2002/04/01 by Alexey K. Mazur, Mazur, Alexey K.
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Biological Physics (physics.bio-ph) #Biomolecules (q-bio.BM) #Chemical Physics (physics.chem-ph) #Experimental and Theoretical Physics Studies #FOS: Biological sciences #FOS: Physical sciences #physics.bio-ph #physics.chem-ph #q-bio.BM
paper · pdf · doi:10.48550/arxiv.physics/0204001
4 two-column pages, 2 integrated eps plates, RevTeX4
arxiv created 2002/04/01 · openalex publication_date 2002/04/01 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Due to its polyionic character the DNA double helix is stable and biologically active only in salty aqueous media where its charge is compensated by solvent counterions. Monovalent metal ions are ubiquitous in DNA environment and they are usually considered as the possible driving force of sequence-dependent modulations of DNA structure that make it recognizable by proteins. In an effort to directly examine this hypothesis, MD simulations of DNA in a water drop surrounded by vacuum were carried out, which relieves the requirement of charge neutrality. Surprisingly, with zero concentration of counterions a dodecamer DNA duplex appears metastable and its structure remains similar to that observed in experiments.