Parallel interaction between nucleic-acid bases

Varying the side groups X in 27b affects both the stability and selectivity of the complexes (lateral discrimination), and allows the receptor-substrate interactions in biological systems to be modelled, for instance, the interaction between nicotinamide and tryptophan [2.109b]. One may attach to 27b amino acid residues (leading to parallel peptides [2.109] as in 27c), nucleic acid bases or nucleosides, saccharides, etc. The structural features of 27 and its remarkable binding properties make it an attractive unit for the construction of macropolycyclic multisite receptors, molecular catalysts, and carriers for membrane transport. Such extensions require sepa-... 

The purine and pyrimidine bases are hydrophobic and relatively insoluble in water at the near-neutral pH of the cell. At acidic or alkaline pH the bases become charged and their solubility in water increases. Hydrophobic stacking interactions in which two or more bases are positioned with the planes of their rings parallel (like a stack of coins) are one of two important modes of interaction between bases in nucleic acids. The stacking also involves a combination of van der Waals and dipole-dipole interactions between the bases. Base stacking helps to minimize contact of the bases with water, and base-stacking interactions are very important in stabilizing the three-dimensional structure of nucleic acids, as described later. 

Base triads do, of course, occur in nucleic acid triplexes. However, tetraplex structures may also contain triads and in RNA structures triads often play a crucial role. Triplexes are formed by the interaction of a third strand in the major groove of a double helix. The duplex has to be composed of a homopurine-homopyrimidine sequence (piuine - R, pyrimidine - Y). The third strand can bind in a parallel or antiparallel orientation to one of the duplex strands. In parallel orientation, a homopyrimidine third strand binds to the homopurine strand of the duplex (YRY). This leads to the two canonical triads TAT and C+GC. Protonation of C (C+) at N3 is required for the formation of two H-bonds between C and G. Therefore, parallel triplexes are pH dependent. These structures have two canonical base triads TAT and C+GC. For an antiparallel orientation of the third strand relative to the binding duplex strand, a homopruine sequence is required that binds to the homopurine strand of the duplex (RRY). This results in the canonical triads GGC, AAT and TAT, where however the TAT triad is different to the corresponding triad in parallel triplexes. In addition to these standard triads, triplexes can also accommodate non-canonical base triads. Fig. 3 shows the two canonical triads C+GC and TAT in an intra-molecular triplex consisting of a DNA duplex and... 

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