Mansi Mavani Graduate Student Department of Physics, OSU Stillwater

1. DNA Nanobiotechnology:Concepts and Applications Mansi Mavani Graduate Student Department of Physics, OSU Stillwater

2. DNA Nanobiotechnology Abstract: • A fusion technology of Nanotechnology and Biotechnology. • DNA nanobiotechnology uses DNA structures and properties for constructing nanostructured material and utilizes those nanostructured materials in biological, engineering, and medical applications. • This review paper focuses on providing information about theoretical background, recent development, current state of art, innovative uses of DNA in multi-disciplinary filed, challenges and future perspective of DNA nanobiotechnology.

3. DNA Nanobiotechnology Background and Introduction: • Discovery of the structure of the DNA in 1953 by Watson and Crick • Nature has been an inspiration • DNA having unique properties, such as a nanoscale structural geometry, information encoding, self-replicating, and self-assembly, have demonstrated it as an excellent fundamental building block material for molecular nanotechnology • DNA can be used as a bottom-up construction medium, a building block for self-assembly and as a nanostructure to construct periodic assemblies and complex nanostructures • Using the DNA as a bottom-up construction molecule to build 3D arrays. Exploring and improving its properties to produce at a higher dimensions

4. DNA Nanobiotechnology Literature Review: • Major work done (by research area): • DNA as a building block (a construction material) REF [1,18-24] (1990-2003) • DNA as a framework (bottom-up construction medium) REF [26] (2000) • DNA to construct periodic assemblies REF [4, 27] (1999-2000) • DNA for diagnosis and drug delivery REF[28] (2001), and etc. • Impact from Chemistry, Molecular Science, Bio and Nano science fields • Enabling technologies are in field of Engineering, Molecular Biology, Computation, Chemistry, Medicine and Health Care • Interesting papers: • Principles and applications of DNA molecules by A. Condon (2) • DNA-programmed self-assembly by T. H. LaBean (1, 6) • Use of DNA as a bottom-up constructive medium by N. C. Seeman et al (3, 4) • self-assembly of DNA tiles for building complex nanostructures by C. Lin et al(5) • Medicine and Health Care applications by T. Kubik et al(30)

5. DNA Nanobiotechnology Theoretical Background: • Structure and properties of DNA (deoxyribonucleic acid) Figure. 1(b) DNA replication (13) Figure. 1 (a) The chemical structure of DNA (13)

6. DNA Nanobiotechnology Theoretical Background: (Contd.) • DNA nanobiotechnology fundamentals • DNA functional properties: sequence, structure and folding pathway Figure 2. DNA nanobiotechnology basic. (a) Sticky-ended cohesion. (b) Self-assembly of branched DNA molecules with complementary sticky-end pairs. This figure is taken from REF [3].

7. DNA Nanobiotechnology Current Research and Application : • DNA computation applications by J. H. Reif, T. H. LaBean, et al (1, 22) • Invention of parallel reaction discovery by C. T. Calderone and M. W. Kanan (31, 32) Figure 3. Exploiting DNA sequences: DNA computation. The “select and prune” parallel computation method used by Adleman (33) to determine path through a network. This figure is taken from REF [2]

8. DNA Nanobiotechnology Current Research and Application : (Contd.) • DNA scaffolding by N.C. Seeman (3, 4, 11, 14, 24, 27) • Diagnosis and release of drug by Y. Benenson, et al (28, 29) Figure 4. Structural DNA nanotechnology applications. (A) Scaffolding biological macromolecules and (B) Scaffolding nanoelectronics by N. C. Seeman (14). This figure is taken from REF [14]

9. DNA Nanobiotechnology Current Research and Application : (Contd.) • Applications of DNA sequences: • Sensitive molecular detection • DNA-templated synthesis • Parallel reaction discovery • Computing with DNA • Organization of nano-electronic components and other materials, etc. • Applications of DNA structures: • Molecular detection • DNA scaffolding • Nanoelectronic assembly • Algorithmic self-assembly, etc. • Applications of DNA-folding pathways: • Molecular detection • Diagnosis and drug release (28, 29) • Binding and release of a protein target, etc.

10. DNA Nanobiotechnology Future Directions : • Future applications: • DNA computation • Drug discovery through DTS • Designing electronic circuit structures using DNA self-assembly techniques • DNA motors to perform DNA like tasks and enhancement to nanorobots • Development of in vivo nano-sensors, etc. • Grand challenge: • To find an error correction method to solve problems in self-assembly methods • Technical challenges: • To explore its electromagnetic, electrochemical and catalytic properties • To produce high order object, arrays and lattices in 3D • To build efficiently self-assembled steady complex structures from nanoscale to macro-scale structures, etc.

11. DNA Nanobiotechnology References: [1] T. H. LaBean, “Introduction to Self-Assembling DNA Nanostructures for Computation and Nanofabrication” (Chapter 2 in Computational Biology and Genome Informatics (eds. Wang, J. T. L., Wu, C. H. & Wang, P. P.), ISBN 981-238-257-7, World Scientific Publishing, 2003). [2] A. Condon, “Designed DNA molecules: principles and applications of molecular nanotechnology,” Nature reviews, Genetics, July 2006, Nature Publishing Group, vol. 7, pp. 565-575. [3] N. C. Seeman, “DNA enables nanoscale control of the structure of matter,” Quarterly Reviews of Biophysics, 2006, Cambridge University Press, pp. 1-9. [4] N. C. Seeman, et al, “Two Dimensions and Two States in DNA Nanotechnology,” Journal of Biomolecular Structure & Dynamics, Conversation 11, Issue #1, SUNY, 2000, Adenine Press. [5] C. Lin, Y. Liu, S. Rinker, H. Yan, “DNA Tile Based Self-Assembly: Building Complex Nanoarchitectures,” ChemPhysChem 2006, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, vol. 7, pp. 1641-1647. [6] K. V. Gothelf, T. H. LaBean, “DNA-programmed assembly pf nanostructure,” Org. Biomol. Chem., 2005, The Royal Society of Chemistry, vol. 3, pp. 4023-4037. [7] M. C. Roco, “Nanotechnology: convergence with modern biology and medicine,” Current Opinion in Biotechnology 2003, vol. 14, pp. 337-346. Please refer to the review paper “DNA Nanobiotechnology” for the rest of references detail.