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Thermodynamic aspects of DNA nanoconstruct stability and design

Thermodynamic aspects of DNA nanoconstruct stability and design
Thermodynamic aspects of DNA nanoconstruct stability and design
In the present study, we use the fluorescent DNA base analog tC° to investigate the thermal stability of a small DNA hexagon and the thermodynamic factors that govern the formation of such a structure. The DNA molecule is becoming increasingly popular as a material for bottom-up construction of nanostructures; however, relatively little attention has been given to the thermodynamics of such biomacromolecule-based constructs. With the goal of increasing information density and structural complexity, the size of the nanoarchitectures decreases and, more importantly, the fine structure is becoming more detailed. In this process the thermal stability and formation of unwanted byproducts will become critical features to consider in the design and assembly of such structures. Using tC° as a fluorescent probe in fluorescence monitored DNA melting allows for individually observing the denaturing of each of the six 10-mer sides in the pseudohexagonal multicomponent system. Experimental results demonstrate that the ring-opening of the cyclized hexamer is virtually exclusive to one side and that the stability of this side is increased as a result of the cyclization. Moreover, a theoretical model describing the formation and melting of the nanostructure is presented. The results show that the cyclized structure is thermodynamically favored over linear polymeric structures under the conditions and concentrations used for the self-assembly.
1932-7447
5941-5946
Sandin, Peter
f7324993-b21e-4575-ae67-fd3223624030
Tumpane, John
b8edc11a-1930-4b53-bdd3-8fd6456be05b
Börjesson, Karl
252a6cb2-9d9f-4e25-8e73-fad787fa8b8e
Wilhelmsson, L. Marcus
bcf4f67a-198c-4c5e-80b8-a78f743509d4
Brown, Tom
a64aae36-bb30-42df-88a2-11be394e8c89
Nordén, Bengt
64d4009e-7456-4490-ac87-8d587334c7e0
Albinsson, Bo
1571067f-df46-43f7-96b9-52dc43278777
Lincoln, Per
f1edcf40-411d-4f54-bd94-d13394c011d4
Sandin, Peter
f7324993-b21e-4575-ae67-fd3223624030
Tumpane, John
b8edc11a-1930-4b53-bdd3-8fd6456be05b
Börjesson, Karl
252a6cb2-9d9f-4e25-8e73-fad787fa8b8e
Wilhelmsson, L. Marcus
bcf4f67a-198c-4c5e-80b8-a78f743509d4
Brown, Tom
a64aae36-bb30-42df-88a2-11be394e8c89
Nordén, Bengt
64d4009e-7456-4490-ac87-8d587334c7e0
Albinsson, Bo
1571067f-df46-43f7-96b9-52dc43278777
Lincoln, Per
f1edcf40-411d-4f54-bd94-d13394c011d4

Sandin, Peter, Tumpane, John, Börjesson, Karl, Wilhelmsson, L. Marcus, Brown, Tom, Nordén, Bengt, Albinsson, Bo and Lincoln, Per (2009) Thermodynamic aspects of DNA nanoconstruct stability and design. The Journal of Physical Chemistry C, 113 (15), 5941-5946. (doi:10.1021/jp808239a).

Record type: Article

Abstract

In the present study, we use the fluorescent DNA base analog tC° to investigate the thermal stability of a small DNA hexagon and the thermodynamic factors that govern the formation of such a structure. The DNA molecule is becoming increasingly popular as a material for bottom-up construction of nanostructures; however, relatively little attention has been given to the thermodynamics of such biomacromolecule-based constructs. With the goal of increasing information density and structural complexity, the size of the nanoarchitectures decreases and, more importantly, the fine structure is becoming more detailed. In this process the thermal stability and formation of unwanted byproducts will become critical features to consider in the design and assembly of such structures. Using tC° as a fluorescent probe in fluorescence monitored DNA melting allows for individually observing the denaturing of each of the six 10-mer sides in the pseudohexagonal multicomponent system. Experimental results demonstrate that the ring-opening of the cyclized hexamer is virtually exclusive to one side and that the stability of this side is increased as a result of the cyclization. Moreover, a theoretical model describing the formation and melting of the nanostructure is presented. The results show that the cyclized structure is thermodynamically favored over linear polymeric structures under the conditions and concentrations used for the self-assembly.

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Published date: 2009

Identifiers

Local EPrints ID: 146687
URI: http://eprints.soton.ac.uk/id/eprint/146687
ISSN: 1932-7447
PURE UUID: e5084547-0380-4605-ab54-5a39bded5b19

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Date deposited: 22 Apr 2010 08:52
Last modified: 17 Jul 2019 00:04

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Contributors

Author: Peter Sandin
Author: John Tumpane
Author: Karl Börjesson
Author: L. Marcus Wilhelmsson
Author: Tom Brown
Author: Bengt Nordén
Author: Bo Albinsson
Author: Per Lincoln

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