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Results for “repeated DNA sequences”

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PubMed1995

[Comparison of repeat DNA sequences in the Erinaceidae mammal family by restriction analysis].

Hedgehog (Erinaceidae) DNA was digested with teh Sau 96 I, Bsp 143 I, Csp 6 I, Taq I, Hinf I, Msp I, Eco 130I, Bcn I, BsuR I restriction endonucleases. The obtained products were end-labeled and electrophoretically separated in polyacrylamide gel. DNA fragments consisting of highly repetitive genomic sequences were detected as a set of bands corresponding to fragments between 30 and 500 bp in length. Comparison of DNA restriction patterns of the species analyzed revealed the presence of species-specific bands as well as common bands. Phylogenetic trees were constructed by means of the maximum parsimony method and the bootstrap procedure. Our data suggest that hedgehog species from arid areas are clearly distinguished from forest species.

Animals↗
PubMed1997

Selective recognition of tandemly repeated DNA sequences by homo- and heterodimers of short peptides.

The non-covalent and specific protein-protein interaction is critical to the specificity and the cooperativity of the DNA-binding by protein dimers. We have designed and synthesized three sets of peptide dimers with covalent- or noncovalent artificial dimerization modules to elucidate the structural and thermodynamic aspects for the sequence-specific DNA-binding by protein dimers. We have investigated the DNA binding of covalent dimer, noncovalent homodimer and noncovalent heterodimer with specific or nonspecific DNA sequences by gel mobility shift assay. Although the amino acid sequence of DNA-binding region of these peptide dimers are the same, the selectivity and the cooperativity of DNA binding by these peptide dimers were found to be different.

Adamantane↗
PubMed2005

Human tandem repeat sequences in forensic DNA typing.

It has been 20 years since the first development of DNA fingerprinting and the start of forensic DNA typing. Ever since, human tandem repeat DNA sequences have been the main targets for forensic DNA analysis. These repeat sequences are classified into minisatellites (or VNTRs) and microsatellites (or STRs). In this brief review, we discuss the historical and current forensic applications of such tandem repeats.

DNA Fingerprinting↗
PubMed2004

A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences.

MOTIVATION: One of the most interesting features of genomes (both coding and non-coding regions) is the presence of relatively short tandemly repeated DNA sequences known as tandem repeats (TRs). We developed a new PC-based stand-alone software analysis program, combining sequence motif searches with keywords such as organs, tissues, cell lines or development stages for finding exact, inexact and compound, TRs. Tandem Repeats Analyzer 1.5 (TRA) has several advanced repeat search parameters/options over other repeat finder programs as it does not only accept GenBank, FASTA and expressed sequence tag (EST) sequence files but also does analysis of multifiles with multisequences. Advanced user-defined parameters/options let the researchers use different motif lengths search criteria for varying motif lengths simultaneously. The outputs show statistical results to be evaluated by the user. The discovery of TRs in ESTs could be useful for both gene mapping and association studies and discovering TRs located in coding regions of important genes that are expressed under various conditions of environment, stress, organ, tissue and development stage. RESULTS: In this paper, we demonstrated applications of TRA using 175 899 ESTs sequences for three Arabidopsis spp. downloaded from GenBank. The EST-SSRs/ESTs ratios were found 43.1%, 15.3% and 2.34% in A.lyrata, A.thaliana and A.halleri, respectively. Analysis revealed that organs, tissues and development stages possessed different amounts of repeats and repeat compositions. This indicated that the distribution of TRs among the tissues or organs may not be random differing from the untranscribed repeats found in genomes. AVAILABILITY: The program can be obtained free by anonymous FTP from ftp.akdeniz.edu.tr/Araclar/TRA.

Arabidopsis↗
PubMed1993

Design of Onchocerca DNA probes based upon analysis of a repeated sequence family.

Repeated DNA sequences have been instrumental in the development of DNA probes for many different parasites. Isolation of such DNA probes has generally been accomplished by differential screening of genomic libraries with total genomic DNA preparations. In the current work, a rational design strategy is presented for the development of oligonucleotide probes based upon repeated sequence families. A repeated sequence family present in the genome of Onchocerca parasites, designated O-150, has been amplified from various samples of genomic DNA using PCR. DNA sequence analysis of the resulting PCR products demonstrated that the sequences may be arranged into clusters within which the individual sequences are identical or nearly identical. Differences among the cluster consensus sequences have been exploited to explain the specificities of previously isolated O-150 based probes and to develop two new oligonucleotide probes. One of these probes hybridizes specifically to Onchocerca volvulus O-150 PCR products, while the second hybridizes specifically to O-150 PCR products from the closely related bovine parasite O. ochengi. These oligonucleotide probes have been used to characterize Onchocerca infective larvae isolated from wild caught infected flies in West Africa. Because repeated sequence families are a common feature of most genomes, including those of parasites, this method should be applicable to the rational design of oligonucleotide probes for other parasitic infections.

Animals↗
PubMed1984

Temporal replication of an interspersed repeated sequence of mouse DNA.

The temporal replication profile of an interspersed repeated DNA sequence (variously named MIF-1, Bam and L1Md) of mouse was determined by isotope analysis of a resolvable restriction fragment differentially labeled in pre- and post-synchrony cultures. While the temporal replication profile of the fragment was similar to that of total nuclear DNA, an average time lag of about 20 min was evident for this interspersed repeated family (called Bam in this paper). In addition, the sequence organisation of Bam homologues were examined for the separable early- and late-replication domains of the hamster genome. The data suggest that late-replicating domains of the rodent genome are slightly enriched in Bam homologous sequences. Furthermore, this repeated sequence family has different sequence organisations in the separable replication domains of hamster.

Animals↗
PubMedDate not supplied

Novel intergenic repeats of Escherichia coli K-12.

An online catalog of intergenic DNA repeat sequence elements is added to the EcoGene Escherichia coli K-12 genome sequence annotation and analysis project (bmb.med.miami.edu/EcoGene). A library of noncoding (intergenic) DNA sequences depleted of known intergenic repeat classes was searched for DNA sequence similarities to identify novel DNA repeat sequence classes.

Base Sequence↗