Interpretation of 3JP,H3' NMR scalar spin-spin coupling constants in DNA becomes more reliable by including distinct structural states such as BI and BII, using the weighted-static or, better still, the recently implemented adiabatic-MD (Ad-MD) method. The calculation method employs an adiabatic ("Ad") dependence of 3JP,H3' coupling on NMR-assigned torsion angle, ε, weighted by P(ε) probability distribution calculated by molecular dynamics (MD). Ad-MD calculations enable cross-validation of the bsc1, OL15, and OL21 force fields and various parametrizations of the Karplus equation describing the dependence of 3JP,H3' coupling on ε torsion (KE). The mean absolute deviation of Ad-MD 3JP,H3' couplings from the experimental values in Dickerson-Drew DNA is comparable to the scatter of 3JP,H3' couplings among four separate NMR experiments. A commonly accepted assumption of homogeneity of one kind of structure-dynamic state within DNA (BI or BII) is questionable because the principal characteristics of relevant P(ε) probabilities (shapes and positioning) vary with DNA sequence. The theory outlined in the present work sets limits to future reparameterization of MD force fields, as relevant to NMR data.

Department of Electrotechnology Electrical Engineering Czech Technical University Technická 2 166 27 Praha 6 Czech Republic

Department of Physical Chemistry Faculty of Science Palacký University Olomouc 17 listopadu 12 77146 Olomouc Czech Republic

Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 166 10 Praha 6 Czech Republic

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Deciphering Dickerson-Drew DNA Equilibrium beyond the BI/BII DNA Dichotomy by Interpretation of 31P NMR Parameters