NDI and DAN DNA: Nucleic Acid-Directed Assembly of NDI and DAN

Two novel DNA base surrogate phosphoramidites <b>1</b> and <b>2</b>, based upon relatively electron-rich 1,5-dialkoxynaphthalene (DAN) and relatively electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (NDI), respectively, were designed, synthesized, and incorporated into DNA oligonucleotide strands. The DAN and NDI artificial DNA bases were inserted within a three-base-pair region within the interior of a 12-mer oligonucleotide duplex in various sequential arrangements and investigated with CD spectroscopy and UV melting curve analysis. The CD spectra of the modified duplexes indicated B-form DNA topology. Melting curve analyses revealed trends in DNA duplex stability that correlate with the known association of DAN and NDI moieties in aqueous solution as well as the known favorable interactions between NDI and natural DNA base pairs. This demonstrates that DNA duplex stability and specificity can be driven by the electrostatic complementarity between DAN and NDI. In the most favorable case, an NDI–DAN–NDI arrangement in the middle of the DNA duplex was found to be approximately as stabilizing as three A–T base pairs

Absorption Properties of a Porous Organic Crystalline Apohost Formed by a Self-Assembled Bis-Urea Macrocycle

We report herein the characterization and binding properties of a microporous crystalline host formed by the self assembly of a bis-urea macrocycle 1. Bis-urea macrocycle 1 has been designed to crystallize into stacked hollow columns. The self-assembly process is guided primarily by hydrogen bonding and aromatic stacking interactions that yield crystals of filled host 1·acetic acid (AcOH). The AcOH guests are bound in the cylindrical cavities of the crystal. The guest AcOH can be removed by heating to form a stable crystalline apohost 1. Apohost 1 displays a type I gas adsorption isotherm with CO2 that is consistent with an open framework microporous material. Apohost 1 binds a range of small molecule guests with specific stoichiometry. The formation of these inclusion complexes does not destroy the crystal framework and therefore apohost 1 can be reused, much like a zeolite. We investigated the structure of apohost 1 and its inclusion complexes by powder X-ray diffraction. The ability of guests to bind and their stoichiometry could be rationalized on the basis of the size, shape, and polarity of the guest molecules. Finally, the shape selectivity of these self-assembled porous materials was demonstrated in competition studies in which apohost 1 preferentially bound p-xylene from a mixture of xylene isomers