DNA conformation is determined by economics in the hydration of phosphate groups

Abstract

Mixed sequence DNA can exist in two right-handed and one left-handed double helical conformations—A, B and Z^1–3. Under conditions of high water activity the B conformation prevails. If the water activity is reduced on addition of salt or organic solvents, transformation occurs to A-DNA or, in DNAs with alternating purine-pyrimidine sequences, to the left-handed Z-DNA. In crystal structure analyses of oligonucleotides, the free oxygen atoms of adjacent phosphate groups along the polynucleotide chain in B-DNA are found at least 6.6 Å apart and individually hydrated⁴ whereas they are as close as 5.3 Å in A-DNA and 4.4 Å in Z-DNA, and bridged by water molecules^5–7. We suggest that this more economical hydration in A- and Z-DNA compared with B-DNA is the underlying cause of B → A and B → Z transitions.