ArticleBiophysical journal2009
Sequence dependencies of DNA deformability and hydration in the minor groove.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Elucidating the Role of Groove Hydration on Stability and Functions of Biased DNA Duplexes in Cell-Like Chemical Environments.Journal of the American Chemical Society · 2024Article
- Examining the Effects of Netropsin on the Curvature of DNA A-Tracts Using Electrophoresis.Molecules (Basel, Switzerland) · 2021Article
- Specifically bound BZIP transcription factors modulate DNA supercoiling transitions.Scientific reports · 2020Article
- Small molecule binders recognize DNA microstructural variations via an induced fit mechanism.Physical chemistry chemical physics : PCCP · 2019Article
- DNA Shape versus Sequence Variations in the Protein Binding Process.Biophysical journal · 2016Article
- Novel alleles of the VERNALIZATION1 genes in wheat are associated with modulation of DNA curvature and flexibility in the promoter region.BMC plant biology · 2016Article
- Prediction of fine-tuned promoter activity from DNA sequence.F1000Research · 2016Article
- Close encounters with DNA.Journal of physics. Condensed matter : an Institute of Physics journal · 2014Review
- Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning.Nucleic acids research · 2014Article
- Small-molecule binding to the DNA minor groove is mediated by a conserved water cluster.Journal of the American Chemical Society · 2013Article
- Molecular dynamics study of the role of the spine of hydration in DNA A-tracts in determining nucleosome occupancy.The journal of physical chemistry. B · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA deformability and hydration are both sequence-dependent and are essential in specific DNA sequence recognition by proteins. However, the relationship between the two is not well understood. Here, systematic molecular dynamics simulations of 136 DNA sequences that differ from each other in their central tetramer revealed that sequence dependence of hydration is clearly correlated with that of deformability. We show that this correlation can be illustrated by four typical cases. Most rigid basepair steps are highly likely to form an ordered hydration pattern composed of one water molecule forming a bridge between the bases of distinct strands, but a few exceptions favor another ordered hydration composed of two water molecules forming such a bridge. Steps with medium deformability can display both of these hydration patterns with frequent transition. Highly flexible steps do not have any stable hydration pattern. A detailed picture of this correlation demonstrates that motions of hydration water molecules and DNA bases are tightly coupled with each other at the atomic level. These results contribute to our understanding of the entropic contribution from water molecules in protein or drug binding and could be applied for the purpose of predicting binding sites.
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