sequence-specific recognition of the HIV-1 long terminal repeat by distamycin: a DNAase I footprinting study

Pharmacological modulation of the interaction between transcription factors and target DNA sequences of cellular and viral genes could have important effects in the experimental therapy of a large variety of human pathologies. For instance, alteration of the DNA/protein interaction might be among the molecular mechanisms of action of DNA-binding drugs, leading to an inhibition of the expression of genes involved in the control of in vitro and in vivo growth of neoplastic cells and virus DNA replication. Natural oligopeptides, such as distamycin, are powerful inhibitors of the interaction between nuclear factors and target DNA sequences and, therefore, have been proposed as compounds retaining antibiotic, antineoplastic and antiviral properties. In this study we performed DNAase I footprinting analysis using a PCR product mimicking a region of the long terminal repeat (LTR) of the human immunodeficiency type 1 (HIV-1) retrovirus. The data obtained suggest that distamycin binds to different regions of the HIV-1 LTR depending on the DNA sequence. Electrophoretic mobility shift assays using both crude nuclear extracts from the Jurkat T-lymphoid cell line and the recombinant proteins transcription factor IID and Sp1 suggest that distamycin differentially inhibits the interaction of these two proteins with their specific DNA target sequences, in good agreement with the results obtained by DNAase I footprinting analysis.

First-trimester human trophoblast is class II major histocompatibility complex mRNA+/antigen

Lack of expression of the polymorphic class I and class II MHC antigens in the cytotrophoblast is one of the major factors determining the privileged immunologic status of the placenta. In this report, we show that first-trimester human placental cytotrophoblast cells display moderate to strong expression of class II MHC (HLA-DR alpha and -DR beta) and Ii chain transcripts, apparently in absence of detectable class II antigens and Ii chain. In addition, DR alpha, DR beta, and Ii mRNAs, but not antigens, are consistently upregulated by IFN-gamma. Constitutive expression and upregulation of mRNAs are detectable in trophoblast cells kept in short term as well as prolonged (2-3 weeks) culture. These results are reminiscent of an analogous mRNA+/antigen- dissociation occurring, in the case of class I MHC gene products, in a subpopulation of first-trimester cytotrophoblast cells. Thus, analogous mechanisms prevent the expression of potentially hazardous class I and II allodeterminants at early stages of semiallogeneic pregnancy.

A chromatographic procedure for fully automated isolation of DNA from human whole blood

Isolation of DNA from peripheral blood constitutes a fundamental step in the molecular diagnosis of genetic disorders, analysis of mutations of oncogenes and detection of nucleic-acid sequences of pathogenic organisms in clinical samples. We investigated whether dextran sedimentation of blood followed by the chromatographic isolation of DNA could be applied to the Biomek-1000 automated laboratory workstation in order to develop a fully automated method of DNA isolation from whole blood. Under our experimental conditions, the Biomek-1000 could perform fully automated DNA isolation from seven human whole blood samples in less than 1.5 h. Our data indicate that the DNA isolated from human blood in this way is suitable for polymerase chain reaction.

Interferon-gamma enhances monoclonal antibody 17-1A-dependent neutrophil cytotoxicity toward colorectal carcinoma cell line SW11-16

17-1A is a murine monoclonal antibody (MAb) specific for the tumor-associated antigen CO17-1A on colorectal carcinoma cells. One of the tumor cell destruction mechanisms induced by in vivo immunotherapy with MAb17-1A has been claimed to be antibody-dependent cellular cytotoxicity (ADCC) by monocytes and NK cells. In the present study we investigated whether human neutrophils (PMN) could be involved in colorectal carcinoma cell lysis and whether IFN-gamma influences this function. We showed that neutrophils are capable of tumor lysis mediated by MAb17-1A, although to a lesser extent than are the mononuclear cells (PBMC). Neutrophil ADCC was, however, markedly increased in the presence of IFN-gamma. Enhancement by IFN-gamma was also observed for PBMC. ADCC by PMN required the binding of MAb17-1A to Fc gamma RIII (CD16) since anti-Fc gamma RIII MAbs efficiently blocked tumor cell lysis. In contrast, in the presence of IFN-gamma the neutralization of Fc gamma RIII did not affect MAb17-1A-mediated cytotoxicity, suggesting that receptors other than Fc gamma RIII were involved in the process. PBMC cytotoxicity was also inhibited by anti-CD16 antibodies but IFN-gamma did not overcome this effect. Finally, the scavenger enzymes superoxide dismutase and catalase did not block ADCC by PMN or PBMC, indicating that oxidants are not key factors in MAb17-1A-mediated lysis; however, in IFN-gamma-activated PMN the oxygen-dependent mechanism was in part involved in tumor lysis.

Detection of hepatitis-C virus by unbalanced polymerase-chain reaction, hybridization to synthetic oligonucleotides and capillary electrophoresis

Polymerase chain reaction (PCR) has been reported as one of the most efficient techniques to detect hepatitis C virus (HCV) RNA. The determination of the specificity of PCR products is usually based on 'nested' PCR, Southern blotting and hybridization of the amplified DNA to radioactive oligonucleotide probes recognizing sequences comprised between the PCR primers. The recent introduction of capillary electrophoresis (CE) to analyse DNA fragments and PCR products appears to be very interesting because this technology is rapid, reproducible, sensitive and could be suitable to detect DNA/DNA and DNA/RNA hybrids. We demonstrate that specific hybridization of an HCV oligonucleotide probe to single stranded HCV-DNA obtained by unbalanced PCR is detectable by capillary electrophoresis, therefore enabling a one-step, non-radioactive protocol to demonstrate the specificity of amplification of HCV sequences by PCR.

Codon usage and evolutionary rates of proteins

The 61 codons and the three terminators were counted in the coding sequences of 31 families of proteins of higher vertebrates. The protein families were ordered according to their evolutionary rate. In each family, the ratio between the Observed and Expected frequency of each codon was obtained (O/E ratio). A strong and significant positive correlation was observed between the O/E ratio of the eight codons AAC, TAT, ATA, GAA, ACA, AAT, ATG and CGA and the evolutionary rate of the protein. A negative and significant correlation was observed for codons AAG and GAG. It was advanced that the functional constraints of proteins can influence the usage of codons, particularly for those trimers which are components of signal sequences. It was also observed that the O/E ratios of the terminators are negatively correlated with the evolutionary rate of the protein they terminate, and the correlation is significant for TAA and TGA, which in vertebrates might be older than TAG.

Methylation state of the human HLA-DRA gene in T-lymphocytes and B-lymphocytes of transgenic mice. Lack of methylation at one 5'-GCGC site is not required for gene expression

A consistent lack of DNA methylation at one or both of two GCGC (Hha I) restriction sites in the 5' region of the HLA-DRA gene has been previously documented by the use of methyl-sensitive restriction enzymes in human cells and tissues, irrespectively of their expression of DR alpha products. Evidence presently available, however, does not exclude that a lack of methylation in this region, although not sufficient, might be necessary for gene expression. In this report, we show that only one of the 5'-GCGC sites is protected, although less efficiently than in man, from CG-->mCG modifications in tissues and cells of transgenic mice carrying an expressed single copy of the HLA-DRA gene/diploid genome. We demonstrate that the two 5' GCGC sites of the HLA-DRA transgene are fully methylated in DR alpha- splenocytes (more than 80% T-lymphocytes), while one of them (the most 5' site) is not methylated in a fraction of DR alpha+ splenocytes (more than 95% B-lymphocytes). These results provide evidence that absence of DNA methylation in the 5' region is not necessary for, but might be associated with and possibly secondary to the expression of the DRA gene.

Sequencing of an RNA transcript of the human estrogen receptor gene: evidence for a new transcriptional event

Two transcripts of the human estrogen receptor (ER) gene have been described, ER mRNA 1 and mRNA 2, different in their 5' untranslated region. By performing reverse transcriptase-polymerase chain reaction with oligonucleotides specific for the 5' genomic region of the human ER gene we have identified a new ER RNA transcript. The sequence analysis of cDNA from MCF7 breast cancer cells and endometrial human tissues demonstrates that this transcript originates further upstream of the initiation transcription sites so far proposed. Primer extension analysis on RNA from MCF7 cells reveals in the upstream region a possible transcription start site at -3090. In agreement with this result, Northern blot analysis shows, in addition to the canonical 6.3 kb ER mRNA, an ER RNA transcript of approx. 7.4 kb in size. The presence of the additional ER mRNA suggests the existence of a new upstream 5' promoter directing transcription of the human ER gene.

Polymerase-chain reaction: analysis of DNA/DNA hybridization by capillary electrophoresis

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Use of an automated laboratory workstation for isolation of genomic DNA suitable for PCR and allele-specific hybridization

In this paper we describe the isolation of genomic DNA by using anion exchange chromatography performed on a Biomek 1000 Automated Laboratory Workstation. This procedure allows the automated isolation of DNA suitable for most molecular analyses employed in diagnosis of genetic pathologies and infectious diseases. The genomic DNA isolated by using the Biomek 1000 was indeed found to be suitable for polymerase chain reaction and allele-specific hybridization.

A new automated method for isolation of genomic DNA from eukaryotic cells

In this study we determine whether the BIOMEK-1000 Laboratory Workstation (Beckman Instruments, Fullerton, CA) can be used to isolate genomic DNA from eukaryotic cells. The results obtained demonstrate that DNA isolated by BIOMEK-1000 is suitable for amplification of genomic sequences by PCR. Our data prove that automated chromatographic DNA isolation employing the BIOMEK-1000 could be used in molecular diagnosis of human pathologies.

DNA binding activity and inhibition of DNA-protein interactions. Differential effects of tetra-p-amidino-phenoxyneopentane and its 2'-bromo derivative

In the present study are reported the differential DNA binding activity of the anti-tumor polyamidine tetra-p-amidinophenoxyneopentane (TAPP-H) and its 2'-halo derivative (TAPP-Br), and their effects on the binding of the recombinant Epstein-Barr virus (EBV) nuclear antigen to a synthetic oligonucleotide mimicking the target DNA sequence present in the EBV genome. In addition, the proliferation kinetics and cell cycle analysis of human leukemia K562 cells treated with TAPP-H and TAPP-Br are reported. The possible in vivo relationship between DNA binding affinity and cytotoxicity is also discussed.

Analysis of upstream sequences of the human estrogen receptor gene

An upstream region of the human estrogen receptor gene (ER) spanning from -2776 to -38 in relation to a previously described exon 1 was sequenced and analyzed for the possible presence of open reading frames (ORF) and regulatory motifs. We identified a long 459 bp ORF beginning at -2301. Most of the transcriptional regulatory motifs present within the ER upstream sequence are distributed either upstream or downstream of this long ORF which displays a TATA box, a CACC motif and a canonical cap site in the 5' flanking region.

Enrichment of oligonucleotide sets with transcription control signals. II: Mammalian DNA

We studied the frequency distribution of oligonucleotides 10 bp long in a sample of 1.6 Mb of mammalian genes, containing 579 sequences from GenBank(R) 55.0, with the aim of detecting transcription control signals. 2216 decamers had a frequency higher than 10 times the mean and were subjected to further statistical analysis. For each of the 2216 decamers (parents), we counted the individual frequencies of the 30 decamers differing from the parent by one base mutation (progeny) and then calculated two variance/mean chi squares for the progeny, with and without the parent. We then studied the distribution of the ratio between the two chi squares. Out of 2216 decamers, 346 had a chi square ratio of 1.9 or larger. In this final set, which corresponds to less than 0.033 per cent of all possible decamers, 18 were found to contain 23 eukaryotic transcription control elements 5-10 bp of length, such as Sp1 and others. Furthermore, when compared to 210 random sets containing 346 decamers, this set contains a highly significant excess of the longer signals.

New isoxazole derivatives of retinoids: synthesis and activity on growth and differentiation of tumor cells

The effects of several newly synthesized isoxazole analogues of retinoids on differentiation and proliferation of 'in vitro' cultured tumor cell lines are reported. Some of the tested compounds exhibit significative differentiating action, inducing adipogenic conversion of the Chinese hamster FH06T1-1 cell line in a range of 2-10 times the activity of retinoic acid and retinol. In addition, most of the compound tested display antiproliferative activity comparable to that of natural retinoids. The reported data could be of interest for experimental anticancer therapy.