ArticleBiophysical journal2005
Ligand-induced DNA condensation: choosing the model.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- An Asymptotic Analysis of Bivalent Monoclonal Antibody-Antigen Binding.Bulletin of mathematical biology · 2025Article
- Unfolding of the chromatin fiber driven by overexpression of noninteracting bridging factors.Biophysical journal · 2021Article
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- Additive Modulation of DNA-DNA Interactions by Interstitial Ions.Biophysical journal · 2020Article
- Branched-Chain Polyamine Found in Hyperthermophiles Induces Unique Temperature-Dependent Structural Changes in Genome-Size DNA.Chemphyschem : a European journal of chemical physics and physical chemistry · 2018Article
- Ion competition in condensed DNA arrays in the attractive regime.Biophysical journal · 2013Article
- Herpes virus genome, the pressure is on.Journal of the American Chemical Society · 2013Article
- Structure-driven homology pairing of chromatin fibers: the role of electrostatics and protein-induced bridging.Journal of biological physics · 2013Article
- FRET-labeled siRNA probes for tracking assembly and disassembly of siRNA nanocomplexes.ACS nano · 2012Article
- Role of amino acid insertions on intermolecular forces between arginine peptide condensed DNA helices: implications for protamine-DNA packaging in sperm.The Journal of biological chemistry · 2011Article
- A lattice model for transcription factor access to nucleosomal DNA.Biophysical journal · 2010Article
- Predicting gene-regulation functions: lessons from temperate bacteriophages.Biophysical journal · 2010Article
- Interaction of a self-assembling peptide with oligonucleotides: complexation and aggregation.Biophysical journal · 2007Article
- General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage lambda.Nucleic acids research · 2007Article
- Morphology and ultrastructure of condensed DNA microparticles formed during PCR.Doklady. Biochemistry and biophysicsArticle
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1 author.
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Abstract
We test and compare different models for ligand-induced DNA condensation. Using 14C-labeled spermidine3+, we measure the binding to condensed DNA at micromolar to molar polyamine concentrations. DNA aggregates at a critical polyamine concentration. Spermidine3+ binding becomes highly cooperative at the onset of aggregation. At higher concentrations, spermidine3+ binding to condensed DNA reaches a plateau with the degree of binding equal to 0.7 (NH(4+)/PO3-). Condensed DNA exists in a wide range of spermidine concentrations with the roughly constant degree of ligand binding. At greater concentrations, the degree of binding increases again. Further spermidine penetration between the double helices causes DNA resolubilization. We show that a simple two-state model without ligand-ligand interactions qualitatively predicts the reentrant aggregation-resolubilization behavior and the dependence on the ligand, Na+, and DNA concentrations. However, such models are inconsistent with the cooperative ligand binding to condensed DNA. Including the contact or long-range ligand-ligand interactions improves the coincidence with the experiments, if binding to condensed DNA is slightly more cooperative than to the starting DNA. For example, in the contact interaction model it is equivalent to an additional McGhee-von Hippel cooperativity parameter of approximately 2. Possible physical mechanisms for the observed cooperativity of ligand binding are discussed.
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