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Results for “DNA sequence analysis”

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At least 163 records · Page 9Linked to original sources
PubMed1999

Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells.

A PCR strategy is described for global amplification of DNA from a single eukaryotic cell that enables the comprehensive analysis of the whole genome. By comparative genomic hybridization, not only gross DNA copy number variations, such as monosomic X and trisomic 21 in single male cells and cells from Down's syndrome patients, respectively, but multiple deletions and amplifications characteristic for human tumor cells are reliably retrieved. As a model of heterogeneous cell populations exposed to selective pressure, we have studied single micrometastatic cells isolated from bone marrow of cancer patients. The observed congruent pattern of comparative genomic hybridization data, loss of heterozygosity, and mutations as detected by sequencing attests to the technique's fidelity and demonstrates its usefulness for assessing clonal evolution of genetic variants in complex populations.

Bone Marrow Cells↗
PubMed1986

DNA sequence analysis of a 5.27-kb direct repeat occurring adjacent to the regions of S-episome homology in maize mitochondria.

The DNA sequence of the 5270-bp repeated DNA element from the mitochondrial genome of the fertile cytoplasm of maize has been determined. The repeat is a major site of recombination within the mitochondrial genome and sequences related to the R1(S1) and R2(S2) linear episomes reside immediately adjacent to the repeat. The terminal inverted repeats of the R1 and R2 homologous sequences form one of the two boundaries of the repeat. Frame-shift mutations have introduced 11 translation termination codons into the transcribed S2/R2 URFI gene. The repeated sequence, though recombinantly active, appears to serve no biological function.

Amino Acid Sequence↗
PubMed1990

DNA sequence analysis of endoglucanase genes from Pseudomonas fluorescens subsp. cellulosa and Pseudomonas sp. NCIB 8634.

The DNA of two previously isolated recombinant clones, one from Pseudomonas sp. NCIB 8634 (= Cellvibrio mixtus) (pPC71) and another from Pseudomonas fluorescens subsp. cellulosa (pPFC4) that express endoglucanase activity in E. coli was sequenced. Plasmid pPC71 had three open reading frames, two of which include portions of plasmid pBR322. The third open reading frame occurs entirely within the Pseudomonas DNA insert and encodes a protein with a molecular mass of 5845 Da. The DNA insert in pPFC4 was found to contain an open reading frame (PFC-ORF) that encodes a protein of 32189 Da. The major endoglucanase produced in E. coli cells carrying pPFC4 is about 30,000 Da. It is concluded that PFC-ORF encodes this endoglucanase. Both ribosome and catabolite gene activator protein binding sites lie upstream from the initiating codon of PFC-ORF. An interesting feature of the PFC-ORF protein is the presence of amino acid motifs Val-Ser-Ser-Ser-Ser and Val-Val-Ser-Ser-Ser-Ser-Ser that occur within a 25 amino acid span.

Amino Acid Sequence↗
PubMed1990

Chemical robot for enzymatic reactions and extraction processes of DNA in DNA sequence analysis.

A chemical robot capable of performing enzymatic reactions and extraction processes of DNA has been developed. The basic functions of this robot include handling of plastic tubes with caps, micropipetting, mixing, microcentrifuging and incubating. As a result, almost all of the pre-electrophoresis steps can be carried out. In addition, because these processes are automated, the working time of each process can be reduced. The reproducibility of the automated operation is equivalent to that of a skilled operator.

Base Sequence↗
PubMed1984

Restriction site bank vectors. II. DNA sequence analysis of plasmid pJRD158.

pJRD158 is a small plasmid vector (3903 bp) derived from pBR327 and specifying resistance to ampicillin and tetracycline. It contains 28 unique restriction sites (and 4 nonunique restriction sites) that can be used for cloning. The DNA sequence and computer-assisted restriction site analysis of pJRD158 are reported. Evidence is also presented that suggests a 2-bp revision of the DNA sequence of pBR322 in the RNA primer region.

Ampicillin↗
PubMed1990

Molecular cloning, genetic characterization and DNA sequence analysis of the recM region of Bacillus subtilis.

In Bacillus subtilis the recM gene, whose product is associated with DNA repair and recombination, has been located between the dnaX and rrnA genes. The recM gene has been cloned and analyzed. Analysis of the nucleotide sequence (3.741-kilobase) around recM revealed five open reading frames (orf). We have assigned recM and dnaX to two of this orf, given the gene order dnaX-orf107-recM-orf74-orf87. The organization of genes of the dnaX-orf107-recM region resembles the organization of genes in the dnaX-orf12-recR region of the Escherichia coli chromosome. Proteins of 24.2 and 17.0 kDa would result from translation of the wild type and in vitro truncated recM genes, and radioactive bands of proteins of molecular weights of 24.5 and 17.0 kDa were detected by the use of the T7promoter-expression system. The RecM protein contains a potential zinc finger domain for nucleic acid binding and a putative nucleotide binding sequence that is present in many proteins that bind and hydrolyze ATP. Strains, in which the recM gene has been insertionally inactivated, were generated and show a phenotype essentially the same as previously described recM mutants.

Adenosine Triphosphate↗
PubMed1994

DNA sequence analysis of the cytosolic acetaldehyde dehydrogenase gene (Ahd-2) in mouse strains with variable ethanol preferences.

Differences in Ahd-2 at the DNA sequence level were characterized in mouse strains with variable ethanol preferences. The 5' region and the region surrounding the active site of Ahd-2 were compared to detect differences which could affect ethanol sensitivity. Only minor differences were found among the strains in the two regions. These differences cannot explain their variable ethanol preference and the implications of sequence identities among the divergent strains in these regions has yet to be determined.

Alcohol Drinking↗
PubMed1998

Sequence assembly validation by multiple restriction digest fragment coverage analysis.

DNA sequence analysis depends on the accurate assembly of fragment reads for the determination of a consensus sequence. This report examines the possibility of analyzing multiple, independent restriction digests as a method for testing the fidelity of sequence assembly. A dynamic programming algorithm to determine the maximum likelihood alignment of error prone electrophoretic mobility data to the expected fragment mobilities given the consensus sequence and restriction enzymes is derived and used to assess the likelihood of detecting rearrangements in genomic sequencing projects. The method is shown to reliably detect errors in sequence fragment assembly without the necessity of making reference to an overlying physical map. An html form-based interface is available at http:/(/)www.ibc.wustl.edu/services/validate. html.

Algorithms↗
PubMed1982

DNA sequence analysis of a mouse pro alpha 1 (I) procollagen gene: evidence for a mouse B1 element within the gene.

In a 3.8-kilobase mouse DNA sequence encoding amino acid sequences for the pro alpha 1(I) chain of type I procollagen, 14 coding sequences were identified which specify a sequence 95% homologous to amino acid residues 568 to 963 of the bovine alpha 1(I) chain. All of these coding sequences were flanked by appropriate splice junctions following the GT/AG rule. These observations suggest, but do not prove, that this pro alpha 1(I) gene is transcriptionally active. Of the 14 coding sequences, 7 were 54 base pairs in length, whereas the remainder were higher multiples of 54 base pairs. Nonrandom utilization of codons pertained throughout all of the coding sequences showing a preference (56%) for U in the wobble position. Two of the intervening sequences encoded imperfect vestiges of coding sequences which exhibited a codon preference different from that of the pro alpha 1(I) gene proper and were not flanked by splice junctions. One intervening sequence encoded a member of the mouse B1 family of middle repetitive sequences. It was flanked by 8-base-pair direct repeats and had a truncated A-rich region, suggesting that it may be a mobile element. Within this element were sequences which could function as a RNA polymerase III split promoter.

Animals↗
PubMed1992

DNA sequence analysis of the dnaK gene of Escherichia coli B and of two dnaK genes carrying the temperature-sensitive mutations dnaK7(Ts) and dnaK756(Ts).

The DNA sequence of the dnaK gene of Escherichia coli was analyzed. The nucleotide sequence of the wild-type dnaK gene of E. coli B differed from that of E. coli K-12 in 15 bp, none of which altered the amino acid sequence. Two temperature-sensitive dnaK mutations were examined by cloning and sequence analyses. Results showed that one dnaK mutation, dnaK7(Ts), was a one-base substitution of T for C at nucleotide position 448 in the open reading frame yielding an amber nonsense codon. The other mutation, dnaK756(Ts), consisted of base substitutions (A for G) at three nucleotide positions, 95, 1364, and 1403, in the open reading frame resulting in an aspartic acid codon in place of a glycine codon.

Amino Acid Sequence↗
PubMed1986

DNA sequence analysis of ARS elements from chromosome III of Saccharomyces cerevisiae: identification of a new conserved sequence.

Four fragments of Saccharomyces cerevisiae chromosome III DNA which carry ARS elements have been sequenced. Each fragment contains multiple copies of sequences that have at least 10 out of 11 bases of homology to a previously reported 11 bp core consensus sequence. A survey of these new ARS sequences and previously reported sequences revealed the presence of an additional 11 bp conserved element located on the 3' side of the T-rich strand of the core consensus. Subcloning analysis as well as deletion and transposon insertion mutagenesis of ARS fragments support a role for 3' conserved sequence in promoting ARS activity.

Base Sequence↗
PubMed1986

Antigenic determinant in human coagulation factor IX: immunological screening and DNA sequence analysis of recombinant phage map a monoclonal antibody to residues 111 through 132 of the zymogen.

As an approach to the study of structure-function relationships in the normal and defective forms of human coagulation factor IX, we have begun to develop a series of monoclonal antibodies against specific sites on the protein. Zymogen and activated forms of normal factor IX were used initially as antigen for the preparation of monoclonal antibodies. Recombinant phage were prepared by cloning small (50- to 500-nucleotide) random DNA fragments from the coding region of a factor IX cDNA clone into the expression vector lambda gt11. Immunological screening of these recombinants with mixtures of monoclonal antibodies identified several immunoreactive phage. Further analysis showed that the monoclonal antibody designated IX-30 was generating the positive signals at a frequency of approximately 1/2,500 recombinants. Subcloning and sequence analysis of the inserted DNA in the immunoreactive phage revealed overlapping in-frame insertions, from which it could be inferred that the site in factor IX recognized by IX-30 is confined to residues 111 through 132 in the light chain. Similar mapping with other monoclonal antibodies should provide additional probes for the protein structure of human factor IX.

Amino Acid Sequence↗
PubMed1993

Spontaneous mutagenesis in Escherichia coli harbouring plasmid pKM101: DNA sequence analysis of forward lacI- mutations.

To investigate the influence of plasmid pKM101 on spontaneous mutagenesis, 198 lacI- mutations generated in Escherichia coli harbouring pKM101 were characterized at the DNA sequence level. pKM101 by itself did not enhance the lacI- forward mutation frequency. In general, the resultant distribution of mutation highlights particular sequences at which a variety of mutational events repeatedly occur, including 5'-(G/C)TGG-3', 5'-CCAGG-3', 5'-GATC-3' and 5'-TCGCG-3' sequences. Specifically, the distribution of mutation within base substitution and deletion classes distinguishes the pKM101 spectrum from the wild-type distribution (i.e. absence of pKM101). An even distribution amongst base substitutions was observed which corresponds to a 2.9- to 6.3-fold increase in occurrence of low frequency events (A-->G,T,C; G-->C); high frequency events in the wild-type distribution (G-->A,T) were not influenced by the presence of pKM101. One complex event was recovered which was comprised of two base substitutions separated by 4 bp. An 11-fold increase in small deletion events (3-6 bp) was also observed. The observed pKM101 spectrum does not closely resemble the mutational consequences of SOS induction in the absence of mutagenic treatment (recA441 spectrum) but does return a distribution like that obtained in E. coli deficient in polymerase I activity (polA1 spectrum).

Amino Acid Sequence↗
PubMed1984

DNA sequence analysis on the IBM-PC.

We have developed, for the IBM-PC microcomputer, a menu driven, interactive set of programs which provide the functions routinely used for DNA sequence data analyses.

Amino Acid Sequence↗