Small-angle neutron scattering and Molecular Dynamics structural study of gelling DNA nanostars

DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed by 196 nucleotides) and to explore the structural signatures of their aggregation process. We report...

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Bibliographic Details
Published in:arXiv.org 2016-05
Main Authors: Fernandez-Castanon, Javier, Bomboi, Francesca, Rovigatti, Lorenzo, Zanatta, Marco, Paciaroni, Alessandro, Comez, Lucia, Porcar, Lionel, Jafta, Charl J, Fadda, Giulia C, Bellini, Tommaso, Sciortino, Francesco
Format: Article
Language:English
Subjects:
Computer simulation
Deoxyribonucleic acid
DNA
Dynamic structural analysis
Form factors
Gelation
Gene sequencing
Molecular dynamics
Neutron scattering
Neutrons
Nucleotides
Oligomers
Stellar evolution
Structure factor
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Summary:DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed by 196 nucleotides) and to explore the structural signatures of their aggregation process. We report small-angle neutron scattering experiments focused on the evaluation of both the form factor and the temperature evolution of the scattered intensity at a nano star concentration where the system forms a tetravalent equilibrium gel. We also perform molecular dynamics simulations of one isolated tetramer to evaluate the form factor theoretically, without resorting to any approximate shape. The numerical form factor is found to be in very good agreement with the experimental one. Simulations predict an essentially temperature independent form factor, offering the possibility to extract the effective structure factor and its evolution during the equilibrium gelation.
ISSN:2331-8422
DOI:10.48550/arxiv.1605.01650