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...

Several categories of human X-Y homologous DNA sequences have been recognized. We report that a locus (DXYS77) approximately 14 kb distal to the pseudoautosomal boundary (PAB) is 93% identical in nucleotide sequence to a locus (DYS148) on the long arm of the Y chromosome (Yq). Within this segment of pseudoautosomal/Yq homology we identified a member of a family of repeats that are concentrated ...

Telomerase is a specialized DNA polymerase that synthesizes telomeric DNA sequences onto chromosome ends. Linear DNA genomes pose a special problem for the DNA replication machinery. Because DNA polymerases function in the 5 to 3 direction and require a primer, part of the lagging strand is predicted to be lost at each round of division. For most eukaryotic chromosomes, sequence loss is balance...

Prokaryotic genomes acquire and eliminate blocks of DNA sequence by lateral gene transfer and spontaneous deletion, respectively. The basic parameters of spontaneous deletion, which are expected to influence the course of genome evolution, have not been determined for any hyperthermophilic archaeon. We therefore screened a number of independent pyrimidine auxotrophs of Sulfolobus acidocaldarius...

Three derivatives of mutant ga10P-308::IS2-I of Escherichia coli were characterized by DNA sequence analysis. Deletions and DNA sequence rearrangements were observed which apparently were initiated at short A-T rich inverted repeats within IS2. Two of the mutants carried newly synthesized DNA sequences which were inverted copies of already existing IS2 sequences. Thus long stretches with twofol...

We describe a system to measure the frequency of both deletions and duplications between direct repeats. Short 17- and 18-bp palindromic and nonpalindromic DNA sequences were cloned into the EcoRI site within the chloramphenicol acetyltransferase gene of plasmids pBR325 and pJT7. This creates an insert between direct repeated EcoRI sites and results in a chloramphenicol-sensitive phenotype. Sel...

Short interspersed elements (SINEs) are ubiquitous in mammalian genomes. Remarkable variety of these repeats among placental orders indicates that most of them amplified in each lineage independently, following mammalian radiation. Here, we present an ancient family of repeats, whose sequence divergence and common occurrence among placental mammals, marsupials and monotremes indicate their ampl...