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Results for “DNA sequence analysis”

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At least 91 records · Page 5Linked to original sources
PubMed1987

DNA sequence analysis of two bovine immunoglobulin CH gamma pseudogenes.

A bovine calf liver DNA library in lambda 2001 bacteriophage has been screened with a human Ig gamma 4 heavy-chain constant-region gene probe. Four hybridizing clones have been identified, and the DNA sequences in two of these, which have high homology with CH gamma genes, are reported here. Within the bovine sequences, four separate exons can be identified, corresponding to the three CH domains and the hinge of gamma heavy-chain genes. Both of these genes contain atypical sequences around one or more of their exon/intron boundaries with consequent loss of splice sites, indicating that these are probably gamma pseudogenes. One sequence codes for a C-terminal peptide which matches the 18-mer C-terminal heavy-chain peptide of bovine serum IgG2, the other encodes a C-terminal peptide unknown in the bovine. These results suggest that evolutionary duplication of CH gamma genes has occurred in the bovine.

Amino Acid Sequence↗
PubMed1983

Random subcloning of sonicated DNA: application to shotgun DNA sequence analysis.

A method for producing random subclones using sonication to fragment the DNA is presented. The sonication is combined with enzymatic repair of the fragment ends and a rigorous size fractionation step to prepare subclones of relatively homogeneous and specific size. Under some conditions sonication is shown to shear A + T-rich sequences preferentially, although under most conditions it will create a random subclone library. The use of these subclone libraries for an improved "shotgun" DNA sequencing strategy is tested on a 17.2-kb (kilobase) fragment of Epstein-Barr virus.

Base Sequence↗
PubMed1991

Mutational specificities of environmental carcinogens in the lacl gene of Escherichia coli H. V: DNA sequence analysis of mutations in bacteria recovered from the liver of Swiss mice exposed to 1,2-dimethylhydrazine, azoxymethane, and methylazoxymethanolacetate.

The host-mediated assay (HMA) was used to determine the spectra of mutations induced in the lacl gene of Escherichia coli cells recovered from the livers of Swiss mice exposed to the carcinogens 1,2-dimethylhydrazine (SDMH), azoxymethane (AOM), and methylazoxymethanolacetate (MAMA). These spectra were further compared with changes induced by dimethylnitrosamine (DMNA) in the HMA methodology. A total of 177 independent lacl mutations arising in the HMA following exposure to SDMH, AOM, and MAMA were analyzed. Single-base substitutions accounted for 97% of all mutations analyzed. The vast majority of the single-base substitutions consisted of G:C----A:T transitions (94% of all mutations). The remaining mutations consisted of A:T----G:C transitions (3% of all mutations) while non-base substitutions accounted for only 3% of the total mutagenesis. The latter mutations consisted of one frameshift mutation and four lacO deletions. The distribution of G:C----A:T transitions induced by the three chemicals in the first 200 bp of the lacl gene was not random, but rather clustered at sites where a target guanine was flanked at the 5' site by a purine residue.

1,2-Dimethylhydrazine↗
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↗
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↗
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↗
PubMed1982

DNA sequence analysis of a Drosophila foldback transposable element rearrangement.

The complete nucleotide sequence of a DNA rearrangement associated with the foldback 4 (FB 4) transposable element is presented. The results demonstrate that the entire loop sequence and almost all of one of the inverted terminal repeats is absent. Moreover, the sequence of the remaining inverted repeat suggests that the FB elements might undergo inversions via recombinations between the two inverted repeats of a single element.

Base Sequence↗