Duplex circles

Aside from the ability to relax (or supercoii) DNA in steps of either 1 or 2, other criteria have been used to distinguish type I and type II enzymes. One useful criterion is the catenation and decatenation of duplex circles (Liu et al., 1980). Type I enzymes, because of their inability to make double-strand breaks, can only catalyze these reactions when at least one circle bears a single-strand nick, whereas type II enzymes can perform these reactions with intact circles (Tse and Wang, 1980). 

Fig. 30. — Packing arrangement of 4-fold antiparallel double helices of potassium hyaluronate (32). (a) Stereo view of a unit cell approximately normal to the line of separation of the two helices. The two chains in each duplex, drawn in open and filled bonds for distinction, are linked by not only direct hydrogen bonds, but also water bridges. Inter double-helix hydrogen bonds are mediated between hydroxymethyl and iV-acetyl groups. Potassium ions (crossed circles) at special positions have only a passive role in the association of hyaluronate chains.

Baumgartner RW, Baumgartner I, Mattie HP et al (1997) Transcranial color-coded duplex sonography in the evaluation of collateral flow through the circle of Willis. Am J Neuro-radiol 18 127-133... 

Fig. 9. View of the partially platinated dodecamer duplex [dCGCGAATTCGCG]2- Pt-Binding sites are indicated by circles [44], Coordinates taken from the Protein Data Bank [49].

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. 

Molecular beacons (MB) are stem-loop hairpin oligonucleotide structures that have a fluorescent dye at one end and a fluorescence quencher at the other. In the hairpin state, the quencher and fluorophore are in close proximity and therefore there is no fluorescence from the probe. However, when the MB binds to a complementary oligonucleotide as a duplex then the fluorophore and quencher are separated and the fluorophore can emit fluorescence. They are particularly useful in monitoring reactions with time, e.g., in PCR, " rolling circle amplification, hybridisation, telomerase activity, ligation... 

Fig. 3 The microRNA (miRNA) pathway. An miRNA is first transcribed as part of an imperfect hairpin in a longer Pol II transcript with 5 cap (open circle) and polyadenosine tail (AAAAAA). The hairpin (pre-miRNA) is removed from the transcript by the nuclear RNase III type enzyme Drosha and its partner, DGCR8. Exportin-5 (Xpo-5) transports the resulting by-product to the cytoplasm, where Dicer liberates a short-lived miRNA duplex. The duplex is unwound, and one strand enters RISC. If the miRNA is mismatched to its target (left), it does not induce cleavage, but may inhibit translation. With a perfect or near-perfect match (right), the target RNA is destroyed by RISC.

Completion of one full circle of replication causes a protein to nick and release the original plus strand and generate a new duplex (called RFII) containing the original minus strand. 

Figure 4.20. Strategies for optical detection of intrinsic DNA bends and kinks. (Top) The FRET approach. The energy transfer donor dye (open circle) is covalently attached to the 5 end of a DNA strand. The complementary strand is labeled on its 5 end with an energy transfer acceptor dye (closed circle). The measured energy transfer is a function of the dye-to-dye distance R and should be different for the double helical straight DNA compared with the double helical bent DNA. (Bottom) The noncovalent probe approach. A probe molecule (shaded circle) is allowed to bind to either straight or bent duplex DNA. Equilibrium binding constants or kinetics of association may be monitored via the spectroscopic properties of the probe.

Shlomai J, Linial M. A nicking en ime from trypanosomatids which specifically affects the topological linking of duplex DNA circles. Purification and characterization. J Biol Chem 1986 261(34) 16219-25. 

Fig. 3. Unlinking and melting of covalently closed DNA by topoisomerase V. (A) Electrophoresis of control relaxed plasmid DNA (1), negatively supercoiled (2), and the same DNA as in (1) but after incubation at 95°C with topo V (3). —SC and U indicate negatively supercoiled and unlinked DNA, respectively. (B) Unlinked DNA strands of pBR322 DNA by electron microscopy. The molecule shown here is magnified approximately 120,000. ssDNA circles are linked onee. (C) An illustration of incomplete melting of circular DNA at high temperature and its complete melting and unlinking by topoisomerase V. Duplex regions and melted strands are shown by thick and thin lines.

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.)...

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