ArticleProceedings of the National Academy of Sciences of the United States of America2013
Entropy-driven collective interactions in DNA brushes on a biochip.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 64 citations in OpenAlex.
- Cell-free immuno-profiling on a genetically programmed biochip.Nature nanotechnology · 2026Article
- Vertical DNA Nanostructure Arrays: Facilitating Functionalization on Macro-Scale Surfaces.ACS nano · 2025Article
- Glycocalyx-induced formation of membrane tubes.Biophysical journal · 2025Article
- Elasticity control of entangled chromosomes: Crosstalk between condensin complexes and nucleosomes.Biophysical journal · 2023Article
- Toward Memory in a DNA Brush: Site-Specific Recombination Responsive to Polymer Density, Orientation, and Conformation.Journal of the American Chemical Society · 2023Article
- Solution properties of spherical gold nanoparticles with grafted DNA chains from simulation and theory.Nanoscale advances · 2022Article
- Nanometer-Scale Force Profiles of Short Single- and Double-Stranded DNA Molecules on a Gold Surface Measured Using a Surface Forces Apparatus.Langmuir : the ACS journal of surfaces and colloids · 2021Article
- Boundary-Free Ribosome Compartmentalization by Gene Expression on a Surface.ACS synthetic biology · 2021Article
- Synthetic Semiflexible and Bioactive Brushes.Biomacromolecules · 2019Article
- Article
- Equilibrium Modeling of the Mechanics and Structure of the Cancer Glycocalyx.Biophysical journal · 2019Article
- Physical biology of the cancer cell glycocalyx.Nature physics · 2018Article
- Multivalent ions induce lateral structural inhomogeneities in polyelectrolyte brushes.Science advances · 2017Article
- DNA Brush-Directed Vertical Alignment of Extensive Gold Nanorod Arrays with Controlled Density.ACS omega · 2017Article
- DNA condensation in one dimension.Nature nanotechnology · 2016Article
- BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE.Biomaterials science · 2014Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cell-free gene expression in localized DNA brushes on a biochip has been shown to depend on gene density and orientation, suggesting that brushes form compartments with partitioned conditions. At high density, the interplay of DNA entropic elasticity, electrostatics, and excluded volume interactions leads to collective conformations that affect the function of DNA-associated proteins. Hence, measuring the collective interactions in dense DNA, free of proteins, is essential for understanding crowded cellular environments and for the design of cell-free synthetic biochips. Here, we assembled dense DNA polymer brushes on a biochip along a density gradient and directly measured the collective extension of DNA using evanescent fluorescence. DNA of 1 kbp in a brush undergoes major conformational changes, from a relaxed random coil to a stretched configuration, following a universal function of density to ionic strength ratio with scaling exponent of 1/3. DNA extends because of the swelling force induced by the osmotic pressure of ions, which are trapped in the brush to maintain local charge neutrality, in competition with the restoring force of DNA entropic elasticity. The measurements reveal in DNA crossover between regimes of osmotic, salted, mushroom, and quasineutral brush. It is surprising to note that, at physiological ionic strength, DNA density does not induce collective stretch despite significant chain overlap, which implies that excluded volume interactions in DNA are weak.
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