Reporter strand

Figure 17. The ligation products of antiparallel double crossover molecules. Ligations of the DAE, DAO, and DAE+J molecules, respectively, from the top to the bottom of the drawing. One domain has been capped by hairpins. Ligation of the DAE molecule leads to a reporter strand, which is drawn more darkly. Ligation of the DAE+J molecule also leads to a reporter strand, similar to the one in DAE. However, ligation of the DAO molecule produces to a polycatenated structure.

It is very hard to analyze such an experiment if it does not produce a reporter strand, either directly, as described for the three-arm and four-arm junction, or after restriction frees it from catenated partners (Li et al. 1996). To characterize the flexibility of double-crossover molecules, it is useful to examine the crossover topology of the products of an oligomerization reaction. These are shown in Figure 17 for DAE, DAO and DAE+J motifs. It is clear that both DAE and DAE+J motifs produce a reporter strand, but DAO does not. Therefore, in our initial experiments, we have analyzed only DAE and DAE+J. In both, these motifs can be shown to behave as rigid species, because they do not cyclize to any appreciable extent. 

Figure 19. Topological structure of 2D antiparallel DX arrays. The four arrays are built from DAO or DAE molecules crossings are separated by an even (E) or odd (O) number of double helical half-turns. Strand polarities are shown by the arrowheads on their 3 ends. Strands are drawn with different thicknesses for clarity. Both DAO lattices contain vertical zigzag strands, only. DAE-E consists of molecular chain mail, and DAE-O produces reporter strands in both the horizontal direction (straight) and the vertical direction (zigzag).

Recently, the DAE-0 and DAO-E lattices have been constructed (E. Winfree et al., 1998). With both it is possible to ligate the strands together to get very long reporter strands. The most effective characterization of these arrays has been achieved without ligating them, merely by visualizing them in the atomic force microscope (AFM). It is possible to include a DAO+J or DAE+J motif in these arrays where the J hairpin points up, sometimes DAO+2J or DAE+2J, with one hairpin pointing up and one down these hairpins have no effect on the topology of the array, just as... 

Figure21 DX-DNA molecules and their ligated products, (a) Five Isomers from DPE to DAO and one derivative DAE+J (b) ligated produots of three antiparallel molecules. Report strands result In ligated DAE and DAE+J, shown as thiok lines, but ligated DAO oontalns polyoatenanes, (Adapted from N.C. Seeman. Annu. Rev. Biophys. Biomol. Struct. 27 225-248, 1998. With permission.)...

Surgical sutures are sterile, flexible strands used to close wounds or to tie off tubular structures such as blood vessels. Made of natural or synthetic fiber and usually attached to a needle, they are available ia monofilament or multifilament forms. Sutures are classified by the United States Pharmacopeia (USP) (1) as either absorbable or nonabsorbable. The USP also categorizes sutures according to size (diameter) and Hsts certain performance requirements. Sutures are regulated by the Food and Dmg Administration (FDA) as medical devices under the Food, Dmg, and Cosmetics (FDC) Act of 1938, the Medical Device Act of 1976, and the Medical Device Reporting regulation of 1995. 

Bell and Hall have incorporated an organometallic unit into a crown by using the ferrocenyl unit as part of the ring or as a third strand. The unit is incorporated either as the 1,1 -diformylferrocene or the corresponding acid. In the former case, the bis-imine is prepared and reduced to give the saturated crown (see structure 24). In the latter case, the acid is converted into its corresponding chloride and thence into the diamide by reaction with a diamine. Diborane reduction affords the saturated amino-crown. Structure 24 could be prepared by either of these methods but the dialdehyde approach was reported to be poor compared to the amide approach which afforded the product in ca. 60% yield . 

A number of bridged crown ethers have been prepared. Although the Simmons-Park in-out bicyclic amines (see Sect. 1.3.3) are the prototype, Lehn s cryptands (see Chap. 8) are probably better known. Intermediates between the cryptands (which Pedersen referred to as lanterns ) and the simple monoazacrowns are monoazacrowns bridged by a single hydrocarbon strand. Pedersen reports the synthesis of such a structure (see 7, below) which he referred to as a clam compound for the obvious reason . Although Pedersen appears not to have explored the binding properties of his clam in any detail, he did attempt to complex Na and Cs ions. A 0.0001 molar solution of the clam compound is prepared in ethanol. The metal ions Na and Cs are added to the clam-ethanol solutions as salts. Ultraviolet spectra of these solutions indicate that a small amount of the Na is complexed by the clam compound but none of the Cs . 

Warshawsky and coworkers have recently reported the synthesis of a class of compounds which they call polymeric pseudocrown ethers . A chloromethylated polystyrene matrix is used here as in 6.6.2, but instead of adding a crown to the backbone, a strand of ethyleneoxy units is allowed to react at two different positions on the chain, thus forming a crown. Such systems must necessarily be statistical, and the possibility exists for forming interchain bridges as well as intrachain species. Nevertheless, polymers which could be successfully characterized in a variety of ways were formed. A schematic representation of such structures is illustrated below as compound 30. ... 

Shortly after their first report of all-oxygen bridged cryptands, Dietrich, Lehn and Sauvage reported incorporation of sulfur in the strands. The experimental methods used were essentially similar to those applied in the syntheses of the parent cryptands. As in previous cases, a diacyl chloride was condensed with a diamine under high dilution conditions. In this case, however, the diamine contained sulfur atoms rather than oxygen. The synthesis of compound 5 was accomplished in two stages as illustrated below in Eq. (8.3). The first cyclization step affords the macrocyclic amine in 55% yield. The macrobicyclic product (5) is formed in 25% yield from the monocyclic diamine and the acid chloride. 

A marked change in burning behavior occurs in properly restricted strands at pressures above 5000 psig, as reported by Irwin et al. (II). Above 5000 psig, the pressure dependence increases sharply and obeys the expression... 

Of course, the network strands cannot be stretched completely. Stretching ratios of 1.4 for PC [31, 90] and of 1.3 for epoxy polymers [37] have been reported. The chain contour length of the strands is an appropriate measure for a simple estimation of the number of strands that are stretched across the deformation zone. The chain contour length of the strands is assumed to be proportional to... 

M L equals the mass of a typical polymer chain devided by the number of atoms in its backbone. Slightly more than 1000 strands (length lc) are needed to cross the deformation zone of width 8 = 2w for all the polymers listed in Table 6.1. It is one of the essential findings of this report that the size of the deformation zone is scaled according to the length of the molecular strands. 

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