Tetrads, structural calculations

An additional series of calculations has been carried out for the complexes of the tetrads with the metal ions. It has been concluded that the stability of such tetrads is controlled by the presence of metal ions. In this presentation, we demonstrate that such cations dominate the H-bonding patterns that govern the structures of the DNA bases polyads. 

For the KHF2 structure, which is a CsCl structure compressed along a tetrad axis, Madelung constants have been calculated for a number of different values of the axial ratio c/a in the pseudo-unit cell 60, 126, 127). However the author 128) has developed a general expression,... 

Quantum-chemical ab initio studies have been performed on triads" " on tetrads " and on a pentad structure. Except for one recent paper we are not aware of further semiempirical calculations on base polyads. Even though semiempirical approaches 5deld occasionally sensible results we know fi om studies on nucleic acid base pairs that a consistent theoretical picture of their structure and energetics did only emerge when ab initio calculations with a consistent treatmait of electron correlation have become feasible. Hence, it is hi y recommraided to adopt non-empirical approaches for studies on base polyads. A detailed comparison of non-empirical, semiempirical and empirical approaches for the description of DNA base interactions has been performed by Hobza et al. ... 

All the tetrads studied thus far have a cyclic topology corresponding to the notation IV.2. Therefore, symmetry constraints have been applied in the calculations which substantially reduce the computational effort. For tetrads consisting of one base type only likely symmetries of the tetrads without metal ions are C41, for planar systems and either C4 or 4 in non-planar structures. Note, however, that applying symmetry constraints may prevent the detection of relevant structures. A ftirther problem of the tetrad studies is that not in all cases the minima obtained have been checked by fiiequency calculations. 

Because of the size of the structures the DFT method seems to be the method of choice. The results are often compared to results obtained fi-om conventional HF calculations without taking into account electron correlation. For the G-tetrad sandwich structure only HF results are available. The preferred DFT approach is the B3LYP me od and a widely used basis set is... 

The intra as well as inter-basepair structural parameters were calculated for the middle three tetrads taking all four strands pairwise and using the NUPARM software [63], For both simulations, local dinucleotide step, intra base-pair and global helical parameters were calculated for the GG base pairs in the middle three tetrads and averaged between 100 to 1100 ps. Only the global helical and... 

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