Fluorescent Hydrophobic Zippers inside Duplex DNA: Interstrand Stacking of Perylene-3,4:9,10-tetracarboxylic Acid Bisimides as Artificial DNA Base Dyes

Assembly of DNA triangles mediated by perylene bisimide caps

Perylene bisimides (PBI) have been synthetically incorporated as caps onto a Y-shaped DNA triple strand. These PBI caps serve as "sticky" ends in the spontaneous assembly of larger DNA ensembles, linking the triangular DNA through stacking interactions. This, in turn, yields a hypsochromic shift in the absorption and a red shift in the fluorescence as characteristic optical readouts. This assembly occurs spontaneously without any enzymatic ligation process and without the use of overhanging DNA as sticky ends. Instead, dimerizations of the PBI chromophores in the assembly are controlled by the DNA as a structural scaffold. Thereby, the PBI-driven assembly is fully reversible. Due to the fact that PBI dimerization does not occur in the single strand, the aggregates can be destroyed by thermal dehybridization of the DNA scaffold and reassembled by reannealing of the DNA construct. In view of the fact that PBI forms stable radical anions, the presented DNA architectures are not only interesting optical biomaterials, but are also promising materials for molecular electronics with DNA.

Introducing structural flexibility into porphyrin-DNA zipper arrays

A more flexible nucleotide building block for the synthesis of new DNA based porphyrin-zipper arrays is described. Changing the rigid acetylene linker between the porphyrin substituent and the 2'-deoxyuridine to a more flexible propargyl amide containing linkage leads in part to an increased duplex stability. The CD spectra reveal different electronic interactions between the porphyrins depending on the type of linker used. Molecular modelling suggests large variation of the relative orientation of the porphyrins within the major groove of the DNA. The porphyrins can be metallated post-synthetically with different metals as shown with zinc, cobalt and copper. The spectroscopic features do not alter drastically upon metallation apart from the CD spectra, and the stability of the metal complex is highly dependent on the nature of the metal. As shown by CD spectroscopy, the zinc porphyrin is rapidly demetallated at high temperatures. Globular structure determination using SAXS indicates that a molecular assembly comprised of a two to four helical bundle dominates in solution at higher concentrations (≥50 μM) which is not observed by spectroscopy at lower concentrations (≤1 μM).

Synthesis and properties of the simplified nucleic acid glycol nucleic acid

The nucleosides of glycol nucleic acid (GNA), with the backbone comprising just the three carbons and one stereocenter of propylene glycol (1,2-propanediol), probably constitute the simplest possible building blocks for a chemically stable nucleic acid that contains phosphodiester bonds. However, it was not until 2005 that the astonishing duplex formation properties of GNA homoduplexes were discovered in our laboratory. The R- and S-enantiomers of GNA, (R)-GNA and (S)-GNA, pair in like-symmetric combinations to form highly stable antiparallel duplexes in a Watson-Crick fashion, with thermal and thermodynamic stabilities exceeding those of analogous duplexes of DNA and RNA. Interestingly, (R)-GNA and (S)-GNA do not significantly cross-pair with each other, either in a parallel or antiparallel fashion. GNA discriminates strongly in favor of the Watson-Crick base-pairing scheme, with only slightly lower fidelity than DNA. Two (S)-GNA homoduplex structures recently determined by X-ray crystallography, one a brominated 6-mer duplex and the other an 8-mer duplex containing two copper(II) ions, reveal that the overall GNA double helix is distinct from canonical A- and B-form nucleic acids. The structure is perhaps best described as a helical ribbon loosely wrapped around the helix axis. Within the backbone, the propylene glycol nucleotides adopt two different conformations, gauche and anti, with respect to the torsional angles between the vicinal C3'-O and C2'-O bonds. A strikingly large backbone-base inclination results in extensive zipper-like interstrand and reduced intrastrand base-base interactions. This strong backbone-base inclination might explain the observation that neither the R- nor S-enantiomer of GNA cross-pairs with DNA, whereas (S)-GNA can interact with RNA strands that are devoid of G:C base pairs. Given the combination of structural simplicity, straightforward synthetic accessibility, and high duplex stability of GNA duplexes, GNA affords a promising nucleic acid scaffold for biotechnology and nanotechnology. Along these lines, we describe the functionalization of GNA duplexes through the incorporation of metal-ion-mediated base pairs. Finally, the properties of GNA discussed here reinforce its candidacy as one of the initial genetic molecules formed during the origins of life on Earth.

DNA as supramolecular scaffold for functional molecules: progress in DNA nanotechnology

Oligonucleotides have recently gained increased attraction as a supramolecular scaffold for the design and synthesis of functional molecules on the nanometre scale. This tutorial review focuses on the recent progress in this highly active field of research with an emphasis on covalent modifications of DNA; non-covalent interactions of DNA with molecules such as groove binders or intercalators are not part of this review. Both terminal and internal modifications are covered, and the various points of attachment (nucleobase, sugar moiety or phosphodiester backbone) are compared. Using selected examples of the recent literature, the diversity of the functionalities that have been incorporated into DNA strands is discussed.

Nucleic acid-guided assembly of aromatic chromophores

The rational formation of aromatic chromophore arrays is an intriguing challenge since ordered collectives of chromophores possess properties that are largely different from those of the individual molecules. Therefore, nucleic acids are increasingly used as scaffolds for the construction of multi-chromophore arrays. This tutorial review provides an introduction to the field of nucleic acid-guided chromophore assemblies for non-specialists and a reference point for those familiar with the area by highlighting the recent developments and describing some of the spectroscopic methods used for the study of oligonucleotide-chromophore conjugates.

DNA as a supramolecular framework for the helical arrangements of chromophores: towards photoactive DNA-based nanomaterials

Nucleic acids have been emerging as supramolecular structural scaffolds for the helical organization of chromophores in the creation of functional nanomaterials mainly because of the their unique structural features and synthetic accessibility. A large number of chromophores have been successfully incorporated into DNA or RNA as C-nucleosides, as base surrogates or as modified sugars using solid phase phosphoramidite chemistry. Moreover, multiple incorporations yield the helical organization of the chromophores inside or outside the DNA or RNA double helix depending upon the conjugation of the chromophores. Significant photophysical interactions are observed in the chromophore stacks resulting in unique optical properties that are significantly different from the monomer properties. In this feature article, multichromophore labelled nucleic acids are reviewed with special emphasis on the self-assembly induced modulation of the optical properties.