Circular genome

Mitochondria are unique organelles in man and higher animals in that they contain their own genome. Mitochondrial DNA (mtDNA) in humans is a small (16.5 kb), circular genome that encodes only 13 proteins, 22 transfer RNA (tRNA), and 2 ribosomal RNA (rRNA) molecules. mtDNA is inherited only from the mother and is present in multiple copies within one mitochondrion. 

Since all DNA polymerases require a primer and work only in the 5 to 3 direction, there s a problem with replicating the 5 ends of the DNA. If an RNA primer has to be laid down and later removed, these ends can t get replicated. For bacteria with a circular genome, this isn t a problem. Eukaryotes have specialized structures called telomeres at the... 

Chloroplasts contain large 120- to 169-kb circular genomes encoding about 100 proteins (Chapter 23). A characteristic feature of most chloroplast DNA is the presence of long inverted repeat sequences (10,058 bp in the liverwort, 25,339 bp in tobacco).463 464 These are separated by 19,813 and 81,095 bp single copy regions in the liverwort and by similar sized regions in tobacco. Plastid DNA exists as a mixture of monomeric molecules with smaller amounts of dimers, trimers, and tetramers.464... 

Cleavage map of the SV40 genome. The zero point of the map is the unique EcoR 1 site. For clarity, the circular genome is shown opened at the R1 site, and the cleavage sites (and resulting fragments) for each restriction enzyme are indicated on a separate line. 

Region in and around the early transcription start sites of the SV40 genome. The base pair number on the circular genome is indicated. There are several transcription start sites. One cluster of start sites (early), used initially after infection, is located about 27 bp downstream from the TATA box. The other cluster of start sites (late early) is used at later times. This cluster of start sites is located... 

Cleavage sites for restriction enzymes occur randomly in the DNA. The frequency of a particular restriction site is dependent on the size of the DNA and the size of the recognition sequence. The probability of finding a particular four-base run in DNA is 1/256 (l/4>base-specific restriction sites in the 5243 base pair, circular genome of the simian virus SV40 is shown in Table 2.7. 

Papillomavirus has a 600-A-diameter shell that encases a histone-bound 8-kb double-stranded, covalently closed circular genome [15]. This... 

Key Words Genome visualization circular genome plots comparative genomics horizontal gene transfer whole genome alignments. 

Several circular genome visualization tools have been developed, and offer a wide variety of features. The Microbial Genome Viewer (1) is one such online tool. Users can choose from several genomes and create plots within the web... 

Sato, N. and Ehira, S. (2003) GenoMap, a circular genome data viewer. Bioinformatics 19, 1583-1584. 

Stothard, P. and Wishart, D. S. (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21, 537-539. 

Detailed understanding of the eukaryotic proteins that participate in DNA replication has come largely from studies with small viral DNAs, particularly SV40 DNA, the circular genome of a small virus that Infects monkeys. Figure 4-34 depicts the multiple proteins that coordinate copying of SV40 DNA at a replication fork. The assembled proteins at a replication fork further illustrate the concept of molecular machines introduced in Chapter 3. These multicomponent... 

Mitochondria and chloroplasts contain multiple copies of double-stranded circular genomes that encode genes required for organelle-specific functions. The complete DNA sequence of representative mitochondrial and chloroplast genomes is known and has been used to characterize genetic mutations. 

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