ArticleNucleic acids research2014
Incorporation of thio-pseudoisocytosine into triplex-forming peptide nucleic acids for enhanced recognition of RNA duplexes.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Synthesis and RNA-Binding Properties of Heteroaryl Amino Pyridine Nucleobases for Triple-Helix-Forming Peptide Nucleic Acids.The Journal of organic chemistry · 2026Article
- 5-Triazolyl uracil improves nucleobase stacking, pyrimidine recognition, biological activity, and specificity of RNA-binding triplex-forming peptide nucleic acids.Nucleic acids research · 2026Article
- Design of an Orally Bioavailable Small Molecule That Modulates the Microtubule-Associated Protein Tau's Pre-mRNA Splicing.ACS chemical biology · 2025Article
- Design of triplex-forming peptide nucleic acid-based fluorescent probes for forced intercalation sensing of double-stranded RNA structures.Analytical sciences : the international journal of the Japan Society for Analytical Chemistry · 2025Review
- Recognition of Noncanonical RNA Base Pairs Using Triplex-Forming Peptide Nucleic Acids.ACS chemical biology · 2025Article
- Isoorotamide-based peptide nucleic acid nucleobases with extended linkers aimed at distal base recognition of adenosine in double helical RNA.Beilstein journal of organic chemistry · 2025Article
- Triplex-forming peptide nucleic acids as emerging ligands to modulate structure and function of complex RNAs.Chemical communications (Cambridge, England) · 2024Review
- Comparison of 2-Aminopyridine and 4-Thiopseudisocytosine PNA Nucleobases for Hoogsteen Recognition of Guanosine in RNA.ACS omega · 2024Article
- Recent Advancements in Development and Therapeutic Applications of Genome-Targeting Triplex-Forming Oligonucleotides and Peptide Nucleic Acids.Pharmaceutics · 2023Review
- 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
- Multicomponent Synthesis of Diaminopurine and Guanine PNA's Analogues Active against Influenza A Virus from Prebiotic Compounds.ACS omega · 2022Article
- Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications.RSC chemical biology · 2022Review
- Fluorobenzene Nucleobase Analogues for Triplex-Forming Peptide Nucleic Acids.Chembiochem : a European journal of chemical biology · 2022Article
- Targeting RNA editing of antizyme inhibitor 1: A potential oligonucleotide-based antisense therapy for cancer.Molecular therapy : the journal of the American Society of Gene Therapy · 2021Article
- The 2-Aminopyridine Nucleobase Improves Triple-Helical Recognition of RNA and DNA When Used Instead of Pseudoisocytosine in Peptide Nucleic Acids.Biochemistry · 2021Article
- Pyridazine Nucleobase in Triplex-Forming PNA Improves Recognition of Cytosine Interruptions of Polypurine Tracts in RNA.ACS chemical biology · 2021Article
- Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases.Journal of computer-aided molecular design · 2021Article
- Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications.Beilstein journal of organic chemistry · 2021Review
- Unnatural bases for recognition of noncoding nucleic acid interfaces.Biopolymers · 2021Review
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Peptide nucleic acids (PNAs) have been developed for applications in biotechnology and therapeutics. There is great potential in the development of chemically modified PNAs or other triplex-forming ligands that selectively bind to RNA duplexes, but not single-stranded regions, at near-physiological conditions. Here, we report on a convenient synthesis route to a modified PNA monomer, thio-pseudoisocytosine (L), and binding studies of PNAs incorporating the monomer L. Thermal melting and gel electrophoresis studies reveal that L-incorporated 8-mer PNAs have superior affinity and specificity in recognizing the duplex region of a model RNA hairpin to form a pyrimidine motif major-groove RNA2-PNA triplex, without appreciable binding to single-stranded regions to form an RNA-PNA duplex or, via strand invasion, forming an RNA-PNA2 triplex at near-physiological buffer condition. In addition, an L-incorporated 8-mer PNA shows essentially no binding to single-stranded or double-stranded DNA. Furthermore, an L-modified 6-mer PNA, but not pseudoisocytosine (J) modified or unmodified PNA, binds to the HIV-1 programmed -1 ribosomal frameshift stimulatory RNA hairpin at near-physiological buffer conditions. The stabilization of an RNA2-PNA triplex by L modification is facilitated by enhanced van der Waals contacts, base stacking, hydrogen bonding and reduced dehydration energy. The destabilization of RNA-PNA and DNA-PNA duplexes by L modification is due to the steric clash and loss of two hydrogen bonds in a Watson-Crick-like G-L pair. An RNA2-PNA triplex is significantly more stable than a DNA2-PNA triplex, probably because the RNA duplex major groove provides geometry compatibility and favorable backbone-backbone interactions with PNA. Thus, L-modified triplex-forming PNAs may be utilized for sequence-specifically targeting duplex regions in RNAs for biological and therapeutic applications.
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