ArticleNucleic acids research2014
Triple helical DNA in a duplex context and base pair opening.
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 14 papers.
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Who cites it
14 citing papers in PubMed.
- Thermodynamic and kinetic considerations in DNA triplex formation revealed by ITC.European biophysics journal : EBJ · 2026Article
- Thermodynamics and Kinetics of the Deintercalation of a Novel Anthracycline from Double-Stranded Oligonucleotide DNA.The journal of physical chemistry. B · 2025Article
- A comprehensive study of Z-DNA density and its evolutionary implications in birds.BMC genomics · 2024Article
- Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNA.Scientific reports · 2023Article
- The effects of RNA.DNA-DNA triple helices on nucleosome structures and dynamics.Biophysical journal · 2023Article
- Three's a crowd - stabilisation, structure, and applications of DNA triplexes.Chemical science · 2022Review
- Recognition of ATT Triplex and DNA:RNA Hybrid Structures by Benzothiazole Ligands.Biomolecules · 2022Article
- Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy.International journal of molecular sciences · 2020Review
- The ability of locked nucleic acid oligonucleotides to pre-structure the double helix: A molecular simulation and binding study.PloS one · 2019Article
- Purine- and pyrimidine-triple-helix-forming oligonucleotides recognize qualitatively different target sites at the ribosomal DNA locus.RNA (New York, N.Y.) · 2018Article
- LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures.Scientific reports · 2017Article
- Role of Pseudoisocytidine Tautomerization in Triplex-Forming Oligonucleotides: In Silico and in Vitro Studies.ACS omega · 2017Article
- Sequence dependency of canonical base pair opening in the DNA double helix.PLoS computational biology · 2017Article
- Next-generation bis-locked nucleic acids with stacking linker and 2'-glycylamino-LNA show enhanced DNA invasion into supercoiled duplexes.Nucleic acids research · 2016Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is fundamental to explore in atomic detail the behavior of DNA triple helices as a means to understand the role they might play in vivo and to better engineer their use in genetic technologies, such as antigene therapy. To this aim we have performed atomistic simulations of a purine-rich antiparallel triple helix stretch of 10 base triplets flanked by canonical Watson-Crick double helices. At the same time we have explored the thermodynamic behavior of a flipping Watson-Crick base pair in the context of the triple and double helix. The third strand can be accommodated in a B-like duplex conformation. Upon binding, the double helix changes shape, and becomes more rigid. The triple-helical region increases its major groove width mainly by oversliding in the negative direction. The resulting conformations are somewhere between the A and B conformations with base pairs remaining almost perpendicular to the helical axis. The neighboring duplex regions maintain a B DNA conformation. Base pair opening in the duplex regions is more probable than in the triplex and binding of the Hoogsteen strand does not influence base pair breathing in the neighboring duplex region.
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