& DNA Nanowires Programmed Self-Assembly of a Quadruplex DNA Nanowire Nason Ma’ani Hessari, [a] Lea Spindler,* [b, c] Tinkara Troha, [c] Wan-Chi Lam, [a] Irena Drevens ˇek- Olenik, [c] and Mateus Webba da Silva* [a] Abstract: The ability to produce, reproducibly and system- atically, well-defined quadruplex DNA nanowires through controlled rational design is poorly understood despite potential utility in structural nanotechnology. The pro- grammed hierarchical self-assembly of a long four-strand- ed DNA nanowire through cohesive self-assembly of GpC and CpG “sticky” ends is reported. The encoding of bases within the quadruplex stem allows for an uninterrupted p-stacking system with rectilinear propagation for hun- dreds of nanometers in length. The wire is mechanically stable and features superior nuclease resistance to double-stranded DNA. The study indicates the feasibility for programmed assembly of uninterrupted quadruplex DNA nanowires. This is fundamental to the systematic in- vestigation of well-defined DNA nanostructures for uses in optoelectronic and electronic devices as well as other structural nanotechnology applications. The ability to produce, reproducibly and systematically, well- defined quadruplex DNA nanowires through controlled ration- al design is poorly understood despite potential utility in struc- tural nanotechnology. We report on the programmed hierarch- ical self-assembly of a long four-stranded DNA nanowire through cohesive self-assembly of GpC and CpG “sticky” ends. The encoding of bases within the quadruplex stem allows for an uninterrupted p-stacking system with rectilinear propaga- tion for hundreds of nanometers in length. The wire is me- chanically stable and features superior nuclease resistance to double-stranded DNA. The study indicates the feasibility for programmed assembly of uninterrupted quadruplex DNA nanowires. This is fundamental to the systematic investigation of well-defined DNA nanostructures for use in optoelectronic and electronic devices as well as other structural nanotechnol- ogy applications. The control of bottom-up organization of DNA with nano- scale precision has been the central goal for the development of a wide array of nanotechnologies. Developments in structur- al DNA nanotechnology have mostly focused on Watson–Crick base-pairing. [1] In four-stranded DNA architectures known as quadruplexes these rules are insufficient for folding. DNA quadruplexes form from association of four hydrogen-bond aligned bases into a pseudoplanar element: a tetrad, (G:G:G:G). The basic requirement for formation of a quadruplex is the association of two-stacked tetrads with the same groove-width combinations. [2] These DNA architectures have three limiting groove sizes generically designated as wide, narrow, and medium. Stacked tetrads form one-dimensional p systems with potential utility in the production of electronic and optoelectronic devices. [3] Currently the essential requirements for the systematic and reproducible production of structurally well-defined quadru- plex DNA nanowires remains poorly understood (for reviews see ref. [4]). It is clear that control of structural properties of the wire, such as nature of the bases of the stem, their base- stacking arrangements, stem groove-widths, and strand direc- tionality, are fundamental to a systematic rational modulation of the putative tunable physical properties. Having previously established some of the principles that can be utilized to con- trol the self-assembly of unimolecular quadruplex, [2] herein we report an instance in which we have utilized quadruplex fold- ing principles to design a quadruplex DNA nanowire with con- trolled structural periodicity. Our design strategy is illustrated in Scheme 1. We utilized the segments 5’-GGAGG to form medium grooves crossed by a looping adenine, resulting in two-stacked (G:G:G:G) tetrads defining a quadruplex stem. These units were designed to be linked through two pairs of 5’-GpC overhangs forming two (G:C:G:C) stacked tetrads. The sequence for this portion thus assumes the form d(GCGGAGG). We previously tested this self- assembly approach, and determined the resultant atomic detail solution structures of the dimer of dimers utilizing the sequences d(GCGGXGGAT) [X is T, TT, A, and TC]. [5] This tetra- meric structure, in which the GC overhang represents a “sticky end” that can associate into a (G:C:G:C) tetrad, helped provide the concept for linking nanowire subunits presented here. In order to allow for further multimerization of these bimo- lecular architectures we added a CpG overhang to the 3’ end of the sequence. The sequence now assumes the form d(GCGGAGGCG). Coupling of two of the dimer of dimers through two pairs of these CpG-3’ overhangs should result in the formation of two further (G:C:G:C) stacked tetrads as shown in Scheme 1. We hypothesized that this design would [a] Dr. N. Ma’ani Hessari, Dr. W.-C. Lam, Dr. M. Webba da Silva Biomedical Sciences Research Institute, University of Ulster Cromore Road, Coleraine, BT51 1SA (UK) E-mail : mm.webba-da-silva@ulster.ac.uk [b] Dr. L. Spindler Faculty of Mechanical Engineering, University of Maribor Smetanova 17, 2000 Maribor (Slovenia) E-mail : lea.spindler@uni-mb.si [c] Dr. L.Spindler, T. Troha, Prof. I.Drevensˇek-Olenik Josef Sefan Institute, Jamova 39, 1000 Ljubljana (Slovenia) Chem. Eur. J. 2014, 20, 3626 – 3630 # 2014 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim 3626 Communication DOI: 10.1002/chem.201300692