Practical aspects of structural and dynamic DNA nanotechnology
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Practical considerations of DNA as a material DNA is a biological polymer with a covalent backbone composed of alternating sugar and phosphate groups. The nucleotide side chains come in four varieties: adenine (A), cytosine (C), guanine (G), and thymine (T), and provide the hydrogen-bond donors and acceptors that allow specific base pairing of A to T and C to G of single-stranded DNA (ssDNA) into doublestranded DNA (dsDNA). The DNA sequence provides information storage in the polymer and specifies the complementary sequence and binding partner ssDNA with which dsDNA can be formed. Organisms use DNA to store genetic information, while molecular engineers use DNA to store supramolecular assembly instructions. Figure 1 provides an overview of DNA nanotechnology from a materials science perspective. DNA is soluble in water and can be precipitated by alcohols. Standard aqueous solutions of DNA contain a buffer to maintain a near-neutral pH and a salt (e.g., MgCl2) to provide cations necessary for shielding negative charges to allow the highly charged backbone phosphates to pack tightly together. In solution, the dehybridization of dsDNA into its ssDNA strands occurs below the boiling point of water, with specific value dependent upon sequence length and composition.
Regarding characterization techniques, the molecular size of ssDNA can be determined by denaturing gel electrophoresis, while supramolecular assemblies can be examined by nondenaturing electrophoresis, atomic force microscopy, or electron microscopy. The absorbance of UV light at 260 nm is used to estimate the solution concentration of DNA with extinction coefficients between 0.020–0.027 (µg/ml)−1 cm−1, depending upon nucleobase composition and secondary structure. DNA can be synthesized biologically, enzymatically, or chemically. Chemical synthesis is limited to molecules of a couple hundred bases, while biological or enzymatic production requires greater commitment during setup, but can then produce gram or even kilogram quantities of DNA. Hydrated DNA with high concentrations forms a viscous liquid and can be noncovalently cross-linked into a gel.1 Polymer stiffness/ flexibility measured as persistence length in solution is less than 3 nm for ssDNA, about 50 nm for dsDNA, and orders of magnitude greater for dsDNA helices aligned and joined noncovalently in nano-assemblies. The applied tensile force required to separate two complementary strands of DNA has been measured at 20–50 pN, depending on sequence length.2 Using optical tweezers, a molecule of ssDNA was estimated to have
Pengfei Wang, Wallace H. Coulter Department of Biomedical Engineering, Emory University, and Georgia Institute of Technology, USA; [email protected] Gourab Chatterjee, Department of Electrical Engineering, University of Washington, USA; [email protected] Hao Yan, School of Molecular Sciences, Biodesign Institute, Arizona State University, USA; [email protected] Thomas H. LaBean, North Carolina State University, USA; [email protected] Andrew J. Turberfield, Department of Physics, Un
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