ArticleScientific reports2016
Förster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- BLeaching In-cell Single-molecule burstS (BLISS) reveals a small dynamic fraction of HP1α clusters in undifferentiated embryonic stem cells.bioRxiv : the preprint server for biology · 2026Article
- Single-Molecule Forster Resonance Energy Transfer With a Minimalistic 3D-Printed Setup and Dyes in the Blue-Green Spectral Region.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Unraveling allosteric signaling of G protein-coupled receptors (GPCRs) by single-molecule fluorescence.Biophysical reviews · 2026Review
- Labelizer: systematic selection of protein residues for covalent fluorophore labeling.Nature communications · 2025Article
- Pretrained Deep Neural Network Kin-SiM for Single-Molecule FRET Trace Idealization.The journal of physical chemistry. B · 2025Article
- Single-molecule detection and super-resolution imaging with a portable and adaptable 3D-printed microscopy platform (Brick-MIC).Science advances · 2024Article
- Deep-LASI, single-molecule data analysis software.Biophysical journal · 2024Article
- Single-molecule fluorescence multiplexing by multi-parameter spectroscopic detection of nanostructured FRET labels.Nature nanotechnology · 2024Article
- Single-molecule detection and super-resolution imaging with a portable and adaptable 3D-printed microscopy platform (Brick-MIC).bioRxiv : the preprint server for biology · 2024Article
- Sequence-specific dynamic DNA bending explains mitochondrial TFAM's dual role in DNA packaging and transcription initiation.Nature communications · 2024Article
- Single-molecule reconstruction of eukaryotic factor-dependent transcription termination.Nature communications · 2024Article
- Deep-LASI: deep-learning assisted, single-molecule imaging analysis of multi-color DNA origami structures.Nature communications · 2023Article
- A new twist on PIFE: photoisomerisation-related fluorescence enhancement.Methods and applications in fluorescence · 2023Review
- Interaction of a Dimeric Single-Stranded DNA-Binding Protein (G5P) with DNA Hairpins. A Molecular Beacon Study.The journal of physical chemistry. B · 2023Article
- smFRET Detection of Cis and Trans DNA Interactions by the BfiI Restriction Endonuclease.The journal of physical chemistry. B · 2023Article
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- Nano-biosensor for SARS-CoV-2/COVID-19 detection: methods, mechanism and interface design.RSC advances · 2023Review
- Small RNAs and Hfq capture unfolded RNA target sites during transcription.Molecular cell · 2023Article
- Cooperative action of separate interaction domains promotes high-affinity DNA binding ofProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Nucleotide detection mechanism and comparison based on low-dimensional materials: A review.Frontiers in bioengineering and biotechnology · 2023Review
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Advanced microscopy methods allow obtaining information on (dynamic) conformational changes in biomolecules via measuring a single molecular distance in the structure. It is, however, extremely challenging to capture the full depth of a three-dimensional biochemical state, binding-related structural changes or conformational cross-talk in multi-protein complexes using one-dimensional assays. In this paper we address this fundamental problem by extending the standard molecular ruler based on Förster resonance energy transfer (FRET) into a two-dimensional assay via its combination with protein-induced fluorescence enhancement (PIFE). We show that donor brightness (via PIFE) and energy transfer efficiency (via FRET) can simultaneously report on e.g., the conformational state of double stranded DNA (dsDNA) following its interaction with unlabelled proteins (BamHI, EcoRV, and T7 DNA polymerase gp5/trx). The PIFE-FRET assay uses established labelling protocols and single molecule fluorescence detection schemes (alternating-laser excitation, ALEX). Besides quantitative studies of PIFE and FRET ruler characteristics, we outline possible applications of ALEX-based PIFE-FRET for single-molecule studies with diffusing and immobilized molecules. Finally, we study transcription initiation and scrunching of E. coli RNA-polymerase with PIFE-FRET and provide direct evidence for the physical presence and vicinity of the polymerase that causes structural changes and scrunching of the transcriptional DNA bubble.
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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.