Open Access Highly Accessed Original article

Modeling biominerals formed by apatites and DNA

Guillermo Revilla-López1, Jordi Casanovas2, Oscar Bertran3, Pau Turon4*, Jordi Puiggalí15 and Carlos Alemán15*

Author Affiliations

1 Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona, 08028, Spain

2 Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/ Jaume II nº 69, Lleida, E-25001, Spain

3 Departament de Física Aplicada, EEI, Universitat Politècnica de Catalunya, Pça. Rei 15, Igualada, 08700, Spain

4 B. Braun Surgical S.A. Carretera de Terrasa 121, Rubí (Barcelona), 08191, Spain

5 Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C’, C/Pasqual i Vila s/n, Barcelona, E-08028, Spain

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Biointerphases 2013, 8:10  doi:10.1186/1559-4106-8-10

Published: 8 April 2013

Abstract

Different aspects of biominerals formed by apatite and DNA have been investigated using computer modeling tools. Firstly, the structure and stability of biominerals in which DNA molecules are embedded into hydroxyapatite and fluoroapatite nanopores have been examined by combining different molecular mechanics methods. After this, the early processes in the nucleation of hydroxyapatite at a DNA template have been investigated using molecular dynamics simulations. Results indicate that duplexes of DNA adopting a B double helix can be encapsulated inside nanopores of hydroxyapatite without undergoing significant distortions in the inter-strand hydrogen bonds and the intra-strand stacking. This ability of hydroxyapatite is practically independent of the DNA sequence, which has been attributed to the stabilizing role of the interactions between the calcium atoms of the mineral and the phosphate groups of the biomolecule. In contrast, the fluorine atoms of fluoroapatite induce pronounced structural distortions in the double helix when embedded in a pore of the same dimensions, resulting in the loss of its most relevant characteristics. On the other hand, molecular dynamics simulations have allowed us to observe the formation of calcium phosphate clusters at the surface of the B-DNA template. Electrostatic interactions between the phosphate groups of DNA and Ca2+ have been found to essential for the formation of stable ion complexes, which were the starting point of calcium phosphate clusters by incorporating

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from the solution.

Keywords:
Biominerals; DNA; Encapsulation; Hydroxyapatite; Nanopores; Nucleation