DNA B to D transition can be explained in terms of hydration economy of the minor groove atoms.
Adjacent phosphate oxygen atoms in A and Z-DNA are located much closer together than in the B form and can be hydrated more economically due to the formation of water bridges between them, whereas in the B form phosphates are hydrated individually. This principle of hydration economy of phosphate groups discovered by Saenger and colleagues could not be applied to the B-D transition, which, like the B-A and B-Z transitions, occurs in a situation of water deficiency, because the distances between adjacent phosphates of individual polynucleotide chains in the D form are not much different from B-DNA. It follows from our calculations of B and D-DNA accessibility to solvent performed by the method of Lee & Richards, and from a simulation of solvent structure near DNA, that there is an economy of hydration only for the minor groove atoms. This feature and some experimental data can explain why only a limited range of sequences consisting of A.T or I.C pairs undergo the transition to the D form. The conformational transition in DNAs with such sequences to a poly[d(A]).poly[d(T])-like conformation (Bh-DNA), which is accompanied by a narrowing of the minor groove, can be explained in the same way. Calculations suggest that in the D-form minor groove of different A-T or I-C DNAs there is a double-layer hydration spine similar to that observed by Drew & Dickerson in the A-T tract of the d(C-G-C-G-A-A-T-T-C-G-C-G) dodecamer. The B-D and B-Bh transitions in A + T-rich DNAs can have biological implications, e.g. they can facilitate DNA bending upon the interaction with proteins.
Lipanov
A A
AA
Institute of Molecular Genetics, U.S.S.R. Academy of Sciences, Moscow.
Beglov
D B
DB
Chuprina
V P
VP
D004247:DNA / Q000648:ultrastructure*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011067:Poly dA-dT; D011089:Polydeoxyribonucleotides; D014867:Water
D011089:Polydeoxyribonucleotides; D014867:Water; D011067:Poly dA-dT; C019530:poly(dC-dG); D004247:DNA