Quadruple helix

While some homopolynucleotides such as poly A and poly U can sometimes occur as single-stranded helices, others can form quadruple strands incorporating an appropriate H bonding scheme (10.89b). 

In (poly-G) , for example, which forms a gel-like structure, there are four bases linked together as indicated ( G Quartet ). This scheme allows four helices to run parallel to a four-fold fibre axis. Monovalent cations may be able to stabilise such arrangements by lying at the centre (10.89b). Another new variety of four-stranded DNA with intercalated bases was reported in 1995 [54]. Quadruple helices can be formed by telomeres (Chapter 11) and interaction with lipids may be important [55-58]. 

Qther H-bonding schemes between bases are possible and some synthetic homopolynucleotides may even be capable of forming helices with the bases turned outwards. The latter arrangement is suggested by crystal structure data on the di-nucleotide p dT p dT. 

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Not all DNAs are double helices duplex DNA) Some types of viral DNA are single stranded and even a few DNA triple and quadruple helices are known... 

Figure 5.7 AFM images of fibrous aggregates of D-Glu-8 (1) lying directly on silicon surfaces (a) network of fibers (b) high-resolution phase image of quadruple helices. Reprinted with permission from Ref. 42. Copyright 2000 by the American Chemical Society.

Fuhrhop and coworkers [54] discovered higher aggregates - ropes - consisting of quadruple helices of N-octyl-D-gluconamide 104. 

Further developments involve the investigation of the mechanism of formation of double- and triple helicates and of the effect of variations in ligand structure on their features, the determination of their physico-chemical (thermodynamic, kinetic, electrochemical, photochemical) properties, the exploration of the coordination chemistry of the ligand strands. For instance, it may be possible to obtain quadruple helical complexes with ions of high coordination number such as the lanthanides and linear ligands containing bipy or terpy units. Using cubic metal ions would also be of interest. 

Figure 10.39 X-ray molecular structures of (a) a [3X3] molecular grid, [Ag9(10.41)6]9+, (b) a [4X5] -Ag20 grid and (c) a decametallic quadruple helicate formed by 10.42 (Ag ions shown as large...

A rare example of higher stranded helicates is found in the decanuclear quadruple-helicate 16. Lehn and coworkers reported the dynamic equilibrium... 

The observed differences have been attributed to differences in the intermol-ecular N-H - - 0=C hydrogen bonding, which is the main contributor to the formation of extended quadruple helices in the case of the fibrous gluconamide. 

Comparisons of solution and solid-state NMR spectra as well as NMR spectra from solid supramolecular assemblies and single crystals allowed the exact determination of four conformations of iV-octyl-gluconamide in three solid materials, namely monolayer single crystals, bilayer racemate microcrystals, and D-enantiomer bilayer quadruple helices as well as in DMSO solution (Fig. 4.2.6, inserts) (Svenson et al., 1994a). 

Transmission electron microscopy of such a gel shows micellar fibers, which are several micrometers long and about 8 nm wide. Image analysis reveals regular quadruple helices of molecular bilayer rods or ribbons (Fig. 4.5.8). In cryo-electron microscopy the single helices appear somewhat broader (Fuhrhop et al., 1988 Koning et al., 1993). 

Figure 4.5.8 (a) Transmission electron micrograph and (b) computer image of an N-octyl-D-gluconamide quadruple helical fiber. 

M alkali salt is essential without it guanosine produces well-defined crystals, but no gel. X-ray fiber diffraction studies of the gel indicate the formation of quadruple helices. (Fig. 8.6.5) (Saenger, 1984). Similar quadruple helices are also formed by corresponding DNA (Wheelhouse et al, 1998)... 

Fig. 3.5 TEM and model of A -octylgluconamide quadruple helices. The fibers look similar to covalent collagen fibers and have been stored for months in the dry state without decomposition.

It was recently discovered that telomeres can wind themselves into quadruple helices (Chapter 10.4). Such quadruplexes are believed to inhibit the activity of telemerases and may have anti-cancer potential. 

Besides hydrogen bonds and salt bridges, metal-ligand coordination is another well-known approach to constrnct well-defined supramolecular entities such as double, triple, and quadruple helical structures such as helicates, from otherwise flexible organic molecular strands. For a presentation of these metal-based architectures, the reader is referred to Self-Assembly of Coordination Chains and Helices, Self-Processes. 

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