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At least 127 records · Page 7Linked to original sources
PubMed1995

Sequence analysis of frog rho-crystallin by cDNA cloning and sequencing: a member of the aldo-keto reductase family.

rho-Crystallin is a major enzyme crystallin present in the lenses of amphibian species with a blocked amino terminus. In order to facilitate the determination of the primary sequence of this taxon-specific crystallin, cDNA mixture was synthesized from the poly(A)+mRNA of bullfrog eye lenses. cDNAs encoding rho-crystallin were then amplified by polymerase chain reaction (PCR) using a new protocol of Rapid Amplification of cDNA Ends (RACE). PCR-amplified product corresponding to rho-crystallin was obtained, which was then subcloned into pUC18 vector and then transformed into E. coli strain JM109. Plasmids purified from the positive clones were prepared for nucleotide sequencing by the automatic fluorescence-based dideoxynucleotide chain-termination method. Sequencing more than 15 clones containing DNA inserts coding for rho-crystallin constructed only one unique and complete full-length reading frame of 975 base pairs covering a deduced protein sequence of 324 amino acids including the universal initiating methionine. It shows 96, 59, 46 and 37 percent sequence similarity to another rho-crystallin from European common frog, bovine prostaglandin-F synthase, human aldose reductase and human aldehyde reductase, respectively, revealing the close relationship between rho-crystallins from related amphibian species and its possible evolutionary relatedness with various aldo-keto reductases. In this study a phylogenetic tree for rho-crystallin and related enzymes is constructed based on multiple-sequence alignment program using a combination of distance matrix and approximate parsimony methods. We have thus established the remote phylogenetic relationship between rho-crystallin and some aldehyde/aldose reductases, which may provide a possible link for the recruitment of this crystallin from detoxification-related enzymes and its physiological role in maintaining a transparent and clear lens.

Alcohol Oxidoreductases↗
PubMed1995

Sequence analysis of frog alpha B-crystallin cDNA: sequence homology and evolutionary comparison of alpha A, alpha B and heat shock proteins.

alpha-Crystallin is a major lens protein present in the lenses of all vertebrate species. Recent studies have revealed that bovine alpha-crystallins possess genuine chaperone activity similar to small heat-shock proteins. In order to facilitate the determination of the primary sequence of amphibian alpha B-crystallin, cDNA encoding alpha B subunit chain was amplified using a new "Rapid Amplification of cDNA Ends" (RACE) protocol of Polymerase Chain Reaction (PCR). PCR-amplified product corresponding to alpha B subunit was then subcloned into pUC18 vector and transformed into E. coli strain JM109. Plasmids purified from the positive clones were prepared for nucleotide sequencing by the automatic fluorescence-based dideoxynucleotide chain-termination method. Sequencing more than five clones containing DNA inserts coding for alpha B-crystallin subunit constructed only one complete full-length reading frame of 522 base pairs similar to that of alpha A subunit, covering a deduced protein sequence of 173 amino acids including the universal translation-initiating methionine. The frog alpha B crystallin shows 69, 66 and 56% whereas alpha A crystallin shows 83, 81 and 69% sequence similarity to the homologous chains of bovine, chicken and dogfish, respectively, revealing a more divergent structural relationship among these alpha B subunits as compared to alpha A subunits. Structural analysis and comparison of alpha A- and alpha B-crystallin subunits from eye lenses of different classes of vertebrates also shed some light on the evolutionary relatedness between alpha B/alpha A crystallins and the small heat-shock proteins.

Amino Acid Sequence↗
PubMed1995

Sequence analysis of one major basic beta-crystallin (beta Bp) of amphibian lenses: evolutionary comparison and phylogenetic relatedness between beta- and gamma-crystallins.

beta Bp-Crystallin, a major basic beta-crystallin of vertebrate eye lens, is developmentally regulated during the process of amphibian metamorphosis. In order to facilitate the determination of the primary sequence of this ubiquitous crystallin present in all vertebrate species, cDNA mixture was synthesized from the poly(A)+ mRNA isolated from bullfrog eye lenses. A protocol of Rapid Amplification of cDNA Ends (RACE) was used to amplify cDNAs encoding beta Bp-crystallin by polymerase chain reaction (PCR). PCR-amplified product corresponding to beta Bp-crystallin was then ligated into pGEM-T vector and then transformed into E. coli strain JM109. One complete full-length reading frame of 615 base pairs, which covers a deduced protein sequence of 205 amino acids, including the universal initiating methionine, was revealed by automatic nucleotide sequencing with a fluorescence-based dideoxynucleotide chain-termination method. It shows 83, 74, 78 and 80 percent sequence similarity to the homologous beta 2 crystallins of chicken, rat, bovine, and human species, respectively, revealing the close structural relationship among beta Bp-crystallins even from remotely related species. In this study phylogenetic trees based on nucleotide and protein sequences of various beta- and gamma-crystallins from different vertebrate classes are constructed using a combination of distance matrix and approximate parsimony methods, which corroborate the previous supposition that beta- and gamma-crystallins form a superfamily with a common ancestry.

Amino Acid Sequence↗
PubMed1998

JC9813-A putative novel human papillomavirus identified by PCR-DS.

Papillomaviruses consist of more than 130 viral types described so far. Most of them are human papillomaviruses (HPV) of supergroup A, demonstrating ano-genital tropism and characterized as etiological agents for benign and malignant cervical lesions in women. A PCR-direct sequencing (PCR-DS) approach with P-33 labeled dideoxynucleotides was used to detect and type human papillomaviruses in cervical biopsies. One novel sequence was identified in a LSIL (low-grade squamous intraepithelial lesions) specimen from an HIV-positive English Canadian patient. The structure of the viral gene L1 was determined, yielding a putative novel HPV type of supergroup A (clade A8) named JC9813.

Adult↗
PubMed1996

Detection of apoptosis and DNA replication by differential labeling of DNA strand breaks with fluorochromes of different color.

Selective DNA strand break induction by photolysis (SBIP) at sites that contain incorporated halogenated nucleotides has been recently proposed as a means of analyzing DNA replication and detecting proliferating cells. The presence of numerous in situ DNA strand breaks is also an inherent feature of apoptotic cells. The aim of the present study was to differentially label DNA strand breaks in apoptotic cells vs photolysis-induced breaks in BrdUrd incorporating cells. This would allow one, by multicolor staining, to identify these respective cells in the same sample preparation. Toward this end, exponentially growing HL-60 cells were pulse labeled with BrdUrd and then were subjected to hyperthermia or treated with DNA topoisomerase I inhibitor camptothecin to induce apoptosis. DNA strand breaks in apoptotic cells were first labeled directly with fluorochrome-conjugated dUTP or dCTP, followed by dideoxynucleotide (to terminate chain elongation), in a reaction catalyzed by exogenous terminal deoxynucleotidyl transferase. The cells were subsequently exposed to UV light to photolyze DNA containing the incorporated BrdUrd. The photolysis-induced DNA strand breaks were, in turn, labeled with digoxygenin- or biotin-conjugated dUTP followed by digoxygenin antibody or avidin, respectively, conjugated with fluorochrome of another color. Alternatively, DNA strand breaks were labeled with BrdUTP which was then detected by FITC-conjugated anti-BrdUrd MoAb. Following counterstaining of cellular DNA with a fluorochrome of a third color it was possible to identify apoptotic cells, cells incorporating BrdUrd, and cells having no DNA strand breaks. Cell fluorescence was measured either by flow cytometry or with the microscope-based laser scanning cytometer. The SBIP approach also offers a possibility to study a colocalization of the immunocytochemically detectable cell constituents at the DNA replication points by microscopy. Using this approach the presence of the proliferating cell nuclear antigen at the DNA replication sites was revealed in MCF-7 breast carcinoma cells.

Antibodies, Monoclonal↗
PubMed1993

Ferrochelatase structural mutant (Fechm1Pas) in the house mouse.

The molecular basis of an inherited defect of ferrochelatase in mouse (Fechm1Pas/Fechm1Pas, described by Tutois et al., 1991, J. Clin. Invest. 88:1730-1736) was investigated. cDNA clones encoding ferrochelatase, isolated by amplification of the mRNA from the liver of a mutant mouse using the polymerase chain reaction, were sequenced by the dideoxynucleotide chain-termination method. All the clones carried a T to A transversion at nucleotide 293, leading to a methionine to lysine substitution at position 98 in the protein (mutation M98K). Hybridization with allele-specific oligonucleotides (ASOs) confirmed the mutation at the cDNA and genomic levels. Finally, expression of the mutant ferrochelatase protein in E. coli demonstrated a marked deficiency in activity in agreement with the activity of the deficient enzyme in vivo. This Fechm1Pas/Fechm1Pas mutant mouse represents a useful model for studying the pathophysiological feature of the human disease and the first accessible model for gene therapy in the field of porphyrias.

Animals↗
PubMed1994

Comparative analysis of human DNA variations by fluorescence-based sequencing of PCR products.

Automated, direct cycle sequencing of purified double-stranded PCR products using Taq polymerase and fluorescently labeled dideoxynucleotide terminators provides a robust and highly reproducible method for identifying DNA sequence variations in sequence-tagged sites. We describe a simple and sensitive strategy that reliably detects the presence of DNA variations when sequencing traces from several different individuals are compared. We also demonstrate the use of this strategy to estimate allele frequencies of single nucleotide substitutions in a population. Taken together, this approach provides an automated method for conducting rapid population studies of candidate gene regions that are in linkage or association with a specific disease and for comparative evolutionary analysis of selected regions of the human genome.

Alleles↗
PubMed1993

Direct sequencing of lambda DNA from crude lysates using an improved linear amplification technique.

We describe an improved method for directly sequencing lambda (lambda) DNA that has been isolated from either crude cleared lysates or plate lysates. This protocol does not require that the DNA be obtained from bacteriophage particles that have been purified by caesium chloride centrifugation. Nanogram quantities of lambda DNA are unidirectionally amplified using a radioactively-labelled oligonucleotide primer, and Thermus aquaticus (Taq) DNA polymerase, in the presence of T4 gene 32 protein (gp 32). The amplification/sequencing reactions are then incubated with terminal deoxynucleotidyl transferase (TdT) and all four deoxynucleotide triphosphates to elongate any prematurely-arrested products. This procedure, which is a modification of a previously-published method, results in a significant improvement in the quality and amount of DNA sequence information that can be obtained from lambda templates. Although it was developed to sequence DNA directly from lambda EMBL3 recombinants, it can also be used with cosmid DNA, M13 and plasmid DNA, and polymerase chain reaction (PCR) amplification products, yielding excellent ladders in each case. In addition, our method resolves the nucleotide sequences of double-stranded plasmid templates that are difficult to determine by conventional dideoxynucleotide sequencing protocols because of 'stalling', in which bands appear at the same position in all four lanes.

Bacteriophage lambda↗
PubMed1994

Sequence analysis of the trailer region of sonchus yellow net virus genomic RNA.

The sequence of the 5' terminus (or the "trailer" region) of the minus-sense RNA genome of sonchus yellow net virus (SYNV) was determined by dideoxynucleotide termination sequencing of purified viral RNA and cloned cDNAs. The 5'-terminal nucleotide was identified by nuclease P1 digestion of 32P-end-labeled genomic RNA followed by polyethyleneimine cellulose chromatography. The trailer sequence occupies positions 13,561 to 13,720 relative to the 3' end of the genomic RNA and is composed of 160 nucleotides (nt) adjacent to a dinucleotide forming a portion of the "gene junction" sequence at the terminus of the L protein gene. The trailer sequence is longer than the 144-nt plus-strand leader RNA transcribed from the 3' end of the genomic RNA and is the longest trailer sequence yet reported among the nonsegmented negative-strand viruses. As is characteristic of other rhabdovirus genomes, the 3' and 5' termini of the SYNV genome are complementary and are capable of forming a panhandle structure involving 16 of the 18 terminal nucleotides. However, there is no obvious direct nucleotide sequence relatedness between the SYNV trailer sequence and those of animal rhabdoviruses and paramyxoviruses. The existence of a minus-strand leader RNA of the same polarity as the trailer sequence could not be detected in nucleic acid extracted from infected plants under hybridization conditions suitable for detection of the plus-strand leader RNA. In this regard, SYNV differs from vesicular stomatitis virus and is similar to other rhabdoviruses which also fail to accumulate detectable minus-strand leader RNAs.

Base Sequence↗
PubMed1991

DNA sequence of a Salmonella-specific DNA fragment and the use of oligonucleotide probes for Salmonella detection.

Hybridization specificity of a 1.8-kb HindIII DNA fragment isolated from Salmonella typhimurium by a molecular cloning technique was confirmed by colony hybridization with 327 Salmonella isolates of various serotypes and 56 non-Salmonella isolates including Enterobacteriaceae closely related to Salmonella, such as Escherichia coli, Klebsiella, Citrobacter and Shigella. It was found that this 1.8-kb DNA fragment was highly specific for all the Salmonella isolates tested. The DNA sequence of this 1.8-kb fragment was then determined by the dideoxynucleotide chain termination method. According to this DNA sequence, six oligonucleotide fragments ranging from 17- to 26-mer were then chemically synthesized and tested for their hybridization specificities. Results show that three of the six oligonucleotide fragments are highly specific for all 327 Salmonella strains tested and can be used as probes for the specific detection of Salmonella in foods or other samples.

Base Sequence↗
PubMed1989

Design of some nucleic acid antimetabolites: expectations and reality.

3'-Azido-2'3'-dideoxythymidine (AZT), a thymidine analogue with potent antiretroviral activity against human immunodeficiency virus (HIV) in vitro, has been shown to confer a clinical benefit in patients with advanced acquired immune deficiency syndrome (AIDS). Other 2',3'-dideoxynucleosides, e.g., 2',3'-dideoxy-cytidine and 2',3'-dideoxyadenosine, block the infectivity of HIV against helper/inducer T cells in vitro and protect the cell against the cytopathic effect of the virus. The majority of these antiretroviral agents were synthesized more than twenty years ago as analogues of physiologically important deoxynucleosides in the quest of a more effective cancer chemotherapy. None of the synthetic analogues manifested significant activity when screened against L1210 leukemia in BDF mice despite the fact that the phosphorylation reactions, crucial to the activation of the 2',3'-dideoxynucleosides, are catalyzed by kinases of appropriate target cells. However, the 2',3'-dideoxynucleoside triphosphates, relative to corresponding deoxynucleotides, have a reduced affinity for DNA polymerase alpha, an enzyme that has key DNA synthetic and repair functions in the life of a cell. In contrast, HIV reverse transcriptase, like host cellular DNA polymerase beta (a repair enzyme) and gamma (a mitochondrial enzyme), is much more susceptible to the inhibitory effects of the dideoxynucleotides. This would explain the activity of the fradulent nucleotides at low concentrations against pathogenic retroviruses vis à vis the low cytoxic activity observed with these agents as anti-leukemia drugs.

Animals↗
PubMed1988

Structure of the Saccharomyces cerevisiae URA4 gene encoding dihydroorotase.

The URA4 gene of Saccharomyces cerevisiae, coding for the third enzyme of the pyrimidine pathway, has been cloned through phenotypic complementation of a ura4 mutant of S. cerevisiae. Subcloning of an original 9 kb DNA fragment, carrying the yeast URA4 gene, allowed us to localize the gene on a 2 kb ClaI--BamHI fragment. The sequence of the URA4 structural gene and surrounding DNA was determined by the dideoxynucleotide chain termination method. The URA4 gene encodes a dihydroorotase subunit of calculated molecular weight 40,600. S1 nuclease mapping indicated that transcription of URA4 is initiated at four major start sites located at positions -41, -30, -22 and -18. A set of potentially significant sequences was identified in the 5' OH non-coding region of the gene. The deduced amino acid sequence of dihydroorotase was examined and compared with homologous amino acid sequences of Salmonella typhimurium, Escherichia coli and Drosophila melanogaster. S. cerevisiae dihydroorotase shows 40% homology with the S. typhimurium and E. coli enzymes and 23% homology with the D. melanogaster enzyme. A potential active site has been predicted for dihydroorotase from these comparisons.

Amidohydrolases↗
PubMed1987

The psbA gene of DCMU-resistant Euglena gracilis has an amino acid substitution at serine codon 265.

The psbA gene coding for the herbicide binding QB protein of photosystem II has been sequenced previously (Karabin et al. 1984). A herbicide resistant mutant of Euglena, Euglena gracilis ZR, was studied by sequencing part of the psbA gene and its corresponding mRNA. Sequencing reactions were done by annealing a psbA specific, end-labeled DNA-oligomer to total chloroplast DNA or RNA and extending this primer with reverse transcriptase in the presence of the four dideoxynucleotides. An amino acid substitution from serine to alanine at position 265 was detected. All known herbicide resistant higher plants sequenced to date and the Chlamydomonas mutant DCMU-4 show a change at exactly this same position, but the substitution in higher plants is from serine to glycine.

Amino Acid Sequence↗
PubMed1986

Pig mitochondrial DNA: polymorphism, restriction map orientation, and sequence data.

Restriction endonuclease cleavage patterns of mitochondrial DNA (mtDNA) in pigs were analyzed using 18 enzymes which recognize six nucleotides and 1 four-nucleotide-recognizing enzyme. Pigs including Taiwan native breeds and miniature strains maintained in Japan were examined in this study; four commercial breeds of pigs and Japanese wild boars have been investigated earlier [Watanabe, T., et al. (1985). Biochem. Genet. 23:105]. mtDNA polymorphisms were observed in the cleavage patterns of five restriction enzymes, Bg1II, EcoRV, ScaI, StuI, and TaqI. The results support the previous hypothesis that pigs must be derived from two different maternal origins, European and Asian wild boars, and that a breed, Large White, arises from both European and Asian pigs. Two HindIII cleavage fragments were cloned into the HindIII site of M13mp10 and were partially sequenced by the dideoxynucleotide-chain termination method. Furthermore, DraI and StuI cleavage sites were newly determined on the restriction endonuclease map. On the basis of these results, the restriction endonuclease cleavage map of pig mtDNA was rewritten. Comparing sequence data of pig mtDNA at 237 positions with those of cow, human, mouse, and rat mtDNA, the sequence difference, silent and replacement changes, and transitions and transversions among mammalian species were estimated. The relationships among them are discussed.

Animals↗
PubMed1981

A method for sequencing single-stranded cloned DNA in both directions.

A DNA sequencing method has been developed whereby DNA that has been cloned in a single-stranded bacteriophage vector can be sequenced from both ends. The method involves first making a minus-strand sense template from a single-stranded insert in the vector M13mp2 using a flanking primer, and then sequencing the synthesized template using the dideoxynucleotide termination method (Sanger et al., 1977, 1980) with a second primer. Special conditions are described under which the first primer is easily removed after making the template, and sequencing in the opposite direction can be done in the normal way (Sanger et al., 1980) without separating the double strands. This method renders it possible to read up to twice the amount of sequence data from a long insert and also to check short inserts by producing complementary sequence patterns.

Bacteriophage lambda↗
PubMed1996

Characterization of gamma-crystallin from the eye lens of bullfrog: complexity of gamma-crystallin multigene family as revealed by sequence comparison among different amphibian species.

gamma-Crystallin is the major and most abundant lens protein present in the eye lens of lower vertebrates such as amphibian and piscine species. To facilitate structural characterization of gamma-crystallins isolated from the lens of the bullfrog (Rana catesbeiana), a cDNA mixture was synthesized from the poly(A)+mRNA isolated from fresh eye lenses. cDNA encoding gamma-crystallin was then amplified using polymerase chain reaction (PCR) based on two primers designed according to the relatively conserved N- and C-terminal sequences of known gamma-crystallins from teleostean fishes. PCR-amplified product corresponding to gamma-crystallin isoforms was obtained, which was then subcloned in pUC18 vector and transformed into Escherichia coli strain JM109. Plasmids containing amplified gamma-crystallin cDNAs were purified and prepared for nucleotide sequencing by the dideoxynucleotide chain-termination method. Sequencing several clones containing DNA inserts of about 0.54 kb revealed the presence of two isoforms with an open reading frame of 534 base pairs, covering two gamma-crystallins each with a deduced protein sequence of 177 amino acids including the translation-initiating methionine. These gamma-crystallins of pI 6.364 and 6.366 contain a low-methionine content of 2.81%, in contrast to 11-16% obtained for those gamma-crystallins with high-methionine content from most teleostean lenses. Pairwise sequence comparison of bullfrog gamma-crystallins with those published sequences of gamma-crystallins from carp, shark, Xenopus and another Rana frog, bovine, and human lenses indicates that there is only 46-63% sequence similarity among these species, revealing that amphibians possess a very complex and heterogeneous group of gamma-crystallins even from closely related species of Rana frogs. The sequence analysis and comparison of various isoforms of the frog gamma-crystallin family provide a firm basis for identifying these lens proteins as members of a multigene family more complex than that reported for mammalian gamma-crystallins.

Amino Acid Sequence↗
PubMed1994

DNA fingerprinting involving fluorescence-labeled termini of any enzymatically generated fragments of DNA.

We have developed a new fluorescence-based method for DNA fingerprinting that does not require a fluorescent linker or a synthetic oligonucleotide primer, both of which are normally used for labeling of DNA. Cosmid DNAs are digested with appropriate restriction enzymes and the 3' termini of DNA fragments are labeled with the corresponding, fluorescent dye-conjugated dideoxynucleotide triphosphate terminator (dye-ddNTP) by the Klenow fragment of DNA polymerase I from Escherichia coli, which has 3'-->5' exonuclease and replacement activities as well as its main 5'-->3' polymerase activity. Samples are separated on a DNA-sequencing gel and data are analyzed by application of both the Version 0.3.8a mapper program (Applied Biosystem Inc., Foster City, CA) and our Overlap I program that facilitate rapid analysis of the frequency of overlapping of cosmid DNAs. Using this method we have determined the overlap frequency of DNA fragments of each cosmid clone from the mouse MHC class I gene cluster.

Animals↗
PubMed2006

Simultaneous detection of precore/basal core promoter mutations in hepatitis B virus using arrayed primer extension.

BACKGROUND: Hepatitis B is a major disease that causes serious public health problems worldwide. The loss of HBeAg expression due to point mutations or single nucleotide polymorphisms (SNPs) in the precore/basal core promoter region of the hepatitis B virus (HBV) is associated with hepatocellular cirrhosis and carcinoma. Simultaneous screening for these mutations is strongly advocated for monitoring disease development in HBV-infected patients. The aim of this study is to apply arrayed primer extension (APEX) for the detection of HBV SNPs at the precore/basal core promoter. METHODS AND RESULTS: We optimized APEX for simultaneous detection of eight potential sites of SNPs in the precore/basal core promoter region of HBV. The precore/basal core promoter regions of HBV from 36 HBV-infected patients were amplified by PCR. After purification and DNA fragmentation, the short, single-stranded HBV DNA fragments were allowed to hybridize with the oligonucleotides corresponding to the sites of SNPs immobilized on glass slides, followed by incorporation of different fluorescently labeled dideoxynucleotides. This allows fast and unequivocal discrimination between wild-type and mutant genotypes with high dideoxy-nucleotide incorporation efficiency, sensitivity, and specificity. The coexistence of both genotypes was also detected; this was undetected by DNA sequencing. CONCLUSION: The simultaneous detection of SNPs in HBV precore/basal core promoter by APEX enables large-scale diagnostic analysis, which can be extended to the whole HBV genome.

Base Sequence↗