Helical stacking

A bisignate spectrum is characteristic of exciton coupling between identical chromophores on one molecule (144), an impossibility with the 1 1 heme-hemopexin complex. Bisignate CD spectra have been observed with bilirnbin-albnmin however, bilirubin, nnlike the planar molecnle heme, can adopt an extended, helical stacked conformation... 

Fig. 7-3331 1 316 are thought to be packed into an imperfect helix as indicated in Fig. 7-34. The structure can also be regarded as an array of longitudinal protofilaments. Naturally formed microtubules usually have precisely 13 protofilaments and a discontinuity in the helical stacking of subunits as shown in Fig. 7-34. When grown in a laboratory the microtubules usually have 14 protofilaments317 and rarely 10 or 16 protofilaments with regular helical packing.318 Microtubules of some moths and also of male germ cells of Drosophila have 16-protofilament microtubules without a discontinuity, an architecture that is specified by the geometry of a specific P-tubulin isoform.319...

Fig. 11 Schematic representation of short DNA self-assembly stages, (a) Pairing of complementary strands yield double helices, (b) Blunt-ended or sticky-ended helices stack and form linear aggregates, while helices with unpaired dangling ends cannot aggregate, (c) Helices capable of linear aggregation display N and COL LC phases, (d) Complementary sequences segregate from mixtures of unpaired sequences through the nucleation of LC domains...

Barbera J, Cavero E, Lehmann M, Serrano J-L, Sierra T, Vazquez JT (2003) Supramolecular helical stacking of metallomesogens derived from enantiopure and racemic polycatenar oxazolines. J Am Chem Soc 125 4527-4533... 

Figure 1. Catalysis and template action of RNA and proteins. Catalytic action of one RNA molecule on another one is shown in the simplest case, the "hammerhead ribozyme." The substrate is a tridecanucleotide forming two double-helical stacks together with the ribozyme (n = 34) in the confolded complex. Tertiary interactions determine the detailed structure of the hammerhead ribozyme complex and are important for the enzymatic reaction cleaving one of the two linkages between the two stacks. Substrate specificity of ribozyme catalysis is caused by secondary structure in the cofolded complex between substrate and catalyst. Autocatalytic replication of oligonucleotide and nucleic acid is based on G = C and A = U complementarity in the hydrogen bonded complexes of nucleotides forming a Watson-Crick type double helix. Gunter von Kiedrowski s experi-...

Figure 6 Examples of compounds that in selective solvents produce biomimetic supramolecular polymers that depending on the conditions exhibit a co-operature intramolecular ordering transition from random to highly ordered helical stacks or a nucleated polymerization transition from oligomeric prenuclei to very long, helical polymeric objects (ten Cate and Sijbesma, 2002 Dankers and Meijer, 2007 van Gorp et al., 2002 Brunsveld, 2001 Jonkheijm, 2005 Hirschberg, 2001).

There are two apparently continuous segments of double helix. These segments are like A-form DNA, as expected for an RNA helix (Section 27.1.1). The base-pairing predicted from the sequence analysis is correct. The helix containing the 5 and 3 ends stacks on top of the helix that ends in the T /C loop to form one arm of the L the remaining two helices stack to form the other (Figure 29.6). 

The DNO backbone imposes a helical stacking on the azobenzenes similar to that observed in DNA, with a twist angle of 36° between adjacent azobenzenes, as shown in Figure 1. Most importantly, the helical stacking imposed by the oligopeptide limits considerably the number of potential stable stationary orientations that the azobenzenes may assume upon irradiation. 

Figure 89. Schematic diagram illustrating the aggregation behavior of m phenylene ethynylene oligomers over a range of concentrations. In dilute solution, the oligomers can exist in a random or helical conformation. At increased concentrations they associate intermolecularly, possibly in an extended lamellar-type fashion or as tubular and hexagonal helical stacks.

The folding of oligo(/n-phenyleneethynylene)s (Figure 4) into helical stacks driven by solvophobic effects was reported by Moore and co-workers.46 These... 

However, one of the most intriguing examples in this field, which also demonstrates the power of diffusion NMR to characterize supramolecular systems obtained by self aggregation, is the assignment of the different species that prevail in solution following the reduction of 2,5,8,ll-tetra-tert-butylcycloocta[l,2,3,4-def-,5,6,7,8]bis-biphenylene (65) to its respective tetraanions [59]. In this sample, different species were observed and only diffusion NMR provided a proof, in conjunction with 2-D NOESY, that the different molecular species are indeed different helically-stacked anionic aggregates of 65. When NMR diffusion measurements were performed on the obtained solution, four different diffusion coefficients were found for the mixture. These coefficients that were assigned to the monomer, dimer, trimer and tetramer of 65 (Fig. 6.24). Based on Eq. (6.16) ... 

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