Topology single-stranded

To date, RNA calculations have been performed on a variety of systems of different topologies including helical duplexes, hairpin loops, and single strands from tRNA, rRNA, and ribozymes. In a simulation of an RNA tetraloop of the GRNA type, which is very common and known to be remarkably stable, it was found that without imposing any external infonnation the simulation found the right confonnation even when it started from the wrong one [72]. Studies have used Ewald summation methods to handle the... 

Soybean trypsin inhibitor, papain dl, and rubredoxin have identical topologies six strands of + 1,+ 1,+ 1,. . . proceeding to the left around the barrel if the chain termini are at the bottom. However, handedness is not nearly as meaningful a property for up-and-down topologies as it is for Greek keys, since up-and-down handedness can change on addition or delection of a single strand. 

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]. 

The plectonemic nature of the DNA double-helix makes it a tractable molecule for experiments in molecular topology. This is a very rich vein for the exploration of the topological properties of matter. In this chapter, we have tried to illuminate some of the techniques by which the single-stranded topology of DNA can be directed in synthetic molecules. Catenanes and knots, periodic braids, and Borro-mean rings are available from simple protocols, and it is to be hoped that the physical properties associated with complex topologies (Moffatt 1990) will become available through the medium of DNA constructions. 

Flapan, E Seeman, N.C. (1995) A topological rubber glove obtained from a synthetic single stranded DNA molecule, J. Chem. Soc., Chem. Commute, 2249-2250. 

This milestone in chemical topology84-85 and topological stereochemistry73-86-87 was followed in 1991 by the first rational synthesis of trefoil and figure-eight knots made from single-stranded DNA (Figure 19).S8-89... 

Single-stranded chain. This simple topology is found in... 

Topoisomerase I is the target enzjme for the inhibitory effects of camptothecins. It modulates the topological structure of DNA by inducing transient DNA breaks. Single-strand breaks help to remove excessive positive and negative DNA supercoUs, which arise during DNA replication and transcription. The interaction between the camptothecins and the enzyme results in the formation of a topoisomerase-I-DNA complex (23). 

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