Duplex linear circles

A cut or nick is made in one of the two chains, and the circle rolls, peeling away one end of the cut chain, to yield the equivalent of two single chains, which function as templates for DNA synthesis at a fork. As the circle continues to roll, a linear duplex molecule containing multiple copies of the sequence is generated. The rolling-circle mechanism is also seen as a stage in the replication of some viral DNA molecules. 

Fig. 3. A, "Slipped" circle formation by denaturation and annealing of a permuted collection of DNA duplexes. Notice that in the permuted DNA molecules the circular order of genes is constant, but the ends are repetitious. However, different DNA duplexes may have different repetitious ends. Upon annealing, the single strand fragments at either end of the same linear duplex may contain complementary sequences, which can undergo further reannealing to produce a circular duplex molecule. In some cases the single-stranded regions at the ends of the linear duplex will not be complementary and so will not result in circular duplex structures. (From Thomas. 1967. J. Cell Physio ., 70 (Suppl. 1) 13-34.)...

Fig.4. Rolling circle mechanism of replication of some viral DNAs. The circular parent DNA is first cleaved ("nicked") enzymatically. New nucleotide units are added to the 3 terminus of the broken strand, and the continuous growth of the new strand displaces the 5 tail of the broken strand from the rolling circular template. Thus, the 5 tail becomes a linear template for synthesis of a new complementary strand. The duplex originating from the 5 tail is then cieaved from the other daughter dupiex by a nuclease.

Fig. 8 2D DNA arrays, (a) Two DX molecules tile the plane. Conventional DX molecule, A, and a DX + J molecule, B, are seen to tile the plane. The extra domain black circles) on B leads to stripes In the array. The molecules are 4 x 16 nm, so the stripes are 32 nm apart, as seen in the AFM image on the right, (b) Four DX molecules (A-D ) tile the plane. This arrangement is similar to (a), but there is only one DX + J molecule, D, so the stripes are separated by 64 nm, as seen on the right, (c) TX array. Two TX tiles, A and B, are connected by complementarity between their first and third double helical domains, resulting in spaces between the tiles. D is a linear duplex that fits in the yellow rows, and C is a TX re-phased by three nucleotide pairs, and the rephased version is labeled C it fits into the gray rows and extends a double helical domain beyond the AB plane in both directions, as shown on the right...

Fig. 5- Duplex AAV linear monomers which did not form circles or oligomers when exposed to annealing conditions (< 1 %) were digested to the extent of 1 % using exonuclease III and annealed in 2 X SSC (0.30 M NaCl, 0.03 M Na citrate) at either 45° C ( ) or 55° C (o) for various periods of time. The percentage of circles and dimers formed is plotted. (No dimers were observed at 55° C)...

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