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.

Targeting microRNAs as a Therapeutic Strategy to Reduce Oxidative Stress in Diabetes

“…Of note, a novel type of oligonucleotide (highly stable and highly resistant to degradation) is represented by Locked Nucleic Acids (LNA) based oligos. LNA are bicyclic nucleic acids that bind the 2 O to the 4 C, locking sugar into a 3 endo conformation [95], thus significantly improving a sequence's stability and specificity. As a matter of fact, the first miRNA-based drug was developed using LNA containing phosphorothioate modifications and specifically targets miR-122 by inhibiting its expression.…”

Thermodynamics of DNA Hybridization from Atomistic Simulations

“…is true, and iii) hybridization entropy can be driven from a correlation between hybridization enthalpy and entropy. In another work, by Ren and coworkers, 62 relative hybridization free energy of DNA analogs have been estimated using an atomistic polarizable force field via alchemical transition method. However, we note that although the calculations in both work can report on melting temperature and thermodynamic quantities of hybridization, they cannot estimate the free energy surface of hybridization.…”

Thermodynamics of DNA Hybridization from Atomistic Simulations

“…Lomzov et al 25 used atomistic models to calculate DNA's melting temperature from the difference in the total energy of hybridized states and that of unhybridized states, assuming that (i) the volume change upon hybridization is negligible, (ii) the difference in total energy between double-and single-stranded states is the same as the hybridization enthalpy (which is, of course, correct when assumption i is true), and (iii) hybridization entropy can be derived from a correlation between hybridization enthalpy and entropy. In another work, by Ren and co-workers, 26 the relative hybridization free energy between RNA and modified nucleic acids was estimated using an atomistic polarizable force field via an alchemical transition method. However, we note that, although the calculations in both of these works can yield melting temperatures and thermodynamic quantities associated with hybridization, they cannot yield the free energy landscape of DNA hybridization, i.e., the free energy as a function of one or more order parameters.…”