Highly sensitive nuclease assay based on chemically-modified DNA or RNA

Nucleolytic enzymes are associated with various diseases, and several methods have been developed for their detection. DNase expression is modulated in such diseases as acute myocardial infarction, transient myocardial ischemia, oral cancer, stomach cancer, and malignant lymphoma, and DNase I is used in cystic fibroma therapy. RNase is used to treat mesothelial cancer because of its antiproliferative, cytotoxic, and antineoplastic activities. Angiogenin, an angiogenic factor, is a member of the RNase A family. Angiogenin inhibitors are being developed as anticancer drugs. In this review, we describe fluorometric and electrochemical techniques for detecting DNase and RNase in disease. Oligonucleotides having fluorescence resonance energy transfer (FRET)-causing chromophores are non-fluorescent by themselves, yet become fluorescent upon cleavage by DNase or RNase. These oligonucleotides serve as a powerful tool to detect activities of these enzymes and provide a basis for drug discovery. In electrochemical techniques, ferrocenyl oligonucleotides with or without a ribonucleoside unit are used for the detection of RNase or DNase. This technique has been used to monitor blood or serum samples in several diseases associated with DNase and RNase and is unaffected by interferents in these sample types

Electrochemical Detection of Duplex DNA Using Intercalation-Triggered Decomplexation of Ferrocene with β-Cyclodextrin

The redox peak of ferrocenylnaphthalene diimide used as a threading intercalator shifted positively due to the formation of its complex with β-cyclodextrin. This complex collapsed upon the addition of double-stranded DNA, and its redox potential shifted negatively. This behavior was applied for the homogenous detection of a polymerase chain reaction (PCR) product from Porphyromonas gingivalis, which is important for the diagnosis of periodontal disease, and its quantitative detection was achieved with a detection limit of 2.7 nM

Electrochemical RNase A Detection Using an Electrode with Immobilized Ferrocenyl Deoxyribooligonucleotide Containing Cytidine Residue

A ferrocenyl deoxyribooligonucleotide (FcODN(rC)) with contiguous cytosine bases and a single ribonucleotide, cytidine, was immobilized on a gold electrode, and this electrode was used to detect RNase A. RNase A activity in a solution was assessed using cyclic voltammetry, and it was found that the current response of the sensor electrode decreased with increasing enzyme concentration. An extremely low detection limit of 1.0×10−11 g mL−1 RNase A was observed, with 15–90 % changes in the current signal. RNase activity can be an indicator of a number of diseases; therefore, this probe has great potential for applications in medical diagnostics

Linker Effect of Ferrocenylnaphthalene Diimide Ligands in the Interaction with Double Stranded DNA

Ferrocenylnaphthalene diimide ligands 1-7 were synthesized by joining a piperazino or N-methylamino linker of the naphthalene diimide skeleton with ferrocenecarboxylic, ferroceneacetic, or ferrocenepropionic parts. Their interaction with double stranded DNA (dsDNA) was studied kinetically and electrochemically. Association rate constants of these ligands were found to correlate with their intramolecular stacking ability between the ferrocene and naphthalene diimide planes: Ligands which can adopt a stacked conformation in buffer solution were unfavorable in the association with dsDNA, resulting in a smaller association rate constant. Dissociation rate constants of these ligands carrying the bulky piperazino linker were smaller than that of those carrying an N-methylamino one. Binding constants were dictated by the balance of these two factors. These ligands were applied to the electrochemical detection of the amount of dsDNA on the electrode. Ligand 6 having the highest affinity for dsDNA gave rise to the largest current increase upon dsDNA formation in the electrochemical hybridization assay

Electrochemical RNase A Detection Using an Electrode with Immobilized Ferrocenyl Deoxyribooligonucleotide Containing Cytidine Residue

A ferrocenyl deoxyribooligonucleotide (FcODN(rC)) with contiguous cytosine bases and a single ribonucleotide, cytidine, was immobilized on a gold electrode, and this electrode was used to detect RNase A. RNase A activity in a solution was assessed using cyclic voltammetry, and it was found that the current response of the sensor electrode decreased with increasing enzyme concentration. An extremely low detection limit of 1.0×10−11 g mL−1 RNase A was observed, with 15–90 % changes in the current signal. RNase activity can be an indicator of a number of diseases; therefore, this probe has great potential for applications in medical diagnostics

Application of naphthalene diimide in biotechnology

Naphthalene diimide (NDI) is an electron-deficient, robust, and planar molecule. These characteristics make it highly applicable to electronic devices that take advantage of their electric character, for imide group-based supramolecular materials that utilize hydrogen bonding, or for sensing materials with a combination of functional groups. Water-soluble NDI binds to a DNA duplex via the threading intercalation mode. Such NDI has enabled the development of unique DNA analytical techniques, functional DNA polymers, and supramolecular polymers. A ferrocene-containing NDI, possessing electrochemically active sites, has been applied to an electrochemical gene detection system and utilized in the precision analysis of genes and single nucleotide polymorphisms. Recently, a DNA quadruplex was identified as one of the noncanonical DNA structures formed by a guanine quartet (G4). The latter serves as one of the control units of gene expression and is associated with cancer development. A stable complex was formed between electron-deficient NDI and the electron-rich G4 planes. Since the G4 stabilizer is recognized as an anticancer agent with relatively few side effects, NDI derivatives may serve as potential candidates for anticancer therapeutics or for designing a unique cancer-detection system

Linker Effect of Ferrocenylnaphthalene Diimide Ligands in the Interaction with Double Stranded DNA

Ferrocenylnaphthalene diimide ligands 1-7 were synthesized by joining a piperazino or N-methylamino linker of the naphthalene diimide skeleton with ferrocenecarboxylic, ferroceneacetic, or ferrocenepropionic parts. Their interaction with double stranded DNA (dsDNA) was studied kinetically and electrochemically. Association rate constants of these ligands were found to correlate with their intramolecular stacking ability between the ferrocene and naphthalene diimide planes: Ligands which can adopt a stacked conformation in buffer solution were unfavorable in the association with dsDNA, resulting in a smaller association rate constant. Dissociation rate constants of these ligands carrying the bulky piperazino linker were smaller than that of those carrying an N-methylamino one. Binding constants were dictated by the balance of these two factors. These ligands were applied to the electrochemical detection of the amount of dsDNA on the electrode. Ligand 6 having the highest affinity for dsDNA gave rise to the largest current increase upon dsDNA formation in the electrochemical hybridization assay

Cooperative Binding of Ferrocenylnaphthalene Diimide Carrying β-Cyclodextrin Converts Double-Stranded DNA to a Rod-Like Structure

Ferrocenylnaphthalene diimide carrying β-cyclodextrin (β-CD), 1, intercalated into double-stranded DNA with a binding affinity of K = (6.6 ± 0.8) × 104 M–1 and a binding site size of n = 4, with a high positive cooperative parameter of ω = 14. β-CD and ferrocene moieties of the compound contributed to the formation of the intermolecular inclusion complex on DNA. Binding of 1 resulted in conversion of the DNA duplex to a rod-like form, which was cleaved upon adamantylamine addition

Ferrocenyl naphthalene diimides as tetraplex DNA binders

Seven ferrocenyl naphthalene diimide (FND) ligands were synthesized. Each had a higher affinity for tetraplex DNA than for either single- or double-stranded DNA. The FND binding affinities were > 105 M− 1 in 0.10 M AcOH-AcONa or AcOH-AcOK (pH 5.5) containing 0.10 M NaCl or KCl. The FNDs with the highest binding affinities for tetraplex DNA showed 23- or 8-times higher preference for tetraplex DNA than for single- or double-stranded DNA, respectively. The current signals generated from the seven FNDs bound to the tetraplex DNA immobilized on the electrode were found to correlate with the binding affinities of these ligands for the tetraplex DNA. Furthermore, using the telomerase repeat amplification protocol assay, the FND ligands could be categorized into three groups: (a) inhibiting both telomerase and Taq polymerase, (b) inhibiting telomerase alone, and (c) inhibiting neither telomerase nor Taq polymerase

Naphthalene diimide carrying two cysteine termini at both imide linkers as a molecular staple

Naphthalene diimide (1) carrying cysteines at the termini of amide substituents were synthesized to act as a molecular staple of double stranded DNA. Since 1 is able to bind to double stranded DNA with threading intercalation, the complex of 1 with double stranded DNA can be topologically immobilized on a gold surface through the S[BOND]Au linkage as confirmed by cyclic voltammetric experiment. Ferrocenyl-double stranded 23-mertic oligonucleotide, dsFcODN, was immobilized on gold electrode with 1.0×1012 molecules cm−2 when electrode was treated with 2.0 µM dsFcODN and 4.0 µM 1 for 1 h at room temperature. The coverage density was similar to that obtained for the terminal thiol-modified oligonucleotide. Compound 1 was applied to detect the 321-meric PCR product of P. gingivalis, which is important in the diagnosis of periodontal disease. This experiment, coupled with the use of ferrocenylnaphthalene diimide, FND as electrochemical indicator for double stranded DNA, resulted in quantitative detection of PCR product within the range of 10 pg µL−1–10 ng µL−1 (15 nM–15 µM). The 1 and FND established a simple and rapid detection method of double stranded PCR product with a detection limit of 10 pg µL−1 (15 nM)