DNA triple helix stabilisation by a naphthylquinoline dimer

Modulation of DNA structure formation using small molecules

Genome integrity is essential for proper cell function such that genetic instability can result in cellular dysfunction and disease. Mutations in the human genome are not random, and occur more frequently at "hotspot" regions that often co-localize with sequences that have the capacity to adopt alternative (i.e. non-B) DNA structures. Non-B DNA-forming sequences are mutagenic, can stimulate the formation of DNA double-strand breaks, and are highly enriched at mutation hotspots in human cancer genomes. Thus, small molecules that can modulate the conformations of these structure-forming sequences may prove beneficial in the prevention and/or treatment of genetic diseases. Further, the development of molecular probes to interrogate the roles of non-B DNA structures in modulating DNA function, such as genetic instability in cancer etiology are warranted. Here, we discuss reported non-B DNA stabilizers, destabilizers, and probes, recent assays to identify ligands, and the potential biological applications of these DNA structure-modulating molecules.

Synthesis of novel 1,10-phenanthroline derivatives and it used as probes for sensitive detection of Zn2+ and Cd2+ metal ions - Spectroscopic and theoretical approach

A novel class of unexpected 1,10-phenanthrolinederivatives were synthesized from 2,3-dihydroacridin-4(1H)-ones with 3-aminonaphthalen-2-carboxylic acid in presence of phosphorus oxychloride at 130°C and simple perceptive emission intensity increasing assay was developed effectively to detect the very low concentrations of Zn²⁺ and Cd²⁺ ions. Emission intensity of compounds 3(a-c) directly related to the concentrations of Zn²⁺ and Cd²⁺ ions was due to metal chelating enhanced fluorescence (CHEF) effect and also its further validated by fluorescence lifetime measurement. Furthermore, the sensing mechanism for compounds 3(a-c) of Zn²⁺ and Cd²⁺ were sustained by theoretical calculations. Computational analysis results reveals that compounds 3(a-c) are more interested in Zn²⁺ ions than that of Cd²⁺ ions, while, compound 3c is more interested with Zn²⁺ and Cd²⁺ ions than those of the rest of the compounds. In addition, this proposed detection analysis has the direct application for monitoring Zn²⁺ and Cd²⁺ concentrations in tap and drinking water samples.

Preferential binding of anticancer drugs to triplex DNA compared to duplex DNA: a spectroscopic and calorimetric study

Binding study of adriamycin and actinomycin to triplex DNA formed on the promoter region of hmgb1 gene using spectroscopic and calorimetric technique.

Biophysical insight into the interaction of the bioflavonoid kaempferol with triple and double helical RNA and the dual fluorescence behaviour of kaempferol

Binding of kaempferol with triple and double helical RNA.

Synthesis of quinolines and acridines by the reaction of 2-(perfluoroalkyl)anilines with lithium and Grignard reagents

This review summarizes the synthesis of quinolines and acridines by the reactions of anionically activated 2-(perfluoroalkyl)anilines. Mechanistic studies including isolation of the intermediate aza-ortho-xylylene are discussed.

Iron/acetic acid mediated synthesis of 6,7-dihydrodibenzo[b,j][1,7]phenanthroline derivatives via intramolecular reductive cyclization

An efficient iron/acetic acid mediated intramolecular reductive cyclization protocol was developed for the synthesis of novel 6,7-dihydrodibenzo[b,j][1,7]phenanthroline derivatives.

Discovery of novel triple helical DNA intercalators by an integrated virtual and actual screening platform

Virtual Screening is an increasingly attractive way to discover new small molecules with potential medicinal value. We introduce a novel strategy that integrates use of the molecular docking software Surflex with experimental validation by the method of competition dialysis. This integrated approach was used to identify ligands that selectively bind to the triplex DNA poly(dA)-[poly(dT)]₂. A library containing ∼2 million ligands was virtually screened to identify compounds with chemical and structural similarity to a known triplex intercalator, the napthylquinoline MHQ-12. Further molecular docking studies using compounds with high structural similarity resulted in two compounds that were then demonstrated by competition dialysis to have a superior affinity and selectivity for the triplex nucleic acid than MHQ-12. One of the compounds has a different chemical backbone than MHQ-12, which demonstrates the ability of this strategy to ‘scaffold hop’ and to identify small molecules with novel binding properties. Biophysical characterization of these compounds by circular dichroism and thermal denaturation studies confirmed their binding mode and selectivity. These studies provide a proof-of-principle for our integrated screening strategy, and suggest that this platform may be extended to discover new compounds that target therapeutically relevant nucleic acid morphologies.

Extended ethidium bromide analogue as a triple helix intercalator: synthesis, photophysical properties and nucleic acids binding

Ethidium bromide has been extended by fusing an additional aromatic ring resulting in a larger intercalator with increased affinity for poly r(A) x r(U), poly d(A) x d(T) and triple helices when compared to the parent heterocycle.

New triple-helix DNA stabilizing agents

Several substituted quinolin-4-amines and heteroaromatic analogs were synthesized and evaluated for interaction with triplex polydA.2polydT and duplex polydA.polydT by using UV-thermal melting experiments. Excellent triple-helix DNA ligands with high affinity toward T.A.T triplets and triple/duplex selectivity were designed through a rational approach.

Triplex selective 2-(2-naphthyl)quinoline compounds: origins of affinity and new design principles

A novel competition dialysis assay was used to investigate the structural selectivity of a series of substituted 2-(2-naphthyl)quinoline compounds designed to target triplex DNA. The interaction of 14 compounds with 13 different nucleic acid sequences and structures was studied. A striking selectivity for the triplex structure poly dA:[poly dT](2) was found for the majority of compounds studied. Quantitative analysis of the competition dialysis binding data using newly developed metrics revealed that these compounds are among the most selective triplex-binding agents synthesized to date. A quantitative structure-affinity relationship (QSAR) was derived using triplex binding data for all 14 compounds used in these studies. The QSAR revealed that the primary favorable determinant of triplex binding free energy is the solvent accessible surface area. Triplex binding affinity is negatively correlated with compound electron affinity and the number of hydrogen bond donors. The QSAR provides guidelines for the design of improved triplex-binding agents.

Bis-4-aminoquinolines: novel triple-helix DNA intercalators and antagonists of immunostimulatory CpG-oligodeoxynucleotides

Six dimeric 2-(2-naphthyl)quinolin-4-amines with a linker between the amino groups and eight dimeric 2-(4-anilino)quinolin-4-amines linked between the anilino groups were synthesized and evaluated for their interaction with duplex/triplex DNA's and as antagonists of immunostimulatory oligodeoxynucleotides with a CpG-motif (CpG-ODN). The most powerful triple-helix DNA intercalator known to date, with high affinity toward T.A.T triplets and triplex/duplex selectivity, was found. The potent antagonism of immunostimulatory CpG-ODN by several bis-4-aminoquinolines is not related to their DNA interactions.

Stability of DNA triplexes on shuttle vector plasmids in the replication pool in mammalian cells

Triple helix-forming oligonucleotides may be useful as gene-targeting reagents in vivo, for applications such as gene knockout. One important property of these complexes is their often remarkable stability, as demonstrated in solution and in cells following transfection. Although encouraging, these measurements do not necessarily report triplex stability in cellular compartments that support DNA functions such as replication and mutagenesis. We have devised a shuttle vector plasmid assay that reports the stability of triplexes on DNA that undergoes replication and mutagenesis. The assay is based on plasmids with novel variant supF tRNA genes containing embedded sequences for triplex formation and psoralen cross-linking. Triple helix-forming oligonucleotides were linked to psoralen and used to form triplexes on the plasmids. At various times after introduction into cells, the psoralen was activated by exposure to long wave ultraviolet light (UVA). After time for replication and mutagenesis, progeny plasmids were recovered and the frequency of plasmids with mutations in the supF gene determined. Site-specific mutagenesis by psoralen cross-links was dependent on precise placement of the psoralen by the triple helix-forming oligonucleotide at the time of UVA treatment. The results indicated that both pyrimidine and purine motif triplexes were much less stable on replicated DNA than on DNA in vitro or in total transfected DNA. Incubation of cells with amidoanthraquinone-based triplex stabilizing compounds enhanced the stability of the pyrimidine triplex.