Other Molecular Duplex Strands

Zimmerman et al. reported a type of ureido-naphthyridine-based duplexes (Fig. 4.22) [47, 48]. Because of the intramolecular hydrogen bonding-mediated molecular folding, there existed a complicated extending-folding equilibrium for 

5 X 10 M. Eight hydrogen bonds-mediated homoduplex 532 could also be constructed with this building block [49]. The dimerization constant was larger than 4.5 X 10 even in a 10 % DMSO-tig-CDCls solution. But it dropped substantially (K = 40 M ) when a 20 % DMSO- fg-CDCls solution was applied. 

An ureido-dipeptide based duplex was reported by Hirao et al. (Fig.4.23) [50]. X-ray single crystal analysis showed that two molecules formed a right-handed helical stmcmre. The chirality center of the amino acid side chains induced this supramolecular chirality. The dimerization constant was determined to be 2.9 X 10 M by H NMR dilution experiments. Interestingly, variable H NMR experiments revealed a unique shuttle movement as depicted in Fig. 4.23. 

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From a chemical perspective, the double-helix produced by two intertwining strands of oligomeric DNA is a fascinating and unique molecular structure. (See Fig. 1 for a structural model of a 12-base pair duplex of B-form DNA.) In it nucleic acid bases are stacked in pairs one on top of the other with a slight twist reminiscent of a spiral staircase [16]. The unique stacking and overlapping of the n- and Tr-electrons of DNA bases may provide a preferred path for electron transfer. Similarly, the exceptional closeness of the stacked bases may have important consequences for charge motion in DNA duplexes. Additionally, the... 

Electron injection from MLCT-excited Ru-polypyridine complexes are used to investigate electron transfer along DNA strands, that is to decide whether DNA can behave as a molecular wire [358-360]. In these studies, derivatives of [Ru(phen)2(dppz)] + act as excited-state electron donors and [Rh (phi)2(bpy)] + as a ground-state electron acceptor. Both complexes are anchored at different DNA sites and the rate of Ru —> Rh photoinduced electron transfer is measured. In another study [361], a [Ru (bpy)2(im)(NH2-)] + unit attached to a terminal ribose of a DNA duplex acted as an excited-state oxidant toward a [Ru (NH3)4(py)(NH2-)] " unit attached at the other end. 

Fig. 3 Sticky-ended cohesion, (a) Cohesion between two molecular overhangs. Two duplex molecules are shown (top). Each has a single-stranded molecular overhang that is complementary to the overhang on the other molecule. When mixed, the two molecules can cohere in solution (center). The four strands can be ligated to form two strands from the original four (bottom). (b) Structural features of stick-ended cohesion. A crystal structure [4] is shown that contains DNA decamers whose cohesion in the direction of the helix axis (horizontal) is directed by dinucleotide sticky ends. This interaction is seen readily In the center box, where the continuity of the chains is interrupted by gaps caused by the absence of phosphate linkages. The two outer boxes contain B-form duplex DNA. It is a half-turn away from the DNA in the center box, so it is upside-down from it, but otherwise the structure is the same. Thus, sticky ends cohere to form B-DNA, and one can use this information in a predictive fashion to estimate the local structures of DNA constructs held together by sticky ends...

Although individually rather weak when compared to ionic or covalent bonds, the cumulative effect of numerous hydrogen bonds results in a rather strong and stable molecular interaction. Finally, the two strands of DNA have to be complementary in that every position an A (or G) appears, the other strand must have a T (or C) present. The base-paired, duplex assumes an a-helical structure. 

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