betadex and naphthalenediimide

An electrochemical DNA detection format has been developed to allow simple and rapid assays with downsized instruments. Since naphthalene diimide derivatives are known to bind to double stranded DNA (dsDNA) with threading intercalation, they are stabilized by pseudo-catenane formation. For example, ferrocenylnaphthalene diimide (FND) can be efficiently concentrated on dsDNA, thus enabling its electrochemical detection. Since dsDNA is formed between single stranded target DNA and DNA probe, the target DNA can be detected electrochemically, using DNA probe-immobilized on the electrode. Further stabilization of naphthalene diimide derivatives as a complex with dsDNA on the electrode is expected to lead to more precise and selective detection of target DNA. This approach was realized by the formation of inclusion complexes of ferrocene with β-cyclodextrin (β-CD) for the FND-dsDNA complexes on the electrode. Combination of adamantylnaphthalene diimide (AND) and ferrocenyl-β-CD (Fc-CD) gave new supramolecular DNA detection assays coupled with DNA probe-immobilized electrodes. The electrochemical signal increased only upon formation of the Fc-CD/AND complex bound to dsDNA on the electrode. Naphthalene diimide carrying ferrocene and β-CD realized "signal on" type detection of dsDNA in homogenous solution. Naphthalene diimide carrying two dithiolene termini provided a new method to immobilize dsDNA on the gold electrode that may be suitable for the electrochemical detection of target DNA.

Topics: beta-Cyclodextrins; DNA; Electrochemistry; Electrodes; Imides; Intercalating Agents; Naphthalenes

Newly synthesized naphthalene diimide carrying two β-cyclodextrins (NDI-β-CyDs) showed improved specificity for the parallel G-quadruplex structure alongside the hybrid G-quadruplex structure. Specifically, the highest binding affinity of NDI-β-CyDs for the telomere RNA G-quadruplex was observed. The binding simulation indicated that β-cyclodextrins might be available for loop nucleobase inclusion under its complex.

Topics: beta-Cyclodextrins; G-Quadruplexes; Imides; Ligands; Naphthalenes; RNA; Telomere

Naphthalene diimide 1 bearing ferrocene and β-cyclodextrin (β-CD) was prepared. Its half-wave potential at 420 mV shifted 40-50 mV upon addition of an excess of adamantylamine, suggesting that the ferrocene of 1 is included in the cavity of β-CD intramolecularly to form a pseudocyclic structure. This unique architecture is retained even where 1 is bound to calf thymus DNA to give rise to a catenane-like structure. Morphology of the DNA complex with 1 was further explored by atomic force microscopy to reveal that the DNA strand tends to bend as the amount of 1 on it increases. Presumably, intermolecular, yet intrastrand, inclusion of ferrocene into β-CD is responsible for this phenomenon. The resulting globular structure reverted partially by the addition of adamantylamine. At a low ratio of 1 to DNA, a novel reduction peak appeared at 320 mV in the differential pulse voltammograms of 1 at the expense of the 420 mV peak. The peak current of the former was proportional to the DNA concentration, thereby enabling quantitation of DNA in a signal-on way. Likewise, a polymerase chain reaction (PCR) product of 754 bp was analyzed successfully with a detection limit of 13 nM.

Topics: Animals; beta-Cyclodextrins; Biosensing Techniques; Cattle; DNA; Electrochemical Techniques; Ferrous Compounds; Imides; Macromolecular Substances; Metallocenes; Molecular Structure; Naphthalenes

The adamantyl moieties of adamantylnaphthalene diimide (AND) can be incorporated into the cavity of ferrocenyl-beta-cyclodextrin even where they are bound to double stranded DNA by threading intercalation. When this ternary complex is formed on the DNA probe-immobilized electrode, electrochemical DNA detection is feasible: the electrode hybridized with target DNA gave rise to a current peak corresponding to the ferrocene oxidation upon treatment with AND and ferrocenyl-beta-cyclodextrin (Fc-beta-CD).

Topics: Adamantane; beta-Cyclodextrins; DNA; Electrochemistry; Electrodes; Ferrous Compounds; Genes; Gold; Hydrogen-Ion Concentration; Imides; Metallocenes; Naphthalenes; Phenanthrolines