Single-stranded circles

This reaction scheme has been extended to other reactions of the type I topoisomerases such as DNA relaxation, knotting, and the annealing of complementary single-strand circles (Brown and Cozzarelli, 1981 Dean et al., 1982 Dean and Cozzarelli, 1985). For this mechanism to operate for all type I reactions, the enzyme must act similarly on nicked and unbroken DNA, and be able to pass either single- or double-stranded DNA through the break (though in the latter case it is not excluded that the strands could be translocated one at a time). 

FIGURE 5.2 A single-strand circle formed by intra-molecular annealing of adenovirus DNA... 

Additional study of the termini of AAV DNA by Koczot et al. (1973) has shown that AAV DNA also contains an inverted terminal nucleotide sequence repetition of the type found in adenovirus DNA (Garon et al., 1972 WoLFSON and Dressler, 1972). This conclusion was based upon the fact that up to 70% of separated plus or minus strands of AAV DNA formed single-stranded circles when annealed and these circles were converted to linear molecules by exonuclease III digestion. It was hypothesized that such single-... 

Fig. 6. Electron micrographs of hydrogen-bonded single-stranded circles formed when purified linear heavy AAV single polynucleotide chains are exposed to annealing conditions. The arrows point to the projections observed on such single-stranded circles...

The linear RCA method can use both target and signal amplification. A DNA circle (such as a plasmid, circular vims or circular chromosome) is amplified by polymerase extension of a complementary primer. Up to 10 tandemly repeated, concantemerized copies of the DNA circle are generated by each primer, resulting in one single-stranded, concantemerized product. ... 

In 4>X174, however, replication begins with a single stranded closed circle, a rather atypical situation. First, primase brings about the synthesis of a short RNA primer, beginning at one or more specific initiation sites on the DNA. 

Figure 1 Action spectra for the induction of single strand break (ssb, open circle) and double strand break (dsb, closed circle) in dry plasmid DNA. Ratio of the cross section of ssb against dsb is also shown in lower panel. Solid line is reconstructed absorption cross section of the plasmid. (From Refs. 12, 13, 22, and 25.)...

The discovery that DNA forms catenanes and knots, some of them extremely complex, initiated a new field of research which has been called Biochemical Topology [21]. In 1967, Vinograd and co-workers detected in HeLa cell mitochondria isolable DNA molecules that consist of independent, double-stranded, closed circles that are topologically interlocked or catenated like the links in a chain [22, 23]. A few years later, catenanes had been observed everywhere that circular DNA molecules were known [24] and the first knot was found by Liu and coworkers in single-stranded circular phage fd DNA treated with Escherichia coli co-protein [25]. In 1980, knots could also be generated in double-stranded circular DNA [26]. 

Unlike the double-stranded nature of DNA, RNA molecules usually occur as single strands. This does not mean they are unable to base-pair as DNA can. Complementary regions within an RNA molecule often base-pair and form complex tertiary structures, even approaching the three-dimensional nature of proteins. Some RNA molecules, such as transfer RNA (tRNA) possess several helical areas and loops as the strand interacts with itself in complementary sections. Other hybrid molecules such as the enzyme RNase P contain protein and RNA portions. The RNA part is highly complex with many circles, loops, and helical regions creating a convoluted structure. 

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