Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes

Abstract

Mixed double helices formed by RNA and DNA strands, commonly referred to as hybrid duplexes or hybrids, are essential in biological processes like transcription and reverse transcription. They are also important for their applications in CRISPR gene editing and nanotechnology. Yet, despite their significance, the hybrid duplexes have been seldom modeled by atomistic molecular dynamics methodology, and there is no benchmark study systematically assessing the force-field performance. Here, we present an extensive benchmark study of polypurine tract (PPT) and Dickerson-Drew dodecamer hybrid duplexes using contemporary and commonly utilized pairwise additive and polarizable nucleic acid force fields. Our findings indicate that none of the available force-field choices accurately reproduces all the characteristic structural details of the hybrid duplexes. The AMBER force fields are unable to populate the C3'-endo (north) pucker of the DNA strand and underestimate inclination. The CHARMM force field accurately describes the C3'-endo pucker and inclination but shows base pair instability. The polarizable force fields struggle with accurately reproducing the helical parameters. Some force-field combinations even demonstrate a discernible conflict between the RNA and DNA parameters. In this work, we offer a candid assessment of the force-field performance for mixed DNA/RNA duplexes. We provide guidance on selecting utilizable force-field combinations and also highlight potential pitfalls and best practices for obtaining optimal performance.

Figure 1

Dickerson–Drew dodecamer (DD) and polypurine tract hybrid duplex (PPT) structures and sequences. The DNA and RNA sequence letters are colored blue and red, respectively.

Figure 2

Histograms of the DNA sugar puckers, inclination and x-displacement in MD simulations of the PPT structure. Example of nucleotides possessing C3′-endo and C2′-endo puckers is shown at top left corner. The individual ff combinations are color-coded in the graphs according to the legend in the bottom right corner. Black dots on the x-axes indicate average experimental values.

Figure 3

Histograms of the dihedral angles in MD simulations of the DD structures. Distribution of the ζ (zeta) dihedral angle in pure DNA and RNA and the hybrid DD structures, using the OL21/OL3 (top) and CHARMM36 ffs (bottom). The visualized data sets are representative of the development observed also for the other dihedrals. The top graph is representative of a performance seen also with the other AMBER ffs.

Figure 4

Histograms of the sugar puckers and dihedral angles in MD simulations of the DD structures. (a) α and γ dihedrals observed for the RNA strand in simulations of the DD_RNA and DD_hybrid structures using the ROC-RNA ff (combined with OL21 ff for the hybrid). (b) ζ dihedral angle in DD_DNA and DD_hybrid structures, using the OL21/OL3 and DES-Amber ffs. Correlated behavior was observed for the ε dihedral as it pertains to the BI/BII B-form substates. (c) Sugar puckers observed for the DD structures using the DES-Amber ff.

Figure 5

Anisotropic base pair buckle observed in the hybrid DNA/RNA experimental structures and simulations. (a) 2D scheme of the anisotropic buckle of the hybrids. Note that the extent of the V-shaped deformation of the base pairs is greatly exaggerated for illustrative purposes. (b) Distribution of the buckle in MD simulations of the PPT structure. Black dot on the x-axis indicates the average experimental value.