ArticleMethods in enzymology2011
Quantitative methods for measuring DNA flexibility in vitro and in vivo.
Article in Methods in enzymology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed, 31 citations in OpenAlex.
- LOOP-TAG: massively-parallel measurement of length-dependent protein-mediated DNA looping probabilities by tagmentationbioRxiv : the preprint server for biology · 2026Article
- Artificial repression looping control by regulated autoinhibition of transcription activator-like effector dimer proteins.Nucleic acids research · 2026Article
- Engineered transcription activator-like effector dimer proteins confer DNA loop-dependent gene repression comparable to Lac repressor.Nucleic acids research · 2024Article
- High-Resolution Characterization of DNA/Protein Complexes in Living Bacteria.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Designed architectural proteins that tune DNA looping in bacteria.Nucleic acids research · 2021Article
- Characterization of Gene Repression by Designed Transcription Activator-like Effector Dimer Proteins.Biophysical journal · 2020Article
- Homolog comparisons further reconcile in vitro and in vivo correlations of protein activities by revealing over-looked physiological factors.Protein science : a publication of the Protein Society · 2019Article
- Evidence for a bind-then-bend mechanism for architectural DNA binding protein yNhp6A.Nucleic acids research · 2019Article
- Single and double box HMGB proteins differentially destabilize nucleosomes.Nucleic acids research · 2019Article
- Dependence of DNA looping onInternational journal of biochemistry and molecular biology · 2019Article
- Bacterial gene control by DNA looping using engineered dimeric transcription activator like effector (TALE) proteins.Nucleic acids research · 2018Article
- Optical Trapping Nanometry of Hypermethylated CPG-Island DNA.Biophysical journal · 2017Article
- Using synthetic biology to make cells tomorrow's test tubes.Integrative biology : quantitative biosciences from nano to macro · 2016Review
- Speeding up biomolecular interactions by molecular sledding.Chemical science · 2016Article
- Supercoiling Effects on Short-Range DNA Looping in E. coli.PloS one · 2016Article
- High-resolution mapping of architectural DNA binding protein facilitation of a DNA repression loop in Escherichia coli.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Mechanical properties of base-modified DNA are not strictly determined by base stacking or electrostatic interactions.Biophysical journal · 2014Article
- Bacterial promoter repression by DNA looping without protein-protein binding competition.Nucleic acids research · 2014Article
- Mechanical properties of DNA-like polymers.Nucleic acids research · 2013Article
- Molecular basis for sequence-dependent induced DNA bending.Chembiochem : a European journal of chemical biology · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The double-helical DNA biopolymer is particularly resistant to bending and twisting deformations. This property has important implications for DNA folding in vitro and for the packaging and function of DNA in living cells. Among the outstanding questions in the field of DNA biophysics are the underlying origin of DNA stiffness and the mechanisms by which DNA stiffness is overcome within cells. Exploring these questions requires experimental methods to quantitatively measure DNA bending and twisting stiffness both in vitro and in vivo. Here, we discuss two classical approaches: T4 DNA ligase-mediated DNA cyclization kinetics and lac repressor-mediated DNA looping in Escherichia coli. We review the theoretical basis for these techniques and how each can be applied to quantitate biophysical parameters that describe the DNA polymer. We then show how we have modified these methods and applied them to quantitate how apparent DNA physical properties are altered in vitro and in vivo by sequence-nonspecific architectural DNA-binding proteins such as the E. coli HU protein and eukaryotic HMGB proteins.
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.