ArticleScientific reports2017
Toehold-enhanced LNA probes for selective pull down and single-molecule analysis of native chromatin.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 16 citations in OpenAlex.
- Beyond the mono-nucleosome.Biochemical Society transactions · 2025Review
- Anti-gene oligonucleotide clamps invade dsDNA and downregulateMolecular therapy. Nucleic acids · 2024Article
- LNA blockers for improved amplification selectivity.Scientific reports · 2023Article
- Analysis of Yeast RNAP I Transcription of Nucleosomal Templates In Vitro.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Establishment and Maintenance of Open Ribosomal RNA Gene Chromatin States in Eukaryotes.Methods in molecular biology (Clifton, N.J.) · 2022Review
- A critical role for linker DNA in higher-order folding of chromatin fibers.Nucleic acids research · 2021Article
- Single-Molecule Techniques to Study Chromatin.Frontiers in cell and developmental biology · 2021Review
- Modified Nucleic Acids: Expanding the Capabilities of Functional Oligonucleotides.Molecules (Basel, Switzerland) · 2020Review
- Multiplexed Nanometric 3D Tracking of Microbeads Using an FFT-Phasor Algorithm.Biophysical journal · 2020Article
- Chromatin fibers stabilize nucleosomes under torsional stress.Nature communications · 2020Article
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The organization of DNA into chromatin is thought to regulate gene expression in eukaryotes. To study its structure in vitro, there is a need for techniques that can isolate specific chromosomal loci of natively assembled chromatin. Current purification methods often involve chemical cross-linking to preserve the chromatin composition. However, such cross-linking may affect the native structure. It also impedes single molecule force spectroscopy experiments, which have been instrumental to probe chromatin folding. Here we present a method for the incorporation of affinity tags, such as biotin, into native nucleoprotein fragments based on their DNA sequence, and subsequent single molecule analysis by magnetic tweezers. DNA oligos with several Locked Nucleic Acid (LNA) nucleotides are shown to selectively bind to target DNA at room temperature, mediated by a toehold end in the target, allowing for selective purification of DNA fragments. The stability of the probe-target hybrid is sufficient to withstand over 65 pN of force. We employ these probes to obtain force-extension curves of native chromatin fragments of the 18S ribosomal DNA from the yeast Saccharomyces cerevisiae. These experiments yield valuable insights in the heterogeneity in structure and composition of natively assembled chromatin at the single-molecule level.
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