ArticleNucleic acids research2013
FRETmatrix: a general methodology for the simulation and analysis of FRET in nucleic acids.
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 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed.
- Evidence for intrinsic DNA dynamics and deformability in damage sensing by the Rad4/XPC nucleotide excision repair complex.Nucleic acids research · 2025Article
- Review of FRET biosensing and its application in biomolecular detection.American journal of translational research · 2023Review
- Impact of DNA sequences on DNA 'opening' by the Rad4/XPC nucleotide excision repair complex.DNA repair · 2021Article
- Unraveling the Compositional and Molecular Features Involved in Lysozyme-Benzothiazole Derivative Interactions.Molecules (Basel, Switzerland) · 2021Article
- Intermolecular dark resonance energy transfer (DRET): upgrading fluorogenic DNA sensing.Nucleic acids research · 2021Article
- Light-induced modulation of DNA recognition by the Rad4/XPC damage sensor protein.RSC chemical biology · 2021Article
- Tethering-facilitated DNA 'opening' and complementary roles of β-hairpin motifs in the Rad4/XPC DNA damage sensor protein.Nucleic acids research · 2020Article
- Getting DNA and RNA out of the dark with 2CNqA: a bright adenine analogue and interbase FRET donor.Nucleic acids research · 2020Article
- Interaction of metallocene dichlorides with apo-human transferrin: A spectroscopic study and cytotoxic activity against human cancer cell lines.International journal of molecular biology (Edmond, Okla.) · 2020Article
- A Porphyrin-DNA Chiroptical Molecular Ruler With Base Pair Resolution.Frontiers in chemistry · 2020Article
- Conformation and Aggregation of Human Serum Albumin in the Presence of Green Tea Polyphenol (EGCg) and/or Palmitic Acid.Biomolecules · 2019Article
- Interbase FRET in RNA: from A to Z.Nucleic acids research · 2019Article
- Electronic Modifications of Fluorescent Cytidine Analogues Control Photophysics and Fluorescent Responses to Base Stacking and Pairing.Chemistry (Weinheim an der Bergstrasse, Germany) · 2019Article
- Enhanced spontaneous DNA twisting/bending fluctuations unveiled by fluorescence lifetime distributions promote mismatch recognition by the Rad4 nucleotide excision repair complex.Nucleic acids research · 2018Article
- Fluorescent nucleobase analogues for base-base FRET in nucleic acids: synthesis, photophysics and applications.Beilstein journal of organic chemistry · 2018Review
- Orientation-dependent FRET system reveals differences in structures and flexibilities of nicked and gapped DNA duplexes.Nucleic acids research · 2017Article
- Fluorescent RNA cytosine analogue - an internal probe for detailed structure and dynamics investigations.Scientific reports · 2017Article
- Studying Z-DNA and B- to Z-DNA transitions using a cytosine analogue FRET-pair.Nucleic acids research · 2016Article
- Twist-open mechanism of DNA damage recognition by the Rad4/XPC nucleotide excision repair complex.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Structure-based model for light-harvesting properties of nucleic acid nanostructures.Nucleic acids research · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Förster resonance energy transfer (FRET) is a technique commonly used to unravel the structure and conformational changes of biomolecules being vital for all living organisms. Typically, FRET is performed using dyes attached externally to nucleic acids through a linker that complicates quantitative interpretation of experiments because of dye diffusion and reorientation. Here, we report a versatile, general methodology for the simulation and analysis of FRET in nucleic acids, and demonstrate its particular power for modelling FRET between probes possessing limited diffusional and rotational freedom, such as our recently developed nucleobase analogue FRET pairs (base-base FRET). These probes are positioned inside the DNA/RNA structures as a replacement for one of the natural bases, thus, providing unique control of their position and orientation and the advantage of reporting from inside sites of interest. In demonstration studies, not requiring molecular dynamics modelling, we obtain previously inaccessible insight into the orientation and nanosecond dynamics of the bases inside double-stranded DNA, and we reconstruct high resolution 3D structures of kinked DNA. The reported methodology is accompanied by a freely available software package, FRETmatrix, for the design and analysis of FRET in nucleic acid containing systems.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.