ArticleScientific reports2017
Focus on PNA Flexibility and RNA Binding using Molecular Dynamics and Metadynamics.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Article
- Solid-Phase Synthesis Approaches and U-Rich RNA-Binding Activity of Homotrimer Nucleopeptide Containing Adenine Linked toInternational journal of molecular sciences · 2025Article
- Comparative molecular dynamics calculations of duplexation of chemically modified analogs of DNA used for antisense applications.NAR genomics and bioinformatics · 2024Article
- Solid Phase Synthesis and TAR RNA-Binding Activity of Nucleopeptides Containing Nucleobases Linked to the Side Chains via 1,4-Linked-1,2,3-triazole.Biomedicines · 2024Article
- Antisense and Functional Nucleic Acids in Rational Drug Development.Antibiotics (Basel, Switzerland) · 2024Review
- Parameterization of the miniPEG-Modified γPNA Backbone: Toward Induced γPNA Duplex Dissociation.Journal of chemical theory and computation · 2023Article
- Antispacer peptide nucleic acids for sequence-specific CRISPR-Cas9 modulation.Nucleic acids research · 2022Article
- An overview of structural approaches to study therapeutic RNAs.Frontiers in molecular biosciences · 2022Review
- Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals.Crystals · 2021Article
- Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases.Journal of computer-aided molecular design · 2021Article
- The proto-Nucleic Acid Builder: a software tool for constructing nucleic acid analogs.Nucleic acids research · 2021Article
- Thermodynamic Origin of Differential Excipient-Lysozyme Interactions.Frontiers in molecular biosciences · 2021Article
- Delivery of Peptide Nucleic Acids Using an Argininocalix[4]arene as Vector.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Energy Landscapes of Deoxyxylo- and Xylo-Nucleic Acid Octamers.The journal of physical chemistry. B · 2020Article
- Antibacterial Peptide Nucleic Acids-Facts and Perspectives.Molecules (Basel, Switzerland) · 2020Review
- Structural Insights on Tiny Peptide Nucleic Acid (PNA) Analogues of miRNA-34a: AnFrontiers in chemistry · 2020Article
- Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides.Journal of chemical theory and computation · 2019Article
- Review
- RNA-Templated Concatenation of Triplet Nucleic-Acid Probe.Chembiochem : a European journal of chemical biology · 2018Article
- Synthesis and Improved Cross-Linking Properties of C5-Modified Furan Bearing PNAs.Molecules (Basel, Switzerland) · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Peptide Nucleic Acids (PNAs) can efficiently target DNA or RNA acting as chemical tools for gene regulation. Their backbone modification and functionalization is often used to increase the affinity for a particular sequence improving selectivity. The understanding of the trading forces that lead the single strand PNA to bind the DNA or RNA sequence is preparatory for any further rational design, but a clear and unique description of this process is still not complete. In this paper we report further insights into this subject, by a computational investigation aiming at the characterization of the conformations of a single strand PNA and how these can be correlated to its capability in binding DNA/RNA. Employing Metadynamics we were able to better define conformational pre-organizations of the single strand PNA and γ-modified PNA otherwise unrevealed through classical molecular dynamics. Our simulations driven on backbone modified PNAs lead to the conclusion that this γ-functionalization affects the single strand preorganization and targeting properties to the DNA/RNA, in agreement with circular dichroism (CD) spectra obtained for this class of compounds. MD simulations on PNA:RNA dissociation and association mechanisms allowed to reveal the critical role of central bases and preorganization in the binding process.
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