Double-strand helices

RNA exists as a single strand, whereas DNA exists as a double-stranded helical molecule. However, given the proper complementary base sequence with opposite polarity, the single strand of RNA—as demonstrated in Figure 35-7—is capable of folding back on itself like a hairpin and thus acquiring double-stranded characteristics. 

The four histone groups that are composed of ho-mogeneous proteins, H2A, H2B, H3, and H4, make up the nucleosome core. Each core consists of two copies of the four histones. The double-stranded DNA is wrapped twice around each core in a left-handed superhelix. A superhelix is the name given to the additional helix made by the double-stranded, helical DNA as it is wrapped around the nucleosome core. A familiar superhelix in everyday life is a twisted spiral telephone cord. The nucleosome core of histones do not recognize specific DNA structures rather, they can bind to any stretch of DNA as long as it is not too close to a neighboring nucleosome. The order of contact of histones to the DNA is as follows ... 

Alternatively, the denatured single strands can be made to reanneal to form double-stranded helices. Complementary strands will hybridize to each other. However, if there are sequence differences between two strands, one from each allele, they remain unpaired in the heteroduplex and, as a result, form open loops that reduce migration in the electrophoretic gel. This is the basis of heteroduplex analysis, in which distinct electrophoretic patterns are seen for different alleles, similar to that seen in SSCP (01). 

DNA codes for its own synthesis at the time of cell division. Thus, DNA acts as the agent of inheritance. As is developed below, DNA is a double-stranded helical molecule—the famous double helix—in which the two strands are complementary. DNA is the repository of information that is expressed in synthesis of the proteins of the cell. Therefore, DNA acts as the determinant of the biochemical personality of the cell. ... 

We encountered the properties of hydrophilic and hydrophobic molecules in our thoughts about driving forces for formation of three-dimensional protein structures. Specifically, proteins fold in a way that puts most of the hydrophobic amino acid side chains into the molecular interior, where they can enjoy each other s company and avoid the dreaded aqueous environment. At the same time, they fold to get the hydrophilic amino acid side chains onto the molecular surface, where they happily interact with that enviromnent. The same ideas are important for the double-stranded helical structure of DNA. The hydrophobic bases are localized within the double hehx, where they interact with each other, and the strongly hydrophilic sugar and phosphate groups are exposed on the exterior of the double helix to the water environment. Now, we need to understand something more about structural features that control these properties. 

The two major types of nucleic acids are DNA and RNA. Nucleic acids are polyphosphate esters containing the phosphate, sugar, and base moieties. Nucleic acids contain one of five purine or pyrimidine bases that are coupled within double-stranded helices. DNA, which is an essential part of the cell s chromosome, contains the information for the synthesis of protein molecules. For double-stranded nucleic acids, as the two strands separate, they act as a template for the construction of a complementary chain. The reproduction or duplication of the DNA chains is called replication. The DNA undergoes semiconservative replication where each of the two new strands contains one of the original strands. 

The question of energy transfer is introduced also by the fact that polynucleotides frequently exist not only in single-strand forms but also entirely or partially as double-strand helices in which pyrimidine residues on one chain are hydrogen bonded to purine residues on the other chain. The reactivity of the pyrimidine residue can be strongly affected by the presence of its purine partner. An example of this will be found further on. 

DNA in cells exists mainly as double-stranded helices. The two strands in each helix wind about each other with the strands oriented in opposite directions (antiparallel strands). The bases of the nucleotides are directed toward the interior of the helix, with the negatively charged phosphodiester backbone of each strand on the outside of the helix. This is the famous B-DNA double helix discovered by Watson and Crick (Figure 3.3). 

Molecular Motions Driven by Transition Metal Redox Couples Ion Translocation and Assembling-Disassembling of Dinuclear Double-Strand Helicates... 

Figure 2.13 The dinucleating bis-bidentate ligand 14 forms with M1 metal ions of electronic configuration d10 (e.g., Cu1, Ag1) dimetallic complexes of formula [M2I(14)2]2 +, in which two molecules of 14 are intertwined to give a double helix. Ligands of the type 14 are named helicands and complexes such as 15 are called helicates. In this particular case, we have a double-strand helicate.

The occurrence of the redox-driven reversible assembling-disassembling process involving copper complexes of 16 has been verified through cyclic voltammetry experiments at a platinum electrode in a MeCN solution. Figure 2.17 shows the CV profile obtained with a solution of the double-strand helicate complex [ Cu 21 (16)212 +. 

Figure 2.16 The redox-driven disassembling of a dicopper(I) double-strand helicate complex to give two mononuclear copper(II) complexes, in which each strand behaves as a quadridentate ligand. On subsequent reduction, the two mononuclear complexes reassemble to give the helicate. The illustrated process fits well the behavior of copper complexes of 16 in a MeCN solution.

However, it has been recently demonstrated by Pallavicini et al. that the lifetime of the dicopper(II) double-strand helicate [ 2 (16)]4 + can be significantly increased by introducing hindering substituents on the framework of 16. In particular, this was shown to occur with the copper complexes of the bis-bidentate ligand 17.21... 

The bidentate ligand 17 forms bis with Cu1 a double-strand helicate complex, whose structure was elucidated through X-ray diffraction studies and is shown in Fig. 2.19. 

Figure 2.19 The molecular structure of the [Cu2,(17>212 1 double-strand helicate complex cation. Cu1 metal centers are represented as spheres. Hydrogen atoms of the two strands have been omitted for clarity. Structure redrawn from data deposited at the Cambridge Crystallographic Data Centre CCDC 641164.

Figure 2.20 Cyclic voltammogram of a MeCN solution of [Cu2 (17)2 2 1 double-strand helicate complex. Supporting electrolyte [Bu4N]C104 scan rate 0.2 V/s internal reference electrode Fc+/Fc. Diagram adapted from Ref. 21.

During the 1980s several laboratories prepared and investigated double-stranded helical complexes, systems containing either pyirolic ligands [75, 76] and derivatives [77-79] (with Zn2+, Ag+, Cu+) or oligomers of 2,2 -bipyridine [80, 81]. Helicates [80-84] may consist of up to five copper centers and these systems are reminiscent of the DNA double helix. 

Formation of Double-Stranded Helical Precursors with Polymethylene Linkers... 

The most easily identifiable characteristics are those related to the shape of the complexes, with their double-stranded helical cores. In this respect, the electrochemical and photochemical properties of Cu2(K-84)2+ are not much different from those of the open-chain helical precursor or its O-methylated version. The strong electronic coupling between the two copper centers is clearly a consequence of the 1,3-phenylene bridges between the two complex subunits and the topological properties of the ligand have virtually no influence. 

Most DNAs form a double stranded helical structure in which nitrogen bases from opposing chains form hydrogen bonds with one another. 

Fig. 34. Formation of enantiomeric double-stranded helicates from two tris(bipyridine) strands and three tetrahedrally coordinated metal ions (Cu(l), Ag(l) dotted circles) [9.68].

Cover Illustration Creativity in art and science. The creative power in chemistry is expressed by the design of molecular species, which self-assemble into organized supramolecular assemblies. The cover illustration shows a synthetic double helix, the double stranded helicate containing a tris bipyridine ligand, held together by Cu(l) ions (see Section 9.3.1). The creative power in art is expressed by the sculpture, la Main de Dieu, by Auguste Rodin. Photograph by Bruno Jarret AD AGP, Paris 1955. 

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