ArticleNucleic acids research2013
Recognition of RNA duplexes by chemically modified triplex-forming oligonucleotides.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 71 citations in OpenAlex.
- RNA Triple Helices: From Structures and Mechanisms to Therapeutic Targets.International journal of biological sciences · 2026Review
- Nucleobase-Modified Triplex-Forming Peptide Nucleic Acids for Sequence-Specific Recognition of Double-Stranded RNA and DNA.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Modified Bis-pyrimidine Clamps for Triplex Formation and Their Use in SARS-CoV‑2 Detection.ACS omega · 2025Article
- Recognition of Noncanonical RNA Base Pairs Using Triplex-Forming Peptide Nucleic Acids.ACS chemical biology · 2025Article
- Comparison of 2-Aminopyridine and 4-Thiopseudisocytosine PNA Nucleobases for Hoogsteen Recognition of Guanosine in RNA.ACS omega · 2024Article
- Triplex-Forming Peptide Nucleic Acid Controls Dynamic Conformations of RNA Bulges.Journal of the American Chemical Society · 2023Article
- Recent Development in Biomedical Applications of Oligonucleotides with Triplex-Forming Ability.Polymers · 2023Review
- A single natural RNA modification can destabilize a U•A-T-rich RNA•DNA-DNA triple helix.RNA (New York, N.Y.) · 2022Article
- Fluorobenzene Nucleobase Analogues for Triplex-Forming Peptide Nucleic Acids.Chembiochem : a European journal of chemical biology · 2022Article
- Targeting SARS-CoV-2 Variants with Nucleic Acid Therapeutic Nanoparticle Conjugates.Pharmaceuticals (Basel, Switzerland) · 2021Article
- Pyridazine Nucleobase in Triplex-Forming PNA Improves Recognition of Cytosine Interruptions of Polypurine Tracts in RNA.ACS chemical biology · 2021Article
- Unnatural bases for recognition of noncoding nucleic acid interfaces.Biopolymers · 2021Review
- Triplex-Forming Peptide Nucleic Acids with Extended Backbones.Chembiochem : a European journal of chemical biology · 2020Article
- LNA units present in [RSC advances · 2020Article
- Sequence-specific recognition of structured RNA by triplex-forming peptide nucleic acids.Methods in enzymology · 2019Article
- Incorporating uracil and 5-halouracils into short peptide nucleic acids for enhanced recognition of A-U pairs in dsRNAs.Nucleic acids research · 2018Article
- Modified RNA triplexes: Thermodynamics, structure and biological potential.Scientific reports · 2018Article
- Interactions of 2'-O-methyl oligoribonucleotides with the RNA models of the 30S subunit A-site.PloS one · 2018Article
- Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids.Journal of visualized experiments : JoVE · 2017Article
- Sequence-selective recognition of double-stranded RNA and enhanced cellular uptake of cationic nucleobase and backbone-modified peptide nucleic acids.RNA (New York, N.Y.) · 2017Article
Corrections and comments
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Authors and funding
9 authors at 5 institutions in 3 countries.
Funding
Abstract
Triplex is emerging as an important RNA tertiary structure motif, in which consecutive non-canonical base pairs form between a duplex and a third strand. RNA duplex region is also often functionally important site for protein binding. Thus, triplex-forming oligonucleotides (TFOs) may be developed to regulate various biological functions involving RNA, such as viral ribosomal frameshifting and reverse transcription. How chemical modification in TFOs affects RNA triplex stability, however, is not well understood. Here, we incorporated locked nucleic acid, 2-thio U- and 2'-O methyl-modified residues in a series of all pyrimidine RNA TFOs, and we studied the binding to two RNA hairpin structures. The 12-base-triple major-groove pyrimidine-purine-pyrimidine triplex structures form between the duplex regions of RNA/DNA hairpins and the complementary RNA TFOs. Ultraviolet-absorbance-detected thermal melting studies reveal that the locked nucleic acid and 2-thio U modifications in TFOs strongly enhance triplex formation with both parental RNA and DNA duplex regions. In addition, we found that incorporation of 2'-O methyl-modified residues in a TFO destabilizes and stabilizes triplex formation with RNA and DNA duplex regions, respectively. The (de)stabilization of RNA triplex formation may be facilitated through modulation of van der Waals contact, base stacking, hydrogen bonding, backbone pre-organization, geometric compatibility and/or dehydration energy. Better understanding of the molecular determinants of RNA triplex structure stability lays the foundation for designing and discovering novel sequence-specific duplex-binding ligands as diagnostic and therapeutic agents targeting RNA.
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Registered trials
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