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 109 records · Page 6Linked to original sources
PubMed1993

Two classes of isocitrate lyase genes are expressed during late embryogeny and postgermination in Brassica napus L.

We have analyzed the structure of genes encoding the glyoxylate cycle enzyme isocitrate lyase from Brassica napus L. and their expression during embryogeny and postgermination. Restriction mapping, nucleotide sequence, and DNA gel blot hybridization analyses of cDNA and genomic clones indicated that there are approximately six isocitrate lyase genes in the B. napus genome that can be divided into at least two subfamilies based upon their divergence in 5' and 3' untranslated regions. We showed previously that isocitrate lyase mRNA accumulates during late embryogeny and postgermination. Here, we present results which indicate that several isocitrate lyase genes are expressed at both stages of development. First, gene-specific probes were used to show that mRNAs encoded by representatives of both gene subfamilies accumulated in both late maturation stage embryos and in seedlings of B. napus. Second, a single B. napus isocitrate lyase gene, together with 3.5 kb and 1.4 kb of 5' and 3' flanking regions, respectively, was expressed in both embryos and seedlings of transgenic tobacco plants. The results indicated that accumulation of isocitrate lyase in late embryogeny and postgermination does not result from the alternate expression of distinct members of the gene family.

Base Sequence↗
PubMed1990

Mapping the active site of ribonuclease P RNA using a substrate containing a photoaffinity agent.

Ribonuclease P RNA is the catalytic moiety of the ribonucleoprotein enzyme that removes precursor sequences from 5'-ends of pre-tRNAs. A photoaffinity cross-linking agent was coupled to the substrate phosphate on which RNase P acts and used to map nucleotides in the vicinity of the catalytic site of this ribozyme. Mature tRNA(Phe) containing a 5'-thiophosphate was synthesized by transcription in vitro using phage T7 RNA polymerase in the presence of guanosine 5'-phosphorothioate. The photoagent (azidophenacyl) was coupled uniquely to the 5'-thiophosphate of the tRNA, the site of action by RNase P. The photoagent-containing tRNA binds to RNase P RNA and is cross-linked by UV irradiation to it at high efficiency (10-30%). Cross-linked conjugates are enzymatically inactive, consistent with the occupancy of the active site of the RNase P RNA by the tRNA. Reversal of the cross-link by phenylmercuric acetate restores activity. The sites of cross-linking in RNase P RNA were determined by primer extension. In order to identify generalities and detect idiosyncrasies, analyses were carried out using RNase P RNAs from three phylogenetically diverse organisms: Bacillus subtilis, Chromatium vinosum and Escherichia coli. In the context of a phylogenetic structure model, two regions of cross-linking are observed in all three RNAs. Two of the RNAs cross-link to a lesser extent at a third structural region and one of the RNAs is cross-linked to a small extent to a fourth region. All the sites of cross-linking between the substrate phosphate in tRNA and the RNase P RNAs are in the conserved core of the structure model, consistent with the importance of the cross-linked residues to the action of this RNA enzyme.

Affinity Labels↗
PubMed1993

Endonuclease VII of phage T4 triggers mismatch correction in vitro.

The reactivity of endonuclease VII (gp49 of phage T4) with DNA-loops of eight, four, or one nucleotide, or any of 12 possible base mismatches was tested in vitro. Endonuclease VII introduces double-strand breaks by nick and counter-nick within six nucleotides 3' from the mispairings. High relative cleavage efficiencies at mismatches in heteroduplexes correlate with their decreased thermal stability and vice versa. A delay between nick and counter-nick was sufficient to allow T4 DNA-polymerase and T4 DNA-ligase to correct a C/C-mismatch in vitro, thereby saving the DNA from double-strand breakage. Very short repair tracks of three to four nucleotides mapped between the mismatch and one of the formerly induced nicks, which were subsequently sealed by DNA ligase.

Bacteriophage T4↗
PubMed1981

Contact-site cross-linking agents.

Contact-site cross-linking agents comprise a heterogeneous grouping of cross-linkers which share the common property of being able to cross-link only very closely juxtaposed residues in macromolecular complexes. We have defined contact-site cross-linking arbitrarily as the covalent joining of residues such that they are constrained to a distance which is equivalent to or less than their closest possible steric approach prior to becoming linked (1). We recognize two classes of contact-site cross-linkers, bridge type and zero-length type. The former, such as formaldehyde, become incorporated during cross-linking as one-atom bridges. The latter, such as the carbodiimides, operate as condensing agents with the result that the cross-linked residues become interjoined directly. Contact-site cross-linkers have been used in several ways as specific probes of both the static and dynamic aspects of macromolecular structure. They can yield precise structural information about macromolecular contacts when actual sites of cross-linking are determined by peptide or nucleotide mapping techniques. In this way exact contacts between histones in the nucleosome, between protein and RNA in the ribosome, and between RNA polymerase and DNA have been determined. Contact-site cross-linkers have also been used to probe the perturbation of contacts following macromolecular conformational changes. Certain histone-histone 'cross-linkable' sites are rendered unreactive after induction of chromatin conformational changes thus serving to localize sites of perturbation.

Binding Sites↗
PubMed1990

A universal primer mixture for sequence determination at the 3' ends of cDNAs.

We have devised a universal primer which can be used to sequence the 3'-ends of cloned cDNAs containing a polyA tail. The primer consists of an equimolar mixture of three primers: 20 T nucleotides followed by either an A, C, or G nucleotide (5'----3'). With this primer mixture and the dideoxynucleotide chain termination method, we determined the 3'-terminal sequence of human beta-actin cDNA in an Okayama-Berg vector, in four parallel sets of reactions containing either a single primer (T20G, T20C, or T20A) or an equimolar mixture of all three primers. Priming with both T20A and the triple mixture gave clearly readable results that agree with the known sequence of the human beta-actin gene, and we have applied this method successfully to several other cDNAs in the Okayama-Berg expression vector. Use of this universal primer mixture facilitates determination of sequences at the 3'-ends of cDNAs while by-passing the polyA tail region.

Actins↗
PubMed1986

Isolation and allelic polymorphism of cDNA clones and genomic clones of HLA-DP heavy and light chains.

From a human cDNA library constructed from consanguineous HLA-homozygous cell line AKIBA (HLA-A24, Bw52, DR2, Dw12, Cp63 Cp63: a new DP type), cDNA clones encoding the heavy and light chains of an HLA-DP Cp63 alloantigen were isolated and analyzed by restriction enzyme mapping and nucleotide sequence determination. Allelic comparisons of DP alpha and DP beta cDNA sequences showed that the amino acid sequence of the DP alpha chain was less polymorphic than that of the DP beta chain. In the DP beta chain, the polymorphic region was restricted to the beta 1 domain. We also isolated and characterized 15 genomic phage clones spanning a 74 kilobase (kb) pair of the DP region which were found to contain one DP alpha gene, one DP-like alpha gene, one DP beta gene, and one DP-like beta gene. Genomic blot analyses with different HLA-DP type cell lines using DP alpha cDNA as a probe revealed EcoRI fragment length polymorphism around the DP alpha gene.

Alleles↗
PubMed1992

Fractal landscape analysis of DNA walks.

By mapping nucleotide sequences onto a "DNA walk", we uncovered remarkably long-range power law correlations [Nature 356 (1992) 168] that imply a new scale invariant property of DNA. We found such long-range correlations in intron-containing genes and in non-transcribed regulatory DNA sequences, but not in cDNA sequences or intron-less genes. In this paper, we present more explicit evidences to support our findings.

DNA↗
PubMed1993

Fractal landscapes and molecular evolution: modeling the myosin heavy chain gene family.

Mapping nucleotide sequences onto a "DNA walk" produces a novel representation of DNA that can then be studied quantitatively using techniques derived from fractal landscape analysis. We used this method to analyze 11 complete genomic and cDNA myosin heavy chain (MHC) sequences belonging to 8 different species. Our analysis suggests an increase in fractal complexity for MHC genes with evolution with vertebrate > invertebrate > yeast. The increase in complexity is measured by the presence of long-range power-law correlations, which are quantified by the scaling exponent alpha. We develop a simple iterative model, based on known properties of polymeric sequences, that generates long-range nucleotide correlations from an initially noncorrelated coding region. This new model-as well as the DNA walk analysis-both support the intron-late theory of gene evolution.

Actins↗
PubMed2003

Nucleotide changes in the translated region of SCN5A from Japanese patients with Brugada syndrome and control subjects.

The mutations of the SCN5A gene have been implicated to play a pathogenetic role in Brugada syndrome, which causes ventricular fibrillation. To determine the Brugada-associated mutations in Japanese patients, facilitate pre-symptomatic diagnosis, and allow genotype-phenotype studies, we screened unrelated patients with Brugada syndrome for mutations. DNAs from 6 Japanese patients were obtained and the sequence in the translated region of SCN5A was determined. We could not find the mutations reported previously, but found 17 sites of nucleotide change, consisting of 7 synonymous and 10 non-synonymous nucleotide changes in our patients. Among them, two non-synonymous nucleotide changes (G1663A and G5227A) are specific to our patients and these changes were not found in 53 healthy controls. In 4 patients out of 6, no specific nucleotide change for Brugada syndrome could be detected. Our findings demonstrating no patient-specific change in the translated region of the SCN5A gene among two thirds of the small number of patients examined here imply that another gene other than the SCN5A may be associated with this disease, supporting previous investigations in Japan and other countries.

Adult↗
PubMed2000

Structure of the human MMP-19 gene.

The recently identified MMP-19 belongs to the multi-protein family of zinc-binding matrix metalloproteinases (MMP). In order to analyze its genomic organization and to identify transcription factor binding sites that may be involved in the regulation of human MMP-19 expression, the gene coding for MMP-19 has been cloned and sequenced. The MMP-19 gene spans over 7.6kb and is composed of nine exons and eight introns. Furthermore, a 1.9kb fragment of 5'-flanking DNA was isolated and the transcription start point mapped. Nucleotide sequence analysis of its 5'-flanking region revealed several potential transcription factor binding sites typical of MMP promoters. Thus, a TATA-box, a consensus AP-1 binding element, and a putative PEA3 site were identified. The 1.9kb MMP-19 promoter fragment and several deletion constructs thereof were able to drive transcription of the luciferase reporter gene in transiently transfected CHO cells. Finally, it has been shown by an electrophoretic mobility shift assay that the AP-1 consensus sequence is able to bind a HeLa nuclear extract derived AP-1 factor.

Amino Acid Sequence↗
PubMed1986

Complete sequence of HLA-B27 cDNA identified through the characterization of structural markers unique to the HLA-A, -B, and -C allelic series.

Antigen HLA-B27 is a high-risk genetic factor with respect to a group of rheumatoid disorders, especially ankylosing spondylitis. A cDNA library was constructed from an autozygous B-cell line expressing HLA-B27, HLA-Cw1, and the previously cloned HLA-A2 antigen. Clones detected with an HLA probe were isolated and sorted into homology groups by differential hybridization and restriction maps. Nucleotide sequencing allowed the unambiguous assignment of cDNAs to HLA-A, -B, and -C loci. The HLA-B27 mRNA has the structural features and the codon variability typical of an HLA class I transcript but it specifies two uncommon amino acid replacements: a cysteine in position 67 and a serine in position 131. The latter substitution may have functional consequences, because it occurs in a conserved region and at a position invariably occupied by a species-specific arginine in humans and lysine in mice. The availability of the complete sequence of HLA-B27 and of the partial sequence of HLA-Cw1 allows the recognition of locus-specific sequence markers, particularly, but not exclusively, in the transmembrane and cytoplasmic domains.

Base Sequence↗
PubMed1989

Reassessment of structural characteristics of the d(CGCG)2:actinomycin D complex from complete 1H and 31P NMR.

Complexes formed between Actinomycin D (ActD) and the tetranucleotides d(AGCT)2 and d(CGCG)2 were studied in detail by one and two-dimensional 1H and 31P NMR. The 31P two dimensional chemical exchange experiment, at room temperature on saturated complexes (1:1), showed unambiguously that the asymmetrical phenoxazone ring binds to the unique GC site under the two possible orientations in the d(AGCT)2 tetranucleotide but adopts a single orientation in the d(CGCG)2 tetranucleotide. For the d(CGCG)2:Act D saturated complex, complete assignments of all protons and phosphorus signals of the two-nucleotide strands, as well as of the two cyclic pentapeptide chains has allowed us to study in details the conformational features of the complex from NOE and coupling constants analysis. The tetranucleotide remains in a right-handed duplex, but the sugar puckers are modified for residues at the intercalation site. A uniform C2' endo pucker is observed for residues on the strand facing the quinoid side of the phenoxazone ring while a C2' endo-C3-endo equilibrium about 60% of C2' endo is proposed for the two residues on the strand facing the benzenoid side of the phenoxazone ring. In contrast to previous studies on ActD-DNA interactions, we have been able to measure the 3J phosphorus-proton coupling constants at the intercalation site but also adjacent to it, showing that 31P chemical shifts are not simply related to the backbone conformation. Molecular mechanics calculations, using empirical distances deduced from NOE effects as restrained distances during minimizations, led to a model differing mainly from those previously published by orientation of the N methyl groups of both N-Methyl-Valines.

Base Sequence↗
PubMed1993

Altered fidelity of a nucleic acid modifying enzyme, T4 polynucleotide kinase, by safrole-induced DNA damage.

Mouse liver DNA adducted with metabolites of the spice constituent safrole (1-allyl-3,4-methylenedioxybenzene), when analyzed via the bisphosphate version of the 32P-postlabeling assay, exhibits two major adducts, which had been previously identified as N2-(trans-isosafrol-3'-yl)2'-deoxyguanosine 3',5'-bisphosphate (adduct 1) and N2-(safrol-1'-yl)2'-deoxyguanosine 3',5'-bisphosphate (adduct 2). However, analysis of the same DNA preparation by the dinucleotide/monophosphate version of the assay gave two additional spots on PEI-cellulose TLC whose nature was clarified in the present study. Several enzymes (T4 polynucleotide kinase, nuclease P1, venom phosphodiesterase and spleen phosphodiesterase) were utilized to hydrolyze these compounds, and the products co-chromatographed on PEI-cellulose thin layers with radiolabeled and non-radioactive nucleotides of known structure. The additional spots were found to be adducted dinucleotides carrying 32P-label at both the 5'- and 3'-hydroxyls. T4 polynucleotide kinase-catalyzed 3'-phosphorylation was highly specific in that only dinucleoside monophosphate derivatives of adduct 1, with an unmodified purine in the 3'-position, were susceptible to both 5'- and 3'-phosphorylation by the enzyme. Thus, the structures of the two additional 32P-labeled safrole derivatives were pX1pAp and pX1pGp where X1 denotes N2-(trans-isosafrol-3'-yl)2'-deoxyguanosine. The official name of T4 polynucleotide kinase, ATP:5'-dephosphopolynucleotide 5'-phosphotransferase (EC 2.7.1.78), denotes the specific action of this enzyme as a 5'-phosphokinase. Although the enzyme has 3'-phosphatase activity at acidic pH, no 3'-kinase reaction has been previously reported. Possible implications for chemical carcinogenesis of the finding that carcinogen-DNA adducts can specifically alter the fidelity of protein-nucleotide interactions are discussed.

Animals↗
PubMed2000

Control of division gene expression in Escherichia coli.

Duplication of the Escherichia coli bacterial cell culminates in the formation of a division septum that splits the progenitor cell into two identical daughter cells. Invagination of the cell envelope is brought about by the co-ordinated interplay of a family of septation-specific proteins that act locally at mid-cell at a specific time in the cell cycle. The majority of the genes known to be required for septum formation are found within the large mra cluster located at 2 min on the E. coli genetic map (nucleotides 89552-107474). Examination of the controls exerted on the mra operon shows that E. coli uses an extraordinary range of strategies to co-ordinate the expression of the cell division genes with respect to each other and to the cell cycle.

Bacterial Proteins↗
PubMed1987

ATP enhances the binding of simian virus 40 large T antigen to the origin of replication.

Simian virus 40 large T antigen initiates DNA replication by binding to the origin of replication. We examined the binding of T antigen to origin regions I, II, and III under conditions designed for efficient in vitro replication functions. We found that 4 mM ATP enhanced the binding of T antigen to regions I and II of the origin DNA by 4- to 20-fold. DNase-footprinting and fragment assays showed that ATP extended the DNase protection domain of T antigen bound to region II by 5 to 10 base pairs at both ends of the core origin of replication. This alteration suggests a change in the conformation of T antigen, bound DNA, or both.

Adenosine Triphosphate↗
PubMed1984

Construction and partial characterization of recombinant cDNA clones for chicken type I collagen messenger RNAs.

Messenger RNAs for the alpha 1 and alpha 2 chains of type I procollagen were partially purified from total embryonic chicken calvaria using gel chromatography on Sepharose 4B and used to construct recombinant cDNA clones corresponding to both mRNAs. Restriction site mapping, nucleotide sequencing and hybridization to RNA blots were used to show that clones pCAL1 and pCAL2 contain inserted sequences corresponding to the mRNAs for chicken alpha 1 and alpha 2 procollagen chains, respectively.

Animals↗
PubMed1990

[A study of protein engineering for human cardionatrin. I. Synthesis, cloning and expression of a gene analog of human atrial natriuretic polypeptide in E. coli].

An analog of the alpha-human atrial natriuretic polypeptide (alpha-hANP) gene, articulated with a peptidase inhibitor SQ20881 at its N-terminal and two prolines at the C-terminal was expressed in E. coli by cloning the reconstituted plasmid pRHL-1 in vivo. This gene analog, RH-1, comprising 154 base pairs in total, was designed to contain an equivalent of the alpha-hANP gene, capping the peptidase inhibitor SQ20881 at its 5' end with a glutamic acid codon GAA to facilitate enzymatic cleavage of the expressed end product by endoproteinase Glu-C, wedging in two proline codons CCG & CCG before the double terminal codons TGA TAG at the 3' end to retard hydrolysis of the expressed product by exopeptidase, and adding 3 restriction sites to both ends. Synthesis of the RH-1 gene was effected enzymatically by joining in predicted order the ten segments of oligodeoxynucleotides which had been chemically synthesized by the solid-phase phosphite-triester method. The synthetic gene was cloned into vector M13mp18. Phage bearing the gene analog was identified by dot blotting and restriction endonuclease mapping. Nucleotide sequence of the gene was determined by the dideoxynucleotide chain termination method.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1988

Characterization of the sites of proteolytic activation of Newcastle disease virus membrane glycoprotein precursors.

The F1- and F2-polypeptide components of the fusion proteins and the hemagglutinin/neuraminidase proteins of the avirulent Queensland (V4) and virulent Australia-Victoria (AuV) strains of Newcastle disease virus have been isolated and subjected to extensive primary structural analysis including amino-terminal sequence analysis and fast atom bombardment-mass spectrometry mapping. Nucleotide sequence analysis was performed on the gene which encodes the V4 hemagglutinin/neuraminidase protein. Signal peptidase cleavage was found to have occurred at the Ser31-Leu32 peptide bond of the primary translation products of the fusion protein genes. Activation cleavage of the V4 fusion protein precursor generated a sequence of -Gly-Lys-Gln-Gly84 at the carboxyl terminus of the F2-polypeptide and an amino-terminal sequence of the F1-polypeptide commencing with 86Leu-Ile-Gly-. The V4 hemagglutinin/neuraminidase protein gene was found to encode a primary translation product 45 amino acids longer at the carboxyl terminus than obtainable from the corresponding gene of the AuV strain (McGinnes, L. W., and Morrison, T. G. (1986) Virus Res. 5, 343-356). However, post-translational proteolytic processing, exclusive to the primary translation product of the V4 hemagglutinin/neuraminidase protein gene, was found to have removed the last 42 residues of this carboxyl-terminal appendage.

Amino Acid Sequence↗