Double-helical conformation

In recent years there has been a great interest in the elucidation of non-conventional double helical conformations and their biological roles [43,44]. 

In terms of physiological conditions, DNA exists almost totally in the double-helical conformation. Certain oligonucleotides also exhibit the ability to form triple-helixes with the DNA double strands. The stability of DNA secondary structures strongly depends on the environmental conditions, such as ionic strength, pH, temperature and solvents. Temperature is the most widely used environmental variable for the quantitative characterization of the helix-coil transitions. A commonly accepted characteristic of the thermal stability of DNA secondary structures is melting temperature, Tm. The binding of cationic species, such as multivalent... 

While these "energies" are necessarily approximate, they afford a basis for clear discrimination between sterically allowed and sterically forbidden structures. The "energy" approach also offers a means to extrapolate experimental studies (nmr, X-ray, etc.) on the conformation of small model compounds to the polynucleotide level and to test the relevance of the data in a helical complex. In addition, the method provides a starting point for a refined potential energy analysis of double helical conformation and stability. 

The isolated 5 helices were free of any objectionable contacts. Since there is no special relationship between two chains in the 5-fold double helix, the relative orientation parameters, Ay and AW, were obtained from the contacts map for each conformation. For both 5, and 5, double helices, conformations without fatal short contacts could be constructed. These double helices were subjected to a packing analysis in the... 

An indole-terminated tris(macrocycle) designed to be a channel-former and which is an effective carrier in bulk membranes but fails to function in a lipid bilayer owing to hydrogen-bond formation has been described <1996CC2147>. Tryptophan- and tryptamine-derived tetraazacyclooctadecane macrocycles have been synthesized <1996J(P1)2427>. Transannular hydrogen bonding stabilizes a left-handed double-helical conformation of the... 

Owing to base pairing and the double-helical conformation, double-stranded DNA (dsDNA) is an exceptionally stable molecule. Retention of the base pairs in the inner portion of the helix prevents disruption by water molecules. The helical conformation places each monomer in an identical orientation within the molecule and forms the same secondary bonds as every other monomer. This secondary bonding contributes to the overall stabifity. Because the base... 

FABMS) with a double-helical conformation was formed (Figure 4). Each copper atom possesses a distorted tetrahedral geometry, and the complex was shown to persist in solution by H NMR and cyclic voltammetry. In contrast, when hgand (11) was treated with cobalt(II), a 1 1 complex was formed. The crystal structure reveals that the aggregate is not a double helix, and the cobalt possesses a distorted octahedral geometry [23],... 

Figure 4.94 Half a pitch (six residues) of a single gellan chain helix in its parallel double-helical conformation.

B-form DNA is the most common form of DNA in solution and is much the most important biologically speaking. The double helical conformation of B-form DNA also conforms most closely with the original model structure for DNA devised by Watson and Crick. The main architectural features of the B-form DNA double helix are illustrated using ribbon display, ring display and ladder display structures (Figure 1.69 and 1.70). Backbones are shown as... 

In general we may distinguish three different types of conformational changes that can occur in DNA (1) the melting transition from an ordered double-helical (usually B form) state to a disordered state with separated strands (this was discussed in the previous section) (2) a change from one double-helical conformational genus to another such as B to A or B to Z and (3) environmentally induced changes in the conformation of a... 

Fig. 3. Top and side views of three DNA double-helical conformations. In the side views, the base pairs are shown in black and ribbons are traced along the DNA backbones to illustrate the helicity.

Type in RS consists of 60—70% of double he-hcal a(l—4)polyglucan aggregates and only 25-30% of crystaUine stractures. It is assumed that the high content of the double helical conformation, which is similar to that of amylose type B, limits the activity of a-amylases. 

The intercalation process requires (1) planarity and a certain size of the ligand, (2) a base-paired helical secondary structure of the nucleic acid. Proflavine and ethidium bromide have been shown to bind strongly to RNA, and to synthetic polymers in an amount proportional to their degree of double-helical conformation. Single-stranded or denaturated nucleic acids have very flexible structures, which allow the stacking of an amount of dye greater than what is allowed by more rigid double-stranded molecules. 

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