A simulation model of sequence-dependent amplification, unequal crossing over and mutation is analyzed. This model predicts the spontaneous formation of tandem-repetitive patterns of noncoding DNA from arbitrary sequences for a wide range of parameter values. Natural selection is found to play an essential role in this self-organizing process. Natural selection which is modeled as a mechanism f...

We describe the detection of a ubiquitous DNA-binding protein which appears to interact specifically with tandem-repeated minisatellites. The murine 40 kd protein, which we term Msbp-1, was found to be present in all mouse tissues tested. This protein was bound specifically and with high affinity by double-stranded DNA containing a repeat sequence related to the minisatellite 'core' sequence, a...

Forensic Short Tandem Repeat (STR) genotyping is almost exclusively performed by capillary electrophoresis (CE) in specialized laboratories. As an alternative to CE, and enable miniaturized lab-on-a-chip STR profiling, we developed the QueSTR probes, a hybridization-based assay that relies on recognition cleavage of RNA:DNA duplex RNase H2 enzyme. For each allele be genotyped, matching DNA prob...

Current methods for characterizing extrachromosomal nuclear DNA in mammalian cells do not permit single-cell analysis, are often semi-quantitative and frequently biased toward the detection of circular species. To overcome these limitations, we developed Halo-FISH to visualize and quantitatively analyze extrachromosomal DNA in single cells. We demonstrate Halo-FISH by using it to analyze extrac...

Centromeres usually contain large amounts of tandem repeat DNA. Alpha satellite DNA (AS) is the most abundant tandem repeat DNA found in the centromeres of simian primates. The AS of humans contains sequences organized into higher-order repeat (HOR) structures, which are tandem arrays of larger repeat units consisting of multiple basic repeat units. HOR-carrying AS also occurs in other hominoid...

Short regularly spaced repeats (SRSRs) occur in multiple large clusters in archaeal chromosomes and as smaller clusters in some archaeal conjugative plasmids and bacterial chromosomes. The sequence, size, and spacing of the repeats are generally constant within a cluster but vary between clusters. For the crenarchaeon Sulfolobus solfataricus P2, the repeats in the genome fall mainly into two cl...

The abnormal number of repeats found in triplet repeat diseases arises from 'repeat instability', in which the repetitive section of DNA is subject to a change in copy number. Recent studies implicate transcription in a mechanism for repeat instability proposed to involve RNA polymerase II (RNAPII) arrest caused by a CTG slip-out, triggering transcription-coupled repair (TCR), futile cycles of ...

Biochemical evidence is presented which confirms that the DNA repeat length in micrococcal nuclease (spleen endonuclease, nucleate 3'-oligonucleotidohydrolase, EC 3-1-4-7) digests of Chinese hamster ovary chromatin is shorter than that of rat liver chromatin [J.L. Compton, R. Hancock, P. Oudet, and P. Chambon (1976) Eur. J. Biochem., in press]. A survey of available cells has shown that the DNA...

Mutants of simian virus 40 (SV40) lacking parts of the 72- and 21-base-pair repeat regions were made deficient in large T antigen by recombination with dlA 4000, a mutant containing a frameshift deletion near the amino terminus of the T antigen genes. These double mutants were transfected into COS cells, and the amounts of replicated viral DNA were measured at various times thereafter. It was f...

Phylogenetic divergence of the members of the Pongidae family has been based on genetic evidence. The terminal repeat array (T2AG3) has lately been considered as an additional basis to analyze genomes of highly related species. The recent isolation of subtelomeric DNA probes specific for human (HSA) chromosomes 7q and 14q has prompted us to cross-hybridize them to the chromosomes of the chimpan...