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At least 325 records · Page 18Linked to original sources
PubMed1993

Brugia malayi and Brugia pahangi: synthetic biotin labeling of oligonucleotide probes for use in species-specific detection assays.

We have developed a novel, high-yield synthetic approach for the incorporation of multiple biotin residues into a series of species-specific oligonucleotide probes for the detection of filarial parasites. The probes are designed to detect species-specific regions of a highly repeated DNA sequence (HhaI repeat) found in all species of Brugia. The synthetic method described in this paper was used to construct oligomer probes tailed on the 5' end with 1 to 46 biotinylated uridine residues. Probes with 46 biotins were found to be more sensitive than probes with 30 or fewer biotins. We also found that alternating the biotinylated uridine residues with nonbiotinylated thymidine residues improved the sensitivity of the probes. Melting temperature studies indicated that the long tails (up to 91 nucleotides) had only a minimal effect on the Tm of the probes. Conditions were found that optimized the sensitivity of the probes while maintaining their species specificity. Using these conditions, the probes were shown to be sensitive enough to detect single parasites in blood using a chemiluminescent detection system. This method of nonradioactively labeling oligonucleotides for the detection of infectious agents will enable the use of such probes in endemic regions in developing countries.

Animals↗
PubMedDate not supplied

The sources of variation in the human genome and genome instability in human cancers.

The human genome is viewed as a stable collection of about 60,000-70,000 genes--a minority of protein--coding DNA sequences--dispersed in a large majority of noncoding DNA sequences--more than 90 per cent of the entire genome sequences. Some of these ubiquitous noncoding DNA sequences, metonymically called "parasitic DNA," "ballast DNA," "selfish DNA" or "extra DNA," especially, the repeated sequences tandemly organized, are not stable but vary with considerable frequency. Recently, the confused or inadequately known origin of native of pathological variations of these DNA sequences appears to be unravelled, with great implications in genome stability. The human chromosomes, the bearer of genome, store and carry it. Their structure is qualified to perform its fastidious functions. The chromosomal conformation, "with variable geometry," exposed to genetoxic action of different damaging factors and to torsional stress after their fast and repeated changes during mitosis. The exaggerate exceeding of the native variation of human genome in disease states, probably, generates genome instability. The chromosome fragility--the cellular phenotypic expression of these molecular instability--reflects the closely relations between the genome and its carrier. The pattern of DNA replication with asynchrony of different domains of "parcelled" genome and the results of replication, susceptible to be corrected by the action of DNA repair genes, render certain limited regions of genome more vulnerable to damaging. These "target" regions focused damaging effects and exhibit an increased susceptibility to breakage and recombination, often with chromosomal expression. The coincidence of these regions, frequently, with locations of many protooncogenes and sometimes, antioncogenes could be subsequently, starting points for a genuine chain of genomic events related to growth cell and cell division. Cancer multistage accumulation of various genomic disorders in a single cell tends to take advantage of discriminating situations of these regions, which themselves can generate other genetic disorders, involving its in carcinogenesis. The gene expression disorders or the genuine mutations of dominant protooncogenes and the recessive behaviour of antioncogenes explain the nature of human cancers--a mixture of inherited and somatically acquired gene disorders. They attest the recessive characteristic of human cell malignancy and emphasize the decisive role of cancer predisposition which operates in interaction with damaging environmental factors. Seemingly, the pivotal causes of genome instability originate from strange behaviour of certain repeated DNA sequences dispersed throughout the human genome. Perhaps they hold the key to the puzzle of cancer processes.

Chromosome Aberrations↗
PubMed2001

A new repetitive DNA sequence family in the olive (Olea europaea L.).

Two families of repeated DNA sequences were cloned from Olea europaea ssp sativa cv. "Picual". The first repetitive DNA is organized in a tandem repeat of monomers of 178 bp. Sequencing of several clones showed that it is relatively A-T rich (54.49%) and possesses short direct and inverted subrepeats as well as some palindromic sequences. Comparison between the monomers revealed heterogeneity of the sequence primary structure. This repetitive DNA is present in several cultivars of olive cultivates. Comparison of sequences with other repetitive DNAs described in Olea europaea has been carried out. No significant similarity was found. All the obtained results suggest that this repetitive DNA described here is a new family of repetitive DNA. The second repetitive DNA is organized in a tandem repeat of monomers of 78 bp. This second family of repetitive DNA showed significant similarity with other repetitive DNAs previously described in Olea europaea. Their existence in new cultivars of olive is shown.

Base Sequence↗
PubMed1989

Human identification and sex determination of dental pulp, bone marrow and blood stains with a recombinant DNA probe.

Recombinant DNA hybridizing specifically to a 300 nucleotide repeat DNA sequence (BLUR8) of human specificity and to human repeat DNA sequence (pHY10) on the Y chromosome was used for human identification and sex determination of degraded DNA samples of blood stains, dental pulp, and bone marrow. This radioactive technique enabled reliable and sensitive human and sex determination from blood stains that were more than 80 years old. Less than 1 piece of 0.5 cm length thread of blood stain was enough for both tests. DNA from relatively fresh dental pulp and bone marrow was clearly identified. The human identification test, which could recognize up to 0.3 ng DNA correctly, was 3 to 5 times more sensitive than the sex determination test.

Adolescent↗
PubMed1978

Kinetic determination of the genome size of the pea.

Renaturation of pea (Pisum sativum) DNA has been used to estimate the size of the pea genome and the fraction of pea DNA containing repeated DNA sequences. Pea DNA renaturation and single copy tracer renaturation indicate that the size of the pea genome is 0.5 picograms. More than 70% of pea DNA sequences are repeated from 100 to 5,000 times.

Journal Article↗
PubMed2002

B chromosomes of Korean field mouse Apodemus peninsulae (Rodentia, Murinae) analysed by microdissection and FISH.

Organization of B chromosomes in the Korean field mouse Apodemus peninsulae was analyzed. We painted its metaphase chromosomes with whole and partial chromosome paints generated by microdissection and DOP-PCR. The results of the painting indicated that all B chromosomes contained a large amount of repeated DNA sequences. The repeats could be classified in terms of their homology and predominant location. Pericentromeric repeats of B chromosomes were present in many copies in pericentromeric C-blocks of all autosomes and in non-centromeric C-blocks of the sex chromosomes. B arm specific type 1 repeats comprised the main body of the arms of almost all B chromosomes and were present in the arms of A chromosomes as interspersed sequences. B arm-specific type 2 repeats were found at the ends of some B chromosomes that did not undergo compaction at the interphase- metaphase transition and remained uncondensed. On the basis of comparative analysis of localization of B chromosome repeats in the chromosomes of two related species, A. peninsulae and A. agrarius, we suggest a hypothesis of B chromosome origin and evolution in the genus Apodemus.

Animals↗
PubMed1995

Unstable triplet repeat diseases.

Seven inherited human disorders are now associated with the intragenic expansion of triplet repeat DNA sequences. These repeats demonstrate extreme instability in both germline and somatic tissue, accounting for the unusual genetic inheritance patterns and symptom variability associated with these diseases.

Brain Diseases↗
PubMed1998

[Mutation process in mini-satellites].

Minisatellites are tandemly repeated DNA sequences with repeat units in the range 6-100 bp. They are preferentially located in subtelomeric euchromatin of chromosomes of higher eukaryotes. Minisatellite loci frequently show variability in allele length. This variability is a consequence of high frequency of mutations which change repeat copy number of locus. The most part of minisatellite mutations are germline specific and possibly meiotic. Examples of different mutations and involved genomic mechanisms are reviewed in this paper. A possible biological role of minisatellites is discussed.

Chromosome Mapping↗
PubMed1989

[Correlation of polymorphism of heterochromatin segments with hybridization on chromosome preparations of various cloned repeated human DNA sequences].

Comparison between results of measurements of heterochromatic regions detected by differential C and DA/DAP1 staining and the hybridization data of two cloned repeated human DNA sequences one alphoid (pH S05) and the other the satellite DNA III (pPD18) on chromosome preparations was made. A positive correlation of heterochromatic region sizes on several chromosomes and the amount of label over them detected after hybridization with both alphoid and satellite sequences was shown, the correlation with the latter being more pronounced.

Cloning, Molecular↗
PubMedDate not supplied

[Search for expansion of CAG-repeats in DNA sequences expressed in the brain of humans with psychiatric and neurological diseases].

Dynamic mutations due to trinucleotide repeat expansion are a new class of human genome mutations. CAG repeat expansion in the coding region of associated genes is the molecular genetic basis of the several diseases of nervous system. Eight DNA sequences with CAG repeats expressed in human brain were chosen from the GenBank database. The search of CAG expansion was carried out for patients with schizophrenia (brain and blood) and essential tremor. CAG repeat expansion has not been found for the loci. The distribution of allelic sizes is similar in the patients and control samples. Locus HS0073 has shown the polymorphism of the length for CAG repeat alleles. Statistically reliable excess of the homozygotes has been found for schizophrenic patients.

Alleles↗
PubMed2006

Repseek, a tool to retrieve approximate repeats from large DNA sequences.

UNLABELLED: Chromosomes or other long DNA sequences contain many highly similar repeated sub-sequences. While there are efficient methods for detecting strict repeats or detecting already characterized repeats, there is no software available for detecting approximate repeats in large DNA sequences allowing for weighted substitutions and indels in a coherent statistical framework. Here, we present an implementation of a two-steps method (seed detection followed by their extension) that detects those approximate repeats. Our method is computationally efficient enough to handle large sequences and is flexible enough to account for influencing factors, such as sequence-composition biases both at the seed detection and alignment levels. AVAILABILITY: http://wwwabi.snv.jussieu.fr/public/RepSeek/

Algorithms↗
PubMed1983

The rat casein multigene family. I. Fine structure of the gamma-casein gene.

A region approximately 35 kilobase pairs (kb) in length containing the hormonally regulated rat gamma-casein gene has been characterized by examining overlapping clones of genomic rat DNA obtained from two Charon 4A libraries. The entire gamma-casein structural gene is contained in a single 17-kb phage clone. R-loop and restriction enzyme mapping analyses revealed that the gamma-casein gene is approximately 15 kb long and is, therefore, 17.4 times larger than the mature gamma-casein mRNA. The coding regions of the gamma-casein gene are split into at least nine small segments, interspersed with long intervening sequences. Sequence analysis of the 5' end of the gamma-casein gene revealed the presence of a TATA sequence which may play a role in the initiation of gene transcription. The first exon is 44 nucleotides long and encodes part of the 5' noncoding sequences of the gamma-casein mRNA. The first intron was found to contain a short interspersed repeated DNA sequences which shares a 92% homology with a cloned rat repeated DNA sequence found at the 3' end of several other rat genes. In addition, the gamma-casein gene contains several families of highly repeated sequences interspersed throughout the intervening and flanking regions, including a family of evolutionary conserved repeats. Thus, the gamma-casein gene represents an unusually large and complex split mammalian gene.

Animals↗
PubMed1993

Isolation of a repeated sequence from the genome of Bordetella parapertussis with characteristics of an insertion sequence element.

A repeated DNA sequence in the genome of Bordetella parapertussis was identified by means of heteroduplex formation and S1 nuclease treatment. Cloning and sequencing of the repeated sequence, revealed that it comprised 1306 basepairs, contained inverted repeats at its termini, and two large open reading frames. This insertion sequence element was designated IS1001, and was found in about 20 copies in 10 B. parapertussis strains analyzed. Identical hybridization patterns were observed in B. parapertussis when IS1001 was used as a probe. B. pertussis strains did not hybridize to IS1001.

Amino Acid Sequence↗
PubMed1992

Structural heterogeneity in the R173 family of rye-specific repetitive DNA sequences.

The rye-specific R173 family of repeated DNA sequences consists of ca. 15,000 individual copies per diploid rye (Secale cereale) genome and is distributed over all 7 rye chromosomes in a dispersed manner. Individual R173 elements vary in size between 3 and 6 kb, are generally not arranged as tandem repeats and are flanked by both multi-copy and single-copy sequences. DNA sequence analysis of three R173 elements (R173-1, R173-2 and R173-3) demonstrated a high degree of homology in conserved domains. The structure of R173-1 was quite different from the other two elements: long direct repeats, which represent a rye-specific repetitive sequence, were found at the ends and a 600 bp long domain was replaced by an unrelated sequence of approximately equal size. R173-2 and R173-3 were extremely similar to each other with the exception of a terminal truncation of R173-2. No open reading frames for proteins greater than 20 kDa were present and a database search failed to detect significant homologies to published protein sequences. Despite the transposon like genomic organisation of the R173 family, individual elements lacked sequence features frequently associated with transposons and retrotransposons. In contrast, two of the regions flanking R173 elements showed strong DNA homologies to a 850 bp long region of a proposed wheat retrotransposon and to a 300 bp long region downstream of the wheat Glu-D1 gene.

Base Sequence↗
PubMed2004

Detection of inter-spread repeat sequence in genomic DNA sequence.

Various types of periodic patterns in nucleotide sequences are known to be very abundant in a genomic DNA sequence, and to play important biological roles such as gene expression, genome structural stabilization, and recombination. We present a new method, named "STEPSTONE", to find a specific periodic pattern of repeat sequence, inter-spread repeat, in which the tandem repeats of the conserved and the not-conserved regions appear periodically. In our method, at first, the data on periods of short repeat sequences found in a target sequence are stored as a hash data, and then are selected by application of an auto-correlation test in time series analysis. Among the statistically selected sequences, the inter-spread repeats are obtained by usual alignment procedures through two steps. To test the performance of our method, we examined the inter-spread repeats in Mycobacterium tuberculosis and Zamia paucijuga genomic sequences. As a result, our method exactly detected the repeats in the two sequences, being useful for identifying systematically the inter-spread repeats in DNA sequence.

Algorithms↗
PubMed2002

CpG methylation modifies the genetic stability of cloned repeat sequences.

The genetic stability of tandemly repeated DNAs is affected by repeat sequence, tract length, tract purity, and replication direction. Alterations in DNA methylation status are thought to influence many processes of mutagenesis. By use of bacterial and primate cell systems, we have determined the effect of CpG methylation on the genetic stability of cloned di-, tri-, penta- and minisatellite repeated DNA sequences. Depending on the repeat sequence, methylation can significantly enhance or reduce its genetic stability. This effect was evident when repeat tracts were replicated from either direction. Unexpectedly, methylation of adjacent sequences altered the stability of contiguous repeat sequences void of methylatable sites. Of the seven repeat sequences investigated, methylation stabilized five, destabilized one, and had no effect on another. Thus, although methylation generally stabilized repeat tracts, its influence depended on the sequence of the repeat. The current results lend support to the notion that the biological consequences of CpG methylation may be affected through local alterations of DNA structure as well as through direct protein-DNA interactions. In vivo CpG methylation in bacteria may have technical applications for the isolation and stable propagation of DNA sequences that have been recalcitrant to isolation and/or analyses because of their extreme instability.

Abnormalities, Multiple↗