ArticleJournal of chemical theory and computation2019
Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed, 32 citations in OpenAlex.
- Kinetics, thermodynamics, and mechanisms of PMO interactions from computational molecular modeling.Molecular therapy. Nucleic acids · 2026Article
- Enzyme-Responsive Cyclic Gapmer Antisense Oligonucleotides via ThymidineBioconjugate chemistry · 2026Article
- Ionic Strength Impact on miR-141 Detection by bioFET.ACS omega · 2026Article
- RNA-Micelles as Self-Assembling Structures for Efficient Co-Delivery of Synergistic siRNA and Nucleoside Analogues to Treat CRC Lung Metastasis.Advanced functional materials · 2026Article
- Backbone-mediated weakening of pairwise interactions enables percolation in peptide-based mimics of protein condensates.Communications chemistry · 2025Article
- Thermodynamic Parameter Estimation for Modified Oligonucleotides Using Molecular Dynamics Simulations.The journal of physical chemistry. B · 2025Article
- Structural dynamics of therapeutic nucleic acids with phosphorothioate backbone modifications.NAR genomics and bioinformatics · 2024Article
- Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning.Journal of chemical theory and computation · 2024Article
- Detection of miR-155 Using Peptide Nucleic Acid at Physiological-like Conditions by Surface Plasmon Resonance and Bio-Field Effect Transistor.Biosensors · 2024Article
- MicroRNAs Targeting Critical Molecular Pathways in Diabetic Cardiomyopathy Emerging Valuable for Therapy.Cardiovascular & hematological agents in medicinal chemistry · 2024Review
- Nanocarrier-Mediated Delivery of MicroRNAs for Fibrotic Diseases.Molecular diagnosis & therapy · 2024Review
- Hybridization Kinetics of miR-155 on Gold Surfaces as Investigated by Surface Plasmon Resonance and Atomic Force Spectroscopy.ACS omega · 2023Article
- Strategy for Pre-Clinical Development of Active Targeting MicroRNA Oligonucleotide Therapeutics for Unmet Medical Needs.International journal of molecular sciences · 2023Article
- Molecular Dynamics Simulations of Protein RNA Complexes by Using an Advanced Electrostatic Model.The journal of physical chemistry. B · 2022Article
- Computational study on the binding of Mango-II RNA aptamer and fluorogen using the polarizable force field AMOEBA.Frontiers in molecular biosciences · 2022Article
- Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity.Chemical reviews · 2021Review
- Targeting microRNAs as a Therapeutic Strategy to Reduce Oxidative Stress in Diabetes.International journal of molecular sciences · 2019Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.