Anti-parallel strand conformation

Diffraction patterns obtained by Davies and Baldwin [12] indicated that poly d(A-T).poly d(A-T) could assume a conformation with axial periodicity about 24.5 A which they named D-DNA. Similar diffraction patterns were obtained from poly d(I-C).poly d(I-C) by Mitsui et al. [46]. They proposed a novel left-handed double helix with anti-parallel strands and Watson-Crick base-pairs. This eightfold helix contained sugars with an unusual pucker and the bases were placed about 2 A behind the helix axis i.e. on the opposite side from the position of the base-pairs in the A form of DNA. Arnott et al. [47] obtained better quality D-form diffraction patterns from poly d(A-T).poly d(A-T) which they analysed using the linked atom least squares technique. They rejected the left-handed model of Mitsui et al. [46] and claimed... 

It is worthwhile to add the following. The / -sheet structure also has intramolecular hydrogen bonds. For a peptide, if the conformational energy of the / -sheet structure is significantly lower than that of the a-helix, alcohol may induce the peptide to form the / -sheet. In fact, it was experimentally shown for some peptides [46] that the / -hairpin structure linking adjacent strands in an anti-parallel / -sheet is considerably more stabilized by addition of TFE. 

The polysaccharide chains of crystalline B-amylose exist as double stranded helices which have a right-handed six-fold helical conformation of 20.8 A. The helices are anti-parallel and have an open channel in the hexagonal array which is filled with water molecules. Two helices (i.e. twelve D-gluose residues) exist in each unit cell which has the dimensions a = b = 18.50 A and c, the fibre repeat distance, 10.40 A with the angle y being 120°. Similar studies on the crystalline polymorph A-amylose have shown that it also exists as a right-handed double helix in which the chains are parallel. The helices pack in an antiparallel fashion into an orthorhombic unit cell (a = 11.90 A, ft = 17.70 A, and c = 10.52 A). The water content of A-amylose was only about 25% of the value for B-amylose. 

Several G-quadruplex structures have been reported. An intramolecular G-quadruplex from human telomeric DNA in the presence of potassium ions adopts a structure in which three strands run in one direction, the fourth strand in the opposite direction (3 + 1 topology). The structure of this qua-druplex has caused particular interest as it forms diflerent structures depending upon the counterion (Na or K ). Substitution of the guanine bases for 8-bromoguanine gives rise to two dilferent conformations of mixed-parallel/anti-parallel and a chair-t5q)e G-quadruplex. The G-quadruplex from the human Bcl-2 promoter region also forms a mixed parallel/antiparallel structure in solution. " " ... 

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