Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Nucleotide Mapping”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 847 records · Page 47Linked to original sources
PubMed1987

Nucleotide sequence of a bovine lens alpha A-crystallin cDNA.

We have determined the nucleotide sequence of a bovine lens alpha A2-crystallin cDNA clone, designated pBL alpha A2-1. The 793 bp cDNA insert contains coding information for the entire 173 amino acid alpha A2-crystallin polypeptide, as well as non-translated sequences located both upstream and downstream from the coding region. The coding sequences contained in pBL alpha A2-1 are at least 89% homologous with the corresponding sequences from other mammalian alpha A-crystallin genes, and are 78% homologous to the frog alpha A-crystallin coding region. In contrast, the downstream nontranslated sequences of the mammalian alpha A-crystallin transcripts show much greater sequence divergence, with the bovine sequences averaging 47% homology with the corresponding sequences from other mammalian species.

Amino Acid Sequence↗
PubMed1987

The isolation and characterisation of a cDNA clone for human lecithin:cholesterol acyl transferase and its use to analyse the genes in patients with LCAT deficiency and fish eye disease.

We have isolated cDNA clones coding for human lecithin:cholesterol acyl transferase (LCAT) from a liver-specific cDNA library by the use of two oligonucleotide probes based on the protein sequence. The clones span the sequence coding for the entire secreted LCAT, the 3' untranslated sequence and 12 amino acids of the signal peptide. The peptide sequence contains the conserved active site of serine lipases within a hydrophobic domain, flanked by a possible amphipatic alpha-helix. Only one gene for LCAT could be detected in genomic blots. We have used the cDNA as a probe to analyse the LCAT gene in patients suffering from LCAT deficiency and fish eye disease. No rearrangements or abnormal gene fragments were detected in these patients.

Amino Acid Sequence↗
PubMed1987

The human apoB-100 gene: apoB-100 is encoded by a single copy gene in the human genome.

Northern blot analysis of human liver and intestine mRNA revealed two separate apoB mRNA of 14.1 and 7.5 kb in the intestine, and a single 14.1 kb apoB mRNA in the liver. cDNA probes which encode for the 5', middle, and 3' regions of the human apoB-100 mRNA have been utilized to evaluate the number of apoB genes present in the human genome by Southern blot hybridization analysis. Comparison of restriction enzyme digestions of high molecular weight leukocyte DNA and a known apoB genomic clone with cDNA probes for the 5', middle and 3' regions of the apoB-100 mRNA were consistent with only a single apoB gene per human haploid genome. Further analysis with synthetic oligonucleotides definitively established that there is a single apoB-100 gene. The two mRNA species observed in the intestine must be derived from a single nuclear apoB RNA transcript.

Apolipoprotein B-100↗
PubMed1988

Changes of c-mos expression in response to 2-O-tetradecanoylphorbol-13-acetate in undifferentiated teratocarcinoma cells.

Treatment of the cells of the 311 cell line, a pluripotent mouse teratocarcinoma cell line, with 12-O-tetradecanoylphorbol-13-acetate (TPA) modulates c-mos expression. Transient suppression of 6.1 and 4.6 kilobases (kb) transcripts and activation of 1.8 transcript indicate that TPA mediates concurrently positive and negative regulation of c-mos transcription. The results show that the c-mos gene is a TPA-modulated gene. In addition, a TPA-responsive element (GTGACTCA), which exists in the 5'-flanking region of c-mos gene of Balb/c mice [1,2], is suggested to be involved in this response. However, these changes were not accompanied by early marker changes associated with endodermal cell differentiation, i.e., morphological change, induction of plasminogen activator and suppression of glucose transport activity.

3-O-Methylglucose↗
PubMed1989

Interaction of mithramycin with metal ions and DNA.

The interaction of mithramycin with metal ions has been studied by absorbance and fluorescence spectroscopy. Magnesium shifts the drug absorbance spectrum to longer wavelengths and displays a weak binding constant (Kd = 1mM); no interaction with calcium was detected. The drug requires magnesium for binding to DNA and this is characterised by small additional hypochromic and bathochromic changes. Mithramycin does not bind to DNA in the presence of calcium. With 10mM magnesium the drug binds to DNA with an association constant of 9.2 x 10(4) M-1. The inability of calcium to substitute for magnesium has been confirmed by 'footprinting' experiments using both DNase I and hydroxyl radicals.

Base Sequence↗
PubMed1990

High levels of transcription driven by a 400 bp segment of the human G6PD promoter.

A 2850-base-pair-long DNA segment containing the transcriptional start site of the human X-linked gene coding for the housekeeping enzyme glucose-6-phosphate dehydrogenase has been fused to the reporter chloramphenicol acetyl transferase gene. This fusion was introduced into three different mammalian cell lines (HepG2, CVI and HeLa). Strong expression was detected and transcription initiated at the natural start site. By deletion analysis, we determined that a 436 base pair region of this promoter is sufficient for full expression of the chimaeric construct and therefore the remainder of the CpC island surrounding the transcriptional start site and differentially methylated in the active and inactive X chromosome is not necessary for transcriptional activity in this assay. Further sequence deletions from -436 to -116 base pairs decrease the promoter-directed chloramphenicol acetyl transferase activity. Site-directed mutagenesis of a TATA-like sequence present in the G6PD promoter shows that this site is required for a correct start of transcription but not for determining the level of gene expression.

Animals↗
PubMed1990

Preferential modification of guanine bases in DNA by dimethyldioxirane and its application to DNA sequencing.

From gel sequencing experiments with 32P-end-labelled oligodeoxyribonucleotides, it is shown that treatment of DNA with the powerful oxidant dimethyldioxirane, followed by heating in piperidine, causes selective strand scission at the sites of guanine bases. The same specificity for cleavage at guanine was observed with a 45-mer labelled at either the 3'- or 5'-end and with a single and double stranded 34-mer. On account of its speed and operational simplicity, modification with dimethyldioxirane is proposed as a practicable alternative to conventional chemical sequencing procedures for locating guanine bases in DNA.

Base Sequence↗
PubMed1990

Regulation of brain-specific transcription of the mouse myelin basic protein gene: function of the NFI-binding site in the distal promoter.

We investigated brain-specific transcription elements in the distal region (-253 to -54) of the mouse myelin basic protein (MBP) promoter by in vitro transcription using mouse brain nuclear extracts. Using deletion and base substitution mutants, we identified one tissue-specific transcription element at the downstream core of the NFI-site between -115 and -111. Foot-printing assay demonstrated that three transcription factors bind around this element; NFI-related (-130 to -111), M1 (-110 to -97) and Sp1 (-92 to -84). NFI-related factor(s) in brain extracts consisted of a characteristic population which was different from that in other tissues. Methylation interference experiments revealed that this factor(s) interacted with the NFI-downstream core in a brain-specific manner. We suggest the existence of a brain-specific NFI-related factor(s).

Animals↗
PubMed1990

Transcription factor IIA of wheat and human interacts similarly with the adenovirus-2 major late promoter.

Transcription factor IIA (TFIIA) is a necessary component of many RNA polymerase II transcription complexes. Assembly of the transcription complex begins when TFIIA interacts with the promoter. We have previously purified wheat germ TFIIA to homogeneity and demonstrated that it substitutes for human TFIIA in a human in vitro transcription system which utilizes the adenovirus-2 major late promoter (Ad-2 MLP). We now show, by gel retardation assays, that wheat TFIIA interacts with the Ad-2 MLP. Extensively purified human (HeLa) TFIIA interacts with the Ad-2 MLP similarly. Both wheat and human TFIIA interact with a DNA fragment comprising the minimal promoter region (-51/+32) but not with upstream or downstream regions. With both TFIIAs multiple complexes form; the fastest wheat TFIIA/DNA complex appears to be larger than the corresponding human TFIIA/DNA complex. Limited point mutation analysis of the Ad-2 MLP demonstrates that changes at -30 (TATAA region), +1, and -1 diminish TFIIA binding, but a change at -40 does not. DNA footprint analysis of this region is not definitive, but does indicate that following TFIIA binding there are changes in the pattern of hypersensitive sites.

Adenoviridae↗
PubMed1991

Analysis of the human type I insulin-like growth factor receptor promoter region.

We isolated genomic fragments containing the 5' region of the human type I insulin-like growth factor receptor gene. A unique transcription start site was identified, defining a 1038 bp 5'-untranslated region. No TATA or CCAAT elements were identified in the proximal 480 nucleotides of 5'-flanking region. The region surrounding the transcription start site was similar to a recently described "initiator" sequence. The 5'-flanking and 5'-untranslated regions were highly GC-rich, with numerous potential Sp1 binding sites. A potential AP-2 binding site was identified in the 5'-flanking region and a potential thyroid response element was identified in the 5'-untranslated region. The 5' region of the human gene was very similar to that of the rat gene, with conservation of many of the potential regulatory elements.

Animals↗
PubMed1991

Footprint of the sigma protein: a re-examination.

Escherichia coli RNA Polymerase is a multi-subunit enzyme that catalyzes RNA synthesis, using DNA as a template. The sigma subunit of this enzyme plays an important role in the recognition of promoter sites on DNA. Using DNase I footprinting, Utpala Ramesh and Claude F. Meares [(1989) Biochem. Biophys. Res. Comm. 160, 121-125] reported that in the absence of the other subunits, sigma binds specifically to the bacteriophage lambda PR promoter DNA sequence. We are unable to reproduce that result.

Bacteriophage lambda↗
PubMed1988

Chemical probing of the homopurine.homopyrimidine tract in supercoiled DNA at single-nucleotide resolution.

Local structure of the homopurine.homopyrimidine tract in a supercoiled plasmid pEJ4 was studied using chemical probes at single-nucleotide resolution. The conformation of the homopyrimidine strand was probed by osmium tetroxide, pyridine (Os,py) while that of the homopurine strand was tested by diethyl pyrocarbonate (DEPC), i.e. by probes reacting preferentially with single-stranded DNA. At weakly acidic pH values, a strong Os,py attack on three nucleotides at the centre of the (dC-dT)16 block and a weaker attack on two nucleotides at the end of the block were observed. DEPC modified adenines in the 5'-half of the homopurine strand. Os,py modification at the centre of the block corresponded to the loop of the hairpin formed by the homopyrimidine tract, while DEPC modification corresponded to the unstructured half of the homopurine strand in the model of protonated triplex H form of DNA.

Animals↗
PubMed1988

Cloning and sequencing of a Clostridium perfringens sialidase gene.

Escherichia coli was transformed with pUC vectors containing Sau3A restriction fragments (RF) of Clostridium perfringens DNA. Two clones expressed sialidase activity when assayed with the fluorogenic substrate 4-methylumbelliferyl-alpha-D-N-acetylneuraminic acid. A synthetic oligonucleotide representing the N-terminus of the expressed enzyme hybridized with the clostridial insert and with a corresponding 2.1 kb Sau3A RF of the C. perfringens genome. The insert reduced to 1.4 kb, which still encoded active sialidase, has been sequenced. The structural gene encodes 382 amino acids representing an Mr of 42770. A hydrophobic leader sequence is absent. Upstream from the initiation codon ATG, a GA-rich region is found and considered as the Shine-Dalgarno sequence. Homology with the N-terminus of the Vibrio cholerae sialidase gene and with viral sialidase sequences was not found.

Amino Acid Sequence↗
PubMed1988

Molecular cloning and sequence analysis of cDNA encoding human kidney D-amino acid oxidase.

cDNA clones encoding D-amino acid oxidase were isolated from a human kidney cDNA library by hybridization with cDNA for the pig enzyme. The cDNA insert of 2.0 kilobase pairs long provided coding information for a protein consisting of 347 amino acids. The molecular mass of the enzyme was calculated to be 39,410 Da. The amino acid sequence similarity between the pig and human enzymes is 84.4%, and among the active site residues proposed from chemical modification studies, methionine-110 of the pig enzyme was replaced by threonine. Northern blot analysis confirmed the expression of an mRNA of 2.0 kilobases encoding the D-amino acid oxidase in human kidney.

Amino Acid Sequence↗
PubMed1988

Organization of 5'-proximal c-myb exons in chicken DNA. Implications for c-myb tissue-specific transcription.

The organization of 5'-proximal c-myb exons in chicken DNA has been established by restriction enzyme mapping and nucleotide sequencing. Hybridization studies performed with cDNA probes revealed that yolk sac and thymic c-myb RNAs differ in their 5'-termini. A comparison of the genomic c-myb sequence with that of cDNAs isolated from normal thymic and lymphoma avian cells suggests that different promoter regions are used to initiate c-myb transcription in hematopoietic cells of different origins.

Amino Acid Sequence↗
PubMed1989

Supercoil-stabilized left-handed DNA in the plasmid (dA-dT)16 insert formed in the presence of Ni2+.

The (dA-dT)16 insert of the plasmid pAT32 was probed with diethyl pyrocarbonate (DEPC) and nuclease Bal3l in the presence of Ni2+ known to be able to induce transition to left-handed conformation in the synthetic poly(dA-dT).poly(dA-T). It has been shown that this insert in a supercoiled plasmid displays a DEPC modification pattern characteristic of left-handed DNA under conditions not sufficient to induce a left-handed structure in the linear plasmid and poly(dA-dT).poly(dA-T).

DNA Transposable Elements↗
PubMed1989

Processing of transcripts of a dimeric tRNA gene in yeast uses the nuclease responsible for maturation of the 3' termini upon 5 S and 37 S precursor rRNAs.

The rna82 mutation of Saccharomyces cerevisiae inactivates an RNA processing activity responsible for maturation of 3'-terminal sequences upon 5 S and 37 S ribosomal RNA precursors. This study describes a difference in the processing of transcripts of an S. cerevisiae dimeric tRNA gene (tRNA(arg)-tRNA(Asp) in RNA polymerase III in vitro transcription extracts prepared from rna82 and wild-type cells. The mutant extract accumulated additional processing intermediates containing tRNA(Arg) sequences as compared to the extract from wild-type cells. The structure of these intermediates revealed a defect in removal of the 10 nucleotides left 3' to the tRNA(Arg) sequence by the RNase P cleavage immediately 5' to tRNA(Asp). This is the first demonstration of a mutational defect affecting maturation of 3' sequences upon a eukaryotic tRNA precursor.

Base Sequence↗