SEARCH · PubMed Health

Results for “DNA sequencing”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 667 records · Page 37Linked to original sources

PubMed2001

Evolution of the periodicity and the self-similarity in DNA sequence: a Fourier transform analysis.

Fourier transform analysis was applied to elucidate the periodical and self-similar properties in the DNA sequences mainly of beta-globin genes in different species, and the evolutionary change in those properties was then investigated. Map patterns of a two-dimensional DNA walk showed that the stretches of exons are significantly shorter than those of introns, suggesting that the evolution of exons is driven by natural selection, whereas that of introns is generated by unknown internal rules. Using a monomer analysis, we obtained the power spectra of four different bases, A, G, C, and T, in DNA sequences. Periodicities in the short- (2 to 10 base pairs [bp]), medium- (10 to 50 bp) and long-range order (50 to 300 bp) of beta-globin gene sequences could be observed, and power spectral densities of these periodicities were increased with evolution. These results suggest the existence of the internal rules in the occurrence of the synonymous and nonsynonymous substitutions in the sequences, the destabilization of the interaction between DNA and histone protein, and the stabilization of the chromatin structure, respectively. Moreover, 1/f(alpha) analysis of the power spectra (log-log plot) in the far long-range region (160 to 16,000 bp) suggested the increase in the self-similarity (the fractal structure) of DNA sequences with evolution. A general trend of the increase in a 3 bp periodicity with evolution might be functionally related to the CAG trinucleotide repeat diseases such as Huntington chorea, where a marked periodicity of 3 bp could be observed. Fourier transform analysis applied to a DNA sequence offers a great new avenue for extracting information on the evolution of a DNA sequence.

Animals↗

PubMed1998

Sequencing DNA using mass spectrometry for ladder detection.

Sequencing of DNA fragments of 130 and 200 bp using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for DNA ladder detection was demonstrated. With further improvement in mass resolution and detection sensitivity, mass spectrometry shows great promise for routine DNA sequencing in the future.

Bacteriophage lambda↗

PubMed1994

A quantitative test of long-range correlations and compositional fluctuations in DNA sequences.

Recent findings concerning long-range correlations and fractals in intron-containing DNA sequences of living organisms are tested qualitatively and quantitatively. Extending previous studies, we demonstrate that these findings are trivially equivalent to variations of the base-pair composition in different regions of a DNA sequence. It is shown explicitly that a well-defined scaling or fractal exponent does not exist anywhere. Comparisons of natural DNAs with computer-generated, artificial sequences are made. The present study reveals that certain natural DNA sequences (especially those with compact genomes) do have stochastic characteristics which are intrinsically different from artificial sequences. The results for 21 DNA sequences of various types from widely different taxa are reported.

Animals↗

PubMed1992

cDNA sequence of three cysteine-rich clusters in the iron-sulfur subunit of complex II (succinate-ubiquinone oxidoreductase) from Caenorhabditis elegans determined by automated DNA sequencer.

Homology probing by using mixed primers for polymerase chain reaction (PCR) and a subsequent sequence analysis by automated DNA sequencer were applied to determine a partial cDNA sequence of the iron-sulfur subunit of complex II (succinate-ubiquinone oxidoreductase). Complex II is a membrane-bound flavoenzyme, which catalyzes the oxidation of succinate to fumarate in the tricarboxylic acid cycle, and it is a component of the mitochondrial and bacterial respiratory chains. In this study, the partial amino acid sequence of iron-sulfur subunits in Caenorhabditis elegans mitochondria was deduced from the DNA sequence obtained from cDNA-PCR. Mixed oligonucleotide primers corresponding to two conserved regions which appear to be the binding site for the prosthetic group were used. The product of PCR was cloned into plasmid vector pUC 119 and the sequence was determined from double strand plasmid DNA by the dideoxy method using of one-dye, four-lane type the automated DNA sequencer (DSQ-1, Shimadzu). The PCR product contained 483 nucleotides and its deduced amino acid sequence was highly homologous with that in human liver (68.9%) and that of Escherichia coli sdh B product (50.3%). As expected, striking sequence conservation was found around the three cysteine-rich clusters which have been thought to comprise the iron-sulfur centers of the enzyme.

Amino Acid Sequence↗

PubMed2000

Combinatorial approaches to finding subtle signals in DNA sequences.

Signal finding (pattern discovery in unaligned DNA sequences) is a fundamental problem in both computer science and molecular biology with important applications in locating regulatory sites and drug target identification. Despite many studies, this problem is far from being resolved: most signals in DNA sequences are so complicated that we don't yet have good models or reliable algorithms for their recognition. We complement existing statistical and machine learning approaches to this problem by a combinatorial approach that proved to be successful in identifying very subtle signals.

Algorithms↗

PubMed2005

Protein coding sequence identification by simultaneously characterizing the periodic and random features of DNA sequences.

Most codon indices used today are based on highly biased nonrandom usage of codons in coding regions. The background of a coding or noncoding DNA sequence, however, is fairly random, and can be characterized as a random fractal. When a gene-finding algorithm incorporates multiple sources of information about coding regions, it becomes more successful. It is thus highly desirable to develop new and efficient codon indices by simultaneously characterizing the fractal and periodic features of a DNA sequence. In this paper, we describe a novel way of achieving this goal. The efficiency of the new codon index is evaluated by studying all of the 16 yeast chromosomes. In particular, we show that the method automatically and correctly identifies which of the three reading frames is the one that contains a gene.

Journal Article↗

PubMed1980

Identification of the herpes simplex virus DNA sequences present in six herpes simplex virus thymidine kinase-transformed mouse cell lines.

We have used a novel filter hybridization approach to detect and map the herpes simplex virus (HSV) DNA sequences which are present in four HSV thymidine kinase (HSVtk+)-transformed cell lines which were derived by exposure of thymidine kinase negative (tk-) mouse cells to UV light-irradiated HSV type 2 (HSV-2). In addition, we have mapped the HSV-1 DNA sequences which are present in two HSV-1tk+-transformed cell lines produced by transfection of tk- mouse cells with sheared HSV-1 DNA. The results of these studies can be summarized as follows. (i) The only HSV DNA sequences which were common to all HSVtk+-transformed cells were those located between map coordinates 0.28 and 0.32. Thus, this region contains all of the viral DNA sequences which are necessary for the expression of HSV-mediated tk transformation. (ii) Many of the cell lines also contained variable amounts of non-tk gene viral DNA sequences located between map coordinates 0.11 to 0.57 and 0.82 to 1.00, suggesting that incorporation of the viral DNA sequences located between these map coordinates is a relatively random event. (iii) The viral DNA sequences located between map coordinates 0 to 0.11 and 0.57 to 0.82 were uniformly absent from all of the HSVtk+ cell lines tested, suggesting that there is a strong negative selective pressure against incorporation of these viral DNA sequences.

Animals↗

PubMed2003

Nucleosome positioning on yeast plasmids is determined only by the internal signal of DNA sequence occupied by the nucleosome.

The possible role of border factors in determining the nucleosome positioning on a DNA sequence was investigated. To this end a family of recombinant plasmids based on Gal10Cyc1 promoter and neomycin phosphotransferase gene NPTII were created. A DNA sequence adjoining the GalCyc promoter was varied in these plasmids. Three nearly equally represented nucleosome positions on the GalCyc promoter were found. In the basal plasmid an FRT sequence adjoins the GalCyc promoter at the right. It contains an internal signal of multiple positioning. Its replacement with different DNA sequences does not affect nucleosome positioning on the GalCyc promoter. The nucleosome positioning on the GalCyc promoter does not depend on nucleosome positioning (or its absence) on adjoining sequences. The same is true for nucleosome positioning on FRT sequence. It was found also that nucleosomes' positioning on the NPTII gene and their mutual disposition, namely the spacing between neighboring nucleosomes (linker length) are determined by the location of positioning signals only. Generally the nucleosome positioning in our experimental model is determined solely by internal DNA sequence occupied by nucleosome. On the other hand, the action of this internal positioning signal does not extend to neighboring DNA sequences.

Base Sequence↗

PubMed1994