"OL" Force Field Refinements
for RNA and DNA Simulations

OL24 Force Field for DNA

The currently recommended DNA force field, OL24, combines several corrections: β_OL1, ε&zeta_OL1, χ_OL3, α/γ_OL21 correction and Sugar pucker 2024 correction, which are added to the ff99 force field. OL24 is especially recommended for protein-DNA complexes, but also improves upon earlier OL21 and OL15 versions for B-DNA duplexes.

Sugar pucker 2024 correction [18] improves the balance between A and B-DNA forms, which is crucial in protein-DNA complexes, where the A form is often adopted upon protein binding.[17]

χ_OL3 correction replaces the χ_OL4 correction used in previous OL15 and OL21 force fields. Both χ_OL3 and χ_OL4 improve structures containing residues with glycosidic torsion χ in the χ=syn conformation (Z-DNA, Guanine quadruplexes) or where the χ=syn region may be populated (such as in DNA melting simulations). While both χ_OL3 and χ_OL4 correction improve the χ=syn region [6], χ_OL3 provides a better balance between anti and high-anti regions of the χ angle, distinguishing between A and B-DNA [17].

α/γ_OL21 correction introduced in OL21 [16] refines the non-canonical backbone conformations in Z-DNA by removing spurious artifacts generated by previous AMBER force fields. It si also expected to improve non-canonical α/γ conformations in protein-DNA complexes.

εζ_OL1 correction for backbone angles epsilon and zeta is well tested and recommended for DNA double helices, Z-DNA and guanine quadruplexes. It improves description of DNA double helices by increasing helical twist, improving sequence dependence of helical twist, and, most importantly, increasing population of BII backbone substate in BI/BII equilibrium [7]. It also provides better description of Z-DNA and guanine quadruplexes [7].

β_OL1 correction improves description of backbone substates in Z-DNA (ZI/ZII equilibrium) and Guanine quadruplexes (high-beta region in antiparallel G-DNA). It also improves description of BI/BII equilibrium in B-DNA [8].

OL3 Force Field for RNA

We recommend ff99bsc0χ_OL3 combination for RNA. It combines ff99 force field [9] with Barcelona bsc0 correction for α/γ backbone torsions [10] and a χ_OL3(= χ_OL) correction for the glycosidic torsion [4,5] that prevents formation of spurious "ladder like" structures [5,11].

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For further testing and notes on applicability, see refs [12,19,20].

The following table lists refinements used in current and previous OL force fields variants.