U tilization of c omputer s cience for c onstruction and c haracterization of dna n anos tructures

In the upcoming field of DNA nano-science, DNA is used as an entity for building higher order self-assembled structures rather than for storage of genetic information. The application of DNA as a building block relies, like its biological blueprinting function, on the specific pairing between bases holding pairs of DNA molecules together. However, the complexity involved in building even simple DNA architectures is usually so high that designing structures from more than a few base sequences makes the use of computer programs indispensible. Moreover, synthetic DNA nano-structures are often timeconsuming and expensive to build and their structures can be difficult to validate. Therefore, atomistic simulations, which can predict assembly efficiency and physical properties of the designed structures are of great value for both the processes of design and characterization. In this article we summarize examples of computational tools for # FFA and PV contributed equally to this work.  Corresponding authors. Contact information AD: e-mail: desideri@uniroma2.it, Telephone: +39-06-72594376, Fax: +39-06-2022798; BRK: e-mail: brk@mb.au.dk, Telephone: +45-89422608, Fax: +45-89422612. The exclusive license for this PDF is limited to personal website use only. No part of this digital document may be reproduced, stored in a retrieval system or transmitted commercially in any form or by any means. The publisher has taken reasonable care in the preparation of this digital document, but makes no expressed or implied warranty of any kind and assumes no responsibility for any errors or omissions. No liability is assumed for incidental or consequential damages in connection with or arising out of information contained herein. This digital document is sold with the clear understanding that the publisher is not engaged in rendering legal, medical or any other professional services. Felicie F. Andersen, Palle Villesen, Bjarne Knudsen et al. 318 the design and characterization of DNA nano-structures with particular emphasis on a three-dimensional truncated octahedral structure.