ArticleNucleic acids research2017
Orientation-dependent FRET system reveals differences in structures and flexibilities of nicked and gapped DNA duplexes.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs.Biophysical journal · 2023Article
- Direct monitoring of the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization from gaps and overhangs.bioRxiv : the preprint server for biology · 2023Article
- Understanding Self-Assembled Pseudoisocyanine Dye Aggregates in DNA Nanostructures and Their Exciton Relay Transfer Capabilities.The journal of physical chemistry. B · 2022Article
- A molecular toolbox for ADP-ribosyl binding proteins.Cell reports methods · 2021Article
- Intermolecular dark resonance energy transfer (DRET): upgrading fluorogenic DNA sensing.Nucleic acids research · 2021Article
- Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET.RNA (New York, N.Y.) · 2021Article
- A helical amplification system composed of artificial nucleic acids.Chemical science · 2021Article
- Lost in the Crowd: How Does Human 8-Oxoguanine DNA Glycosylase 1 (OGG1) Find 8-Oxoguanine in the Genome?International journal of molecular sciences · 2020Review
- Determinants of cyclization-decyclization kinetics of short DNA with sticky ends.Nucleic acids research · 2020Article
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Authors and funding
4 authors.
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Abstract
Differences in structures and flexibilities of DNA duplexes play important roles on recognition by DNA-binding proteins. We herein describe a novel method for structural analyses of DNA duplexes by using orientation dependence of Förster resonance energy transfer (FRET). We first analyzed canonical B-form duplex and correct structural parameters were obtained. The experimental FRET efficiencies were in excellent agreement with values theoretically calculated by using determined parameters. We then investigated DNA duplexes with nick and gaps, which are key intermediates in DNA repair systems. Effects of gap size on structures and flexibilities were successfully revealed. Since our method is facile and sensitive, it could be widely used to analyze DNA structures containing damages and non-natural molecules.
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