Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides

Abstract

MicroRNAs (miRNAs) are attractive drug candidates for many diseases as they can modulate the expression of gene networks. Recently, we discovered that DNAs targeting microRNA-22-3p (miR-22-3p) hold the potential for treating obesity and related metabolic disorders (type 2 diabetes mellitus, hyperlipidemia, and nonalcoholic fatty liver disease (NAFLD)) by turning fat-storing white adipocytes into fat-burning adipocytes. In this work, we explored the effects of chemical modifications, including phosphorothioate (PS), locked nucleic acid (LNA), and peptide nucleic acid (PNA), on the structure and energy of DNA analogs by using molecular dynamics (MD) simulations. To achieve a reliable prediction of the hybridization free energy, the AMOEBA polarizable force field and the free energy perturbation technique were employed. The calculated hybridization free energies are generally compatible with previous experiments. For LNA and PNA, the enhanced duplex stability can be explained by the preorganization mechanism, i.e., the single strands adopt stable helical structures similar to those in the duplex. For PS, the S and R isomers (Sp and Rp) have preferences for C2'-endo and C3'-endo sugar puckering conformations, respectively, and therefore Sp is less stable than Rp in DNA/RNA hybrids. In addition, the solvation penalty of Rp accounts for its destabilization effect. PS-LNA is similar to LNA as the sugar puckering is dominated by the locked sugar ring. This work demonstrated that MD simulations with polarizable force fields are useful for the understanding and design of modified nucleic acids.

Figure 1.

Common chemical modifications of nucleic acids.

Figure 2.

Structure of the (A) PS-6 [Rp,Rp]-DNA/RNA and (B) PS-10 Sp-DNA/Sp-DNA systems. The nucleotides connected to PS are shown in sticks, while others are shown in cartoon representation. The coordinates of PS-10 were taken from the Protein Data Bank (PDB: 5J3I).

Figure 3.

Sugar puckering conformation in the PS-6 single strand simulations. “PO” means unmodified phosphate linkage. “Sp” and “Rp” mean the two isomers of PS modification. “*” denotes the nucleotide with PS modification on 5’-end. The sugar puckering conformation is measured by pseudo-rotation angle P. An angle near 0 deg means the north conformation or C3’-endo, while an angle near 180 deg means the south conformation or C2’-endo.

Figure 4.

Sugar puckering conformation in the PS-10 single strand simulations. The definition is in Figure 3 caption.

Figure 5.

Structures of DNA and PS antagomirs from MD simulations. The structures from left to right are (A) DNA/RNA, (B) DNA, (C) Sp, (D) Rp and (E) mixed Sp/Rp isomer, corresponding to A-0, A-0, A-11, A-12, and A-14, respectively.

Figure 6.

Solvation structures of the 3’-terminal bases of DNA and Rp antagomir (A-12) from MD simulations. In the duplex, the sulfur atoms are not well solvated (B) due to the steric effect of nearby nucleobases compared to DNA (A). In the single strand (C), the steric effect on solvation is less severe since the backbone is more flexible. For example, the sulfur atoms can have close interaction with nucleobases, which compensates for the under-solvation. Therefore, the under-solvation leads to a penalty for duplex formation.

Figure 7.

Sugar puckering conformation in the simulations of antagomirs A-0, A-11, A-12, A-13 and A-14. The five antagomirs are labeled as PO, Sp7, Rp7, Sp4Rp3, Sp3Rp4, respectively. The definition is in Figure 3 caption.

Figure 8.

Structures of dodecamer single-strand PNA (B) and PNA/RNA hybrid (A) from MD simulations.