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DNA closed nanostructures: a structural and Monte Carlo simulation study

DNA closed nanostructures: a structural and Monte Carlo simulation study
DNA closed nanostructures: a structural and Monte Carlo simulation study
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.
1089-5647
15283-15294
Bombelli, Francesca Baldelli
6afe2a22-054d-4461-8b34-33e261563808
Gambinossi, Filippo
8f600237-8a29-4e52-bbe0-5dea1e0447b4
Lagi, Marco
fbde5c77-d94c-4ff4-8ba8-befcde666434
Berti, Debora
fc2212b2-4a40-4302-8258-e32bf5a3fd25
Caminati, Gabriella
841c7c0f-fff9-4b17-8e41-c35cc76c502a
Brown, Tom
a64aae36-bb30-42df-88a2-11be394e8c89
Sciortino, Francesco
2de3899f-5871-4b8a-b2f6-a3a99ef6e903
Nordén, Bengt
64d4009e-7456-4490-ac87-8d587334c7e0
Baglioni, Piero
695e2f89-0770-4f24-866c-2ef50f274d9d
Bombelli, Francesca Baldelli
6afe2a22-054d-4461-8b34-33e261563808
Gambinossi, Filippo
8f600237-8a29-4e52-bbe0-5dea1e0447b4
Lagi, Marco
fbde5c77-d94c-4ff4-8ba8-befcde666434
Berti, Debora
fc2212b2-4a40-4302-8258-e32bf5a3fd25
Caminati, Gabriella
841c7c0f-fff9-4b17-8e41-c35cc76c502a
Brown, Tom
a64aae36-bb30-42df-88a2-11be394e8c89
Sciortino, Francesco
2de3899f-5871-4b8a-b2f6-a3a99ef6e903
Nordén, Bengt
64d4009e-7456-4490-ac87-8d587334c7e0
Baglioni, Piero
695e2f89-0770-4f24-866c-2ef50f274d9d

Bombelli, Francesca Baldelli, Gambinossi, Filippo, Lagi, Marco, Berti, Debora, Caminati, Gabriella, Brown, Tom, Sciortino, Francesco, Nordén, Bengt and Baglioni, Piero (2008) DNA closed nanostructures: a structural and Monte Carlo simulation study. Journal of Physical Chemistry B, 112 (48), 15283-15294. (doi:10.1021/jp804544u).

Record type: Article

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.

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Published date: 4 December 2008

Identifiers

Local EPrints ID: 146701
URI: https://eprints.soton.ac.uk/id/eprint/146701
ISSN: 1089-5647
PURE UUID: cd97a796-5206-40e4-8625-55fbfbb2d7d9

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Date deposited: 22 Apr 2010 09:01
Last modified: 18 Jul 2017 23:03

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Contributors

Author: Francesca Baldelli Bombelli
Author: Filippo Gambinossi
Author: Marco Lagi
Author: Debora Berti
Author: Gabriella Caminati
Author: Tom Brown
Author: Francesco Sciortino
Author: Bengt Nordén
Author: Piero Baglioni

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