title: DNA closed nanostructures: a structural and Monte Carlo simulation study.
abstract: DNA nanoconstructs are obtained in solution by using six unique 42-mer DNA oligonucleotides, whose sequences have been designed to form a pseudohexagonal structure. The required flexibility is provided by the insertion of two non-base-paired thymines in the middle of each sequence that work as flexible hinges and constitute the corners of the nanostructure when formed. We show that hexagonally shaped nanostructures of about 7 nm diameter and their corresponding linear open constructs are formed by self-assembly of the specifically designed linear oligonucleotides. The structural and dynamical characterization of the nanostructure is obtained in situ for the first time by using dynamic light scattering (DLS), a noninvasive method that provides a fast dynamic and structural analysis and allows the characterization of the different synthetic DNA nanoconstructs in solution. A validation of the LS results is obtained through Monte Carlo (MC) simulations and atomic force microscopy (AFM). In particular, a mesoscale molecular model for DNA, developed by Knotts et al., is exploited to perform MC simulations and to obtain information about the conformations as well as the conformational flexibilities of these nanostructures, while AFM provides a very detailed particle analysis that yields an estimation of the particle size and size distribution. The structural features obtained by MC and AFM are in good agreement with DLS, showing that DLS is a fast and reliable tool for characterization of DNA nanostructures in solution.
authors.affiliation: Department of Chemistry and CSGI, University of Florence, Via della Lastruccia 3 - Sesto Fiorentino, 50019 Florence, Italy.
authors.forename: Francesca Baldelli
authors.initials: FB
authors.lastname: Bombelli
authors.forename: Filippo
authors.initials: F
authors.lastname: Gambinossi
authors.forename: Marco
authors.initials: M
authors.lastname: Lagi
authors.forename: Debora
authors.initials: D
authors.lastname: Berti
authors.forename: Gabriella
authors.initials: G
authors.lastname: Caminati
authors.forename: Tom
authors.initials: T
authors.lastname: Brown
authors.forename: Francesco
authors.initials: F
authors.lastname: Sciortino
authors.forename: Bengt
authors.initials: B
authors.lastname: Norden
authors.forename: Piero
authors.initials: P
authors.lastname: Baglioni
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D008027:Light; D018625:Microscopy, Atomic Force; D008958:Models, Molecular; D015233:Models, Statistical; D009010:Monte Carlo Method; D036103:Nanotechnology; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D012542:Scattering, Radiation; D014466:Ultraviolet Rays
chemical_list: D009841:Oligonucleotides; D004247:DNA