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Biomedical subjects

H Seliger

Publications and source records attributed to H Seliger.

At least 19 recordsLinked to original sources
PubMed1995

Fractal dimension of error sequence dynamics in quantitative modeling of syntheses of short oligonucleotide and single-stranded DNA sequences.

Oligonucleotides are becoming more and more important in molecular biomedicine; for example, they are used as defined primers in polymerase chain reaction and as antisense oligonucleotides in gene therapy. In this paper, we model the dynamics of polymer-supported oligonucleotide synthesis to an inverse power law of driven multi-cycle synthesis on fixed starting sites. The mathematical model is employed by presenting the accompanying view of error sequences dynamics. This model is a practical one, and is applicable beyond oligonucleotide synthesis to dynamics of biological diversity. Computer simulations show that the polymer support synthesis of oligonucleotides and single-stranded DNA sequences in iterated cyclic format can be assumed as scale-invariant. This synthesis is quantitatively described by nonlinear equations. From these the fractal dimension Da (N,d) is derived as the growth term (N = number of target nucleotides, d = coupling probability function). Da(N,d) is directly measurable from oligonucleotide yields via high-performance liquid chromatography or capillary electrophoresis, and quantitative gel electrophoresis. Different oligonucleotide syntheses, including those with large-scale products can be directly compared with regard to error sequences dynamics. In addition, for short sequences the fractal dimension Da (N,d) is characteristic for the efficiency with which a polymer support of a given load allows oligonucleotide chain growth. We analyze the results of separations of crude oligonucleotide product from the synthesis of a 30 mer. Preliminary analysis of a 238 mer single-stranded DNA sequence is consistent with a simulated estimate of crude synthesis product, although the target sequence itself is not detectable. We characterize the oligonucleotide support syntheses by simulated and experimentally determined values of the fractal dimension Da (N,d0) within limitations (d0 = constant (average) coupling probability).

Animals↗
PubMed1993

Cleavage and binding of a DNA fragment containing a single 8-oxoguanine by wild type and mutant FPG proteins.

A 34-mer oligonucleotide containing a single 7,8-dihydro-8-oxoguanine (8-OxoG) residue was used to study the enzymatic and DNA binding properties of the Fpg protein from E. coli. The highest rates of incision of the 8-OxoG containing strand by the Fpg protein were observed for duplexes where 8-OxoG was opposite C (*G/C) or T (*G/T). In contrast, the rates of incision of duplexes containing 8-OxoG opposite G (*G/G) and A (*G/A) were 5-fold and 200-fold slower. Gel retardation studies showed that the Fpg protein had a strong affinity for duplexes where the 8-OxoG was opposite pyrimidines and less affinity for duplexes where the 8-OxoG was opposite purines. KDapp values were 0.6 nM (*G/C), 1.0 nM (*G/T), 6.0 nM (*G/G) and 16.0 nM (*G/A). The Fpg protein also binds to unmodified (G/C) duplex and a KDapp of 90 nM was measured. The cleavage and binding of the (*G/C) duplex were also studied using bacterial crude lysates. Wild type E. coli crude extract incised the 8-OxoG containing strand and formed a specific retardation complex with the (*G/C) duplex. These two reactions were mediated by the Fpg protein, since they were not observed with a crude extract from a bacterial strain whose fpg gene was inactivated. Furthermore, we have studied the properties of 6 mutant Fpg proteins with Cys-->Gly mutations. The results showed that the 2 Fpg proteins with Cys-->Gly mutations outside the zinc finger sequence cleaved the 8-OxoG containing strand, formed complexes with the (*G/C) duplex and suppressed the mutator phenotype of the fpg-1 mutant. In contrast, the 4 Fpg proteins with Cys-->Gly mutations within the zinc finger motif neither cleave nor bind the (*G/C) duplex, nor do these proteins suppress the fpg-1 mutator phenotype.

Amino Acid Sequence↗
PubMed1992

Antisense effect of oligodeoxynucleotides with inverted terminal internucleotidic linkages: a minimal modification protecting against nucleolytic degradation.

The synthesis of a new class of antisense oligonucleotide compounds with 3'-3' and 5'-5' end inversion (INV-oligonucleotides) is described. Besides the advantage of simplicity of synthesis, physico-chemical studies show that these compounds do not disturb Watson-Crick base-pairing. INV-oligonucleotides have a half-life of 30 h in human serum. We show that they are capable of inhibiting SV40 large T-antigen expression in COS-1 cells, both in vitro and in vivo, and by modulation of the expression of cellular oncoprotein p53 in vitro.

Animals↗
PubMed1991

Synthetic oligonucleotides for biomedical applications.

New developments of oligonucleotides for biomedical applications are surveyed. Diagnostic probes were conveniently labelled by enzymatic immunogenic tailing with 5-bromo-deoxyuridine triphosphate. "Antisense" oligonucleotides of potential therapeutic value were stabilized against nucleolytic decay by inversion of terminal internucleotidic linkages. Introduction of 2'-deoxy-2'-fluoro-nucleotide units enhances duplex stability and conveys resistance to ribonucleases.

Base Sequence↗
PubMed1990

Isolation and full structural characterisation of six adrenocorticotropin-like peptides from porcine pituitary gland. Identification of three novel fragments of adrenocorticotropin and of two forms of a novel adrenocorticotropin-like peptide.

A partially purified fraction of extracted porcine pituitary glands which possesses lipolytic and adrenocorticotropic activity has been characterised. It consists of six adrenocorticotropin(ACTH)-like peptides (five of which have not been previously described) which were each purified by sequential reverse-phase (rp) HPLC. Their complete primary structures were determined following amino acid compositional analysis, extensive peptide mapping and partial sequencing. Four of the fragments represent the following ACTH fragments; ACTH(1-31), ACTH(7-34), ACTH(7-36) and ACTH(7-38). By combined analytical rpHPLC and an ACTH radioimmunoassay (with an antiserum exhibiting full cross-reaction with all six ACTH variants isolated here), evidence was obtained from analysis of extracts of whole pituitary that these fragments of ACTH exist in significant amounts relative to intact ACTH(1-39). This suggests that ACTH can undergo more extensive differential proteolytic processing than previously thought. These peptides were found to possess reduced or a complete absence of ACTH-like biological activity. Therefore the biological significance of this processing needs to be resolved. The other two fragments also resembled fragments of ACTH but each possessed the same, single amino acid substitution: a threonine replacing the arginine at the position corresponding to position 8 in the ACTH sequence and had the structures [Thr8]ACTH(1-31) and [Thr8]ACTH(7-31). They possess little ACTH-like biological activity. If these variants are derived from a variant ACTH, this would be a significant finding in view of the site of the amino acid substitution and the highly conserved nature of the ACTH primary structure. The possible physiological and genetic implications are briefly discussed. In this study attempts were also made to identify the DNA coding for the mutant ACTH sequence.

Adrenocorticotropic Hormone↗
PubMed1989

Production of human adrenocorticotropin by cleavage of alkaline-phosphatase-derived fusion proteins containing repetitive recognition sequences for collagenases.

Recombinant plasmids coding for fusion proteins which consist of human adrenocorticotropin joined to N-terminal sequences of Escherichia coli alkaline phosphatase via collagenase-sensitive linkers were constructed and used for the production of these proteins by transformed E. coli cells. It was shown that repetitive linkers of the form -Gly-(Pro-Xaa-Gly)n-Pro- with n greater than or equal to 2 were cleaved by clostridiopeptidase A (Clostridium histolyticum) by orders of magnitude faster than corresponding nonrepetitive sequences (n = 1). The C-terminal cleavage product was Gly-Pro-adrenocorticotropin which could be converted to the authentic hormone by dipeptidyl peptidase IV. On the basis of these enzymatic reactions a procedure for the preparation of pure adrenocorticotropin was developed. Derivatives of alkaline phosphatase containing similar repetitive linker sequences were cleaved by clostridiopeptidase A as efficiently as the adrenocorticotropin fusion proteins.

Adrenocorticotropic Hormone↗
PubMed1989

Polymer support synthesis. XV. Behaviour of non-porous surface-coated silica gel microbeads in oligonucleotide synthesis.

Non-porous silica gel microbeads of diameter 1.5 microns have been investigated as supports for oligonucleotide synthesis. In the preparation of oligothymidylates of chain length up to 150 bases, with 5'-di-p-anisylphenylmethyl-3'-phosphoramidite as an intermediate, the average yields per chain elongation were up to 99%. Lower overall yields were observed in the case of a support which developed a strong tendency towards aggregation after the build up of an oligonucleotide coating.

Autoradiography↗
PubMed1989

Studies on the role of tetrazole in the activation of phosphoramidites.

The mechanism of the tetrazole-activated coupling step in the synthesis of oligonucleotides via phosphoramidites is studied with the help of model reactions: Treatment of diethoxydiisopropylaminophosphane with two equivalents of tetrazole resulted in a diethoxy-tetrazolophosphane, whose (31P)-NMR shift of 126 ppm is identical with the signal observed during internucleotide bond formation. A series of different related diethoxy-phosphorous-acid derivatives were also synthesized; their (31P)-NMR signals between 123.9 and 130.8 ppm are additional evidence for the intermediacy of a tetrazolide species. Further NMR investigations with more basic azoles showed that tetrazole is also active as a proton donor.

Amides↗
PubMed1989

Immunocytochemistry of 5-bromo-2'-deoxyuridine labelled oligonucleotide probes. A novel technique for in situ hybridization.

A synthetic oligonucleotide probe, complementary to oxytocin m-RNA was labelled enzymatically with 5-bromo-2'-deoxyuridine (5-BrdU) and with [gamma-32P]-ATP. The labelled probes were used for in situ hybridization of histological sections of the mouse hypothalamus. A monoclonal antibody to 5-BrdU and the streptavidine-peroxidase technique were used in order to visualize hybridization with the 5-BrdU labelled probe. In situ hybridization with [32P] labelling was detected autoradiographically. With both methods hybridized neurons were visible in the magnocellular hypothalamic nuclei. While immunostaining and radio-labelling provided similar localization of oxytocin m-RNA, only the immunocytochemical technique showed clear cellular resolution of the reaction product. In situ hybridization with 5-BrdU labelled probes followed by 5-brdU immunocytochemistry seems to be a powerful alternative to common autoradiographic techniques.

Adenosine Triphosphate↗
PubMed1988

In situ hybridization with complementary synthetic oligonucleotide and immunocytochemistry: a combination of methods to study transcription and secretion of oxytocin by hypothalamic neurons.

We have constructed an icosameric, anti-sense oligodeoxyribonucleotide probe derived from the published sequence of rat oxytocin gene precursor that was used for in situ hybridization, combined with immunostaining, to characterize the biosynthetic and secretory activity of hypothalamic oxytocin neurons. The population of hybridized neurons overlapped with the pattern of oxytocin immunoreactive cells, except for a fraction of these cells which remained unhybridized. A number of hybridized neurons remained unstained. The differential proportion of hybridized and immunostained neurons are interpreted as differences in secretory turnover of endocrine neurons.

Amino Acid Sequence↗
PubMed1988

Synthesis and structure-activity relationships in the cefpirome series. II. Analogues of cefpirome with different 7-heteroarylacetamido and 3'-ammonium substituents.

The synthesis and antibacterial activity in vitro of 7-(2-heteroarylacetamido)-3-[(2,3- cyclopentenopyridinium)methyl]cephalosporins and of some related compounds with different ammonium functions in 3'-position are described. The 7-[5-amino-1,2,4-thiadiazol-3-yl] and the 7-[4-aminopyrimidin-2-yl] analogues of cefpirome and compounds with 3-aliphatic ammoniummethyl functions have excellent antibacterial activity. Cephalosporins with different N-heterocycles other than pyridine in 3'-position are less active than their 3-pyridiniummethyl analogues. Attachment of a pyridinium group to a cephem at C-3 via a thiomethyl or an aminomethyl bridge causes reduction of antibacterial activity.

Cephalosporins↗
PubMed1987

Concurrent mutations in two different ras genes in acute myelocytic leukemias.

DNA transfection analyses (tumorigenicity assay) and hybridization to mutation specific oligonucleotide probes established point mutations in codon 61 of both, N-ras and Ki-ras genes in fresh leukemic cells of an AML patient. Concurrent activation of N-ras and Ki-ras sequences by point mutations in codons 12 were demonstrated for AML cell line Rc2a. Moreover, using a rapid and sensitive dot-blot screening procedure based on the combination of in vitro amplification of ras specific sequences and oligonucleotide hybridization we could show that ras gene activation was not present in primary leukemic cells of the patient this cell line had been derived from, but rather occurred during later passages of Rc2a.

Animals↗
PubMed1987

Polymer support synthesis. XII. Derivatization with the 4-decyloxytrityl group as an aid in the affinity chromatography of oligo- and polynucleotides.

In a continuation of previous studies on trityl groups substituted with long alkyl chains as affinity-protecting groups for oligonucleotides, the use of the (4-decyloxyphenyl)diphenylmethyl (DTr) group as an aid in the separation of solid-phase products has been investigated. This substituent, which can be introduced and removed from the 5'-position in a similar manner to the di-p-anisylphenylmethyl group, helps in the purification of deoxypolynucleotides with up to 140 bases. Their retention time was shown to depend not only on the length of the nucleotide chain and alkyl substituent, but also on the elution gradient rate. In oligoribonucleotide synthesis, the DTr group allows the purification of partially protected sequences, which are more stable to enzymatic degradation and, therefore, more suitable for handling and storage.

Chromatography, Affinity↗
PubMed1987

RAS gene mutations in acute and chronic myelocytic leukemias, chronic myeloproliferative disorders, and myelodysplastic syndromes.

We report on investigations aimed at detecting mutated RAS genes in a variety of preleukemic disorders and leukemias of myeloid origin. DNA transfection analyses (tumorigenicity assay) and hybridization to mutation-specific oligonucleotide probes established NRAS mutations in codon 12 or 61 of 4/9 acute myelocytic leukemias (AML) and three AML lines. Leukemic cells of another AML patient showed HRAS gene activation. By using a rapid and sensitive dot-blot screening procedure based on the combination of in vitro amplification of RAS-specific sequences and oligonucleotide hybridization we additionally screened 15 myelodysplastic syndromes, 26 Philadelphia chromosome-positive chronic myelocytic leukemias in chronic or acute phase, and 19 other chronic myeloproliferative disorders. A mutation within NRAS codon 12 could thus be demonstrated in a patient with idiopathic myelofibrosis and in another with chronic myelomonocytic leukemia. Moreover, mutated NRAS sequences were detected in lymphocytes, in granulocytes, as well as in monocytes/macrophages of the latter case.

DNA, Neoplasm↗