1. Self-assembling of calcium salt of the new DNA base 5-carboxylcytosine
- Author
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Daniele Passeri, Gustavo Portalone, Marco Rossi, Sergio E. Ruiz-Hernandez, Marco Natali, Simona Irrera, Fabrizio Gala, Giuseppe Zollo, and Melania Reggente
- Subjects
Guanine ,Supramolecular chemistry ,General Physics and Astronomy ,02 engineering and technology ,010402 general chemistry ,X-ray diffraction (XRD) ,01 natural sciences ,Nucleobase ,chemistry.chemical_compound ,Molecular dynamics ,5-carboxylcytosine ,atomic force microscopy (AFM) ,ab initio calculation ,Surfaces and Interfaces ,General Chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,nanomedicine ,molecular dynamics ,0104 chemical sciences ,Surfaces, Coatings and Films ,Thymine ,Crystallography ,chemistry ,Density functional theory ,0210 nano-technology ,DNA ,Cytosine - Abstract
Supramolecular architectures involving DNA bases can have a strong impact in several fields such as nanomedicine and nanodevice manufacturing. To date, in addition to the four canonical nucleobases (adenine, thymine, guanine and cytosine), four other forms of cytosine modified at the 5 position have been identified in DNA. Among these four new cytosine derivatives, 5-carboxylcytosine has been recently discovered in mammalian stem cell DNA, and proposed as the final product of the oxidative epigenetic demethylation pathway on the 5 position of cytosine. In this work, a calcium salt of 5-carboxylcytosine has been synthesized and deposited on graphite surface, where it forms self-assembled features as long range monolayers and up to one micron long filaments. These structures have been analyzed in details combining different theoretical and experimental approaches: X-ray single-crystal diffraction data were used to simulate the molecule-graphite interaction, first using molecular dynamics and then refining the results using density functional theory (DFT); finally, data obtained with DFT were used to rationalize atomic force microscopy (AFM) results.
- Published
- 2017
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