  The DNA duplex may be locally strongly bent in complexes with proteins, for
example, with polymerases or in a nucleosome. At such bends, the DNA helix is
locally in the non-canonical forms A (with a narrow major groove and a large
amount of north sugars) or C (with a narrow minor groove and a large share of
BII phosphates). To model the formation of such complexes by molecular dynamics
methods, the force field is required to reproduce these conformational
transitions for a naked DNA. We analyzed the available experimental data on the
B-C and B-A transitions under the conditions easily implemented in modeling: in
an aqueous NaCl solution. We selected six DNA duplexes which conformations at
different salt concentrations are known reliably enough. At low salt
concentrations, poly(GC) and poly(A) are in the B-form, classical and slightly
shifted to the A-form, respectively. The duplexes ATAT and GGTATACC have a
strong and salt concentration dependent bias toward the A-form. The polymers
poly(AC) and poly(G) take the C- and A-forms, respectively, at high salt
concentrations. The reproduction of the behavior of these oligomers can serve
as a test for the balance of interactions between the base stacking and the
conformational flexibility of the sugar-phosphate backbone in a DNA force
field. We tested the AMBER bsc1 and CHARMM36 force fields and their hybrids,
and we failed to reproduce the experiment. In all the force fields, the salt
concentration dependence is very weak. The known B-philicity of the AMBER force
field proved to result from the B-philicity of its excessively strong base
stacking. In the CHARMM force field, the B-form is a result of a fragile
balance between the A-philic base stacking (especially for G:C pairs) and the
C-philic backbone. Finally, we analyzed some recent simulations of the LacI-,
SOX-4-, and Sac7d-DNA complex formation in the framework of the AMBER force
field.
