Selectively Scissoring Hydrogen-Bonded Cytosine Dimer Structures Catalyzed by Water Molecules
- 20 July 2020
- journal article
- research article
- Published by American Chemical Society (ACS) in ACS Nano
- Vol. 14 (8), 10680-10687
- https://doi.org/10.1021/acsnano.0c05227
Abstract
A single-molecule-level understanding of the activity of solvating water molecules in hydrogen-bonded assemblies would provide insights into the properties of the first hydration shells. Herein, we investigate the solvation of one of the DNA bases, cytosine, whose glassy-state network formed on Au(111) contains diverse types of hydrogen-bonded dimer configurations with hierarchical strengths. Upon water exposure, a global structural transformation from interwoven chain segments to extended chains was identified by scanning tunneling microscopy and atomic force microscopy. Density functional theory calculation and coarse-grained molecular dynamics simulation indicate that water molecules selectively break the weak-hydrogen-bonded dimers at T-junctions, while the stable ones within chains remain intact. The resulting hydrated chain segments further self-assemble into molecular chains by forming strong hydrogen bonds and spontaneously releasing water molecules. Such an intriguing transformation cannot be realized by thermal annealing, indicating the dynamic nature of water molecules in the regulation of hydrogen bonds in a catalytic manner.Keywords
Funding Information
- Ministry of Education of the People's Republic of China
- Ministry of Science and Technology of the People's Republic of China (2016YFA0200700, 2017YFA0205000)
- National Natural Science Foundation of China (21425310, 21622307, 21721002, 21790351, 21790353, 21833007, 21972032, 21973085)
- Chinese Academy of Sciences (XDB36000000)
- Convestro-Tongji Innovation Academy Fund
This publication has 40 references indexed in Scilit:
- Electrostatic Interactions in Protein Structure, Folding, Binding, and CondensationChemical Reviews, 2018
- Water Dynamics in the Hydration Shells of BiomoleculesChemical Reviews, 2017
- Single-molecule dissection of stacking forces in DNAScience, 2016
- Metal-Mediated DNA Base Pairing: Alternatives to Hydrogen-Bonded Watson–Crick Base PairsAccounts of Chemical Research, 2012
- Solution structure of a DNA double helix with consecutive metal-mediated base pairsNature Chemistry, 2010
- Nanoscale Forces and Their Uses in Self‐AssemblySmall, 2009
- Non-covalent interactions in biomacromoleculesPhysical Chemistry Chemical Physics, 2007
- Dielectric Relaxation and Solvation Dynamics of Water in Complex Chemical and Biological SystemsChemical Reviews, 2000
- Self‐Assembly in Natural and Unnatural SystemsAngewandte Chemie-International Edition, 1996
- Molecular Self-Assembly and Nanochemistry: a Chemical Strategy for the Synthesis of NanostructuresScience, 1991