CRYSTAL-STRUCTURES OF A-DNA DUPLEXES

All crystal structures of A-DNA duplexes exhibit a typical crystal pac king, with the termini of one molecule abutting the shallow grooves of symmetry related neighbors, while all other forms (B, Z, and RNA) ten d to form infinitely stacked helices. The A-DNA arrangement leads to t he formation of shallow groove base multiples that have implications f or the structure of DNA in compacted states. The characteristic packin g leaves big solvent channels, which can be sometimes occupied by B-DN A duplexes. Comparisons of the structures of the same oligomer crystal lizing in two different space groups and of different sequences crysta llizing in the same space group show that the lattice forces dominate the A-DNA conformation in the crystals, complicating the effort to elu cidate the influence of the base sequence on the structures. Neverthel ess, in both alternating and nonalternating fragments some sequence ef fects can still be uncovered. Furthermore, several studies have starte d to define the minimal sequence changes or chemical modifications tha t can interconvert the oligomers between different double-helical conf ormers (A-, B-, and Z-form). Overall, it is seen that the rigid nucleo tide principle applies to the oligomeric fragments. Besides the struct ures of the naked DNAs, their interactions with water, polyamines, and metal ions have attracted considerable attention. There are conserved patterns in the hydration, involving both the grooves and the backbon e, which are different from those of B-DNA or Z-DNA. Overall, A-DNA se ems to be more economically hydrated than B-DNA, particularly around t he sugar-phosphate backbone. Spermine was found to be able to bind exc lusively to either of the grooves or to the phosphate groups of the ba ckbone, or exhibit a mixed binding mode. The located metal cations pre fer binding to guanine bases and phosphate groups. The only mispairs i nvestigated in A-DNA are the wobble pairs, yielding structural insight into their effects on helix stabilities and hydration. G . T wobble p airs have been determined in various sequence contexts, where they dif ferentially affect the conformations and stableness of the duplexes. T he structure of a G .C-m5 base pair, which surprisingly also adopted t he wobble conformation, suggests that a similar geometry may transient ly exist for G . C pairs. These results from the crystalline state wil l be compared to the solution state and discussed in relation to their relevance in biology. (C) 1997 John Wiley & Sons, Inc.