ArticleNucleic acids research2019
Stability of an RNA•DNA-DNA triple helix depends on base triplet composition and length of the RNA third strand.
Article in Nucleic acids research, 2019. 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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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.
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Who cites it
24 citing papers in PubMed, 45 citations in OpenAlex.
- RNA•DNA:DNA triplex formation byRNA (New York, N.Y.) · 2026Article
- Functional Characterization of Long Non-Coding RNAs Associated with Reproductive Fitness in Pura Raza Española Mares.Animals : an open access journal from MDPI · 2026Article
- TripLexicon: prediction and analysis of gene regulatory RNA-DNA interactions.Bioinformatics (Oxford, England) · 2025Article
- Triplexes Color the Chromaverse by Modulating Nucleosome Phasing and Anchoring Chromatin Condensates.International journal of molecular sciences · 2025Review
- Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism.Nucleic acids research · 2025Article
- 3plex Web: An interactive platform for RNA:DNA triplex prediction and analysis.Computational and structural biotechnology journal · 2025Article
- Locked Nucleic Acid Oligonucleotides Facilitate RNA•LNA-RNA Triple-Helix Formation and ReduceInternational journal of molecular sciences · 2024Article
- Anti-Gene IGF-I Vaccines in Cancer Gene Therapy: A Review of a Case of Glioblastoma.Current medicinal chemistry · 2024Review
- EphrinA5 regulates cell motility by modulating Snhg15/DNA triplex-dependent targeting of DNMT1 to the Ncam1 promoter.Epigenetics & chromatin · 2023Article
- Article
- The effects of RNA.DNA-DNA triple helices on nucleosome structures and dynamics.Biophysical journal · 2023Article
- Computational Methods to Study DNA:DNA:RNA Triplex Formation by lncRNAs.Non-coding RNA · 2023Review
- 3plex enables deep computational investigation of triplex forming lncRNAs.Computational and structural biotechnology journal · 2023Article
- A universal model of RNA.DNA:DNA triplex formation accurately predicts genome-wide RNA-DNA interactions.Briefings in bioinformatics · 2022Article
- KCNQ1OT1 promotes genome-wide transposon repression by guiding RNA-DNA triplexes and HP1 binding.Nature cell biology · 2022Article
- A single natural RNA modification can destabilize a U•A-T-rich RNA•DNA-DNA triple helix.RNA (New York, N.Y.) · 2022Article
- Deciphering the RNA universe in sperm in its role as a vertical information carrier.Environmental epigenetics · 2022Review
- Sequence-specific recognition of a coding segment of humanRSC advances · 2021Article
- Three-dimensional genome organization via triplex-forming RNAs.Nature structural & molecular biology · 2021Article
- Bifacial PNAs Destabilize MALAT1 by 3' A-Tail Displacement from the U-Rich Internal Loop.ACS chemical biology · 2021Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Recent studies suggest noncoding RNAs interact with genomic DNA, forming an RNA•DNA-DNA triple helix that regulates gene expression. However, base triplet composition of pyrimidine motif RNA•DNA-DNA triple helices is not well understood beyond the canonical U•A-T and C•G-C base triplets. Using native gel-shift assays, the relative stability of 16 different base triplets at a single position, Z•X-Y (where Z = C, U, A, G and X-Y = A-T, G-C, T-A, C-G), in an RNA•DNA-DNA triple helix was determined. The canonical U•A-T and C•G-C base triplets were the most stable, while three non-canonical base triplets completely disrupted triple-helix formation. We further show that our RNA•DNA-DNA triple helix can tolerate up to two consecutive non-canonical A•G-C base triplets. Additionally, the RNA third strand must be at least 19 nucleotides to form an RNA•DNA-DNA triple helix but increasing the length to 27 nucleotides does not increase stability. The relative stability of 16 different base triplets in DNA•DNA-DNA and RNA•RNA-RNA triple helices was distinctly different from those in RNA•DNA-DNA triple helices, showing that base triplet stability depends on strand composition being DNA and/or RNA. Multiple factors influence the stability of triple helices, emphasizing the importance of experimentally validating formation of computationally predicted triple helices.
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Registered trials
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