DNA-interacting Molecules Research Articles

Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules.

Due to the central role of DNA, its interactions with inorganic salts and small organic molecules are important. For example, such interactions play important roles in various fundamental cellular processes in living systems and are involved in many DNA-damage related diseases. Strategies to improve the sensitivity of existing techniques for studying DNA interactions with other molecules would be appreciated in situations where the interactions are too weak. Here we report our development and demonstration of bent DNA bows for amplifying, sensing, and detecting the interactions of 14 inorganic salts and small organic molecules with DNA. With the bent DNA bows, these interactions were easily visualized and quantified in gel electrophoresis, which were difficult to measure without bending. In addition, the strength of the interactions of DNA with the various salts/molecules were quantified using the modified Hill equation. This work highlights the amplification effects of the bending elastic energy stored in the DNA bows and the potential use of the DNA bows for quantitatively measuring DNA interactions with small molecules as simple economic methods; it may also pave the way for exploiting the bent DNA bows for other applications such as screening DNA-interacting molecules and drugs.

Nuclear proteins: finding and binding target sites in chromatin

Fluorescent protein labelling, as well as impressive progress in live cell imaging have revolutionised the view on how essential nuclear functions like gene transcription regulation and DNA repair are organised. Here, we address questions like how DNA-interacting molecules find and bind their target sequences in the vast amount of DNA. In addition, we discuss methods that have been developed for quantitative analysis of data from fluorescence recovery after photobleaching experiments (FRAP).

DNA‐Destabilizing Agents as an Alternative Approach for Targeting DNA: Mechanisms of Action and Cellular Consequences

DNA targeting drugs represent a large proportion of the actual anticancer drug pharmacopeia, both in terms of drug brands and prescription volumes. Small DNA-interacting molecules share the ability of certain proteins to change the DNA helix's overall organization and geometrical orientation via tilt, roll, twist, slip, and flip effects. In this ocean of DNA-interacting compounds, most stabilize both DNA strands and very few display helix-destabilizing properties. These types of DNA-destabilizing effect are observed with certain mono- or bis-intercalators and DNA alkylating agents (some of which have been or are being developed as cancer drugs). The formation of locally destabilized DNA portions could interfere with protein/DNA recognition and potentially affect several crucial cellular processes, such as DNA repair, replication, and transcription. The present paper describes the molecular basis of DNA destabilization, the cellular impact on protein recognition, and DNA repair processes and the latter's relationships with antitumour efficacy.

The hollow fibre model - facilitating anti-cancer pre-clinical pharmacodynamics and improving animal welfare

We describe a modified hollow fibre assay (HFA) for investigating the potential of novel molecules as pharmaceutical agents. In particular the assay provides drug/target interaction data that can facilitate the selection of lead compounds for further evaluation in more sophisticated solid tumour models, whilst successfully implementing the 3Rs - the 'replacement' 'refinement' and 'reduction' of animals. This more ethical and rapid approach to early drug development does not compromise on the validity, sensitivity, predictivity or efficacy of preclinical evaluation. We present novel data using the standard cross-linker mitomycin C (MMC) as a positive control, and two investigational DNA interactive molecules (C1311/ SJG-136). Tumour cells were seeded in fibres and implanted into mice. Following treatment with an intraperitoneal injection, fibres were excised and cells retrieved for pharmacodynamic analysis using the comet assay/fluorescence microscopy. Microscopy results revealed nuclear uptake and localisation within cytoplasmic organelles of HT29 colorectal adenocarcinoma cells following treatment with C1311 (150 mg/kg). Following treatment with SJG-136 (0.3 mg/kg) a 27.3% (p<0.001) DNA cross-linking (s.c.) effect was observed in the HL60 acute promyelocytic leukaemia cell line. DNA cross-linking effects of 55% (i.p) and 50% (s.c.) (p<0.005) were observed in the A549 lung carcinoma cell line following administration of MMC (6 mg/kg). These data are consistent with previous activity defined using solid tumour models, and support the use of the HFA for in vivo pharmacodynamic investigation whilst significantly reducing animal numbers and the influence of tumour growth on the welfare of mice.

Does it bind? An instant binding assay for DNA oligonucleotide interactive small molecules

Ultrafiltration analysis has been used to screen DNA oligonucleotide interactive small molecules for the first time, providing an almost instantaneous indication of the binding affinity, and was used to identify a new class of DNA interactive molecules based on a range of dihydro-imidazo-phenanthridinium-based framework; this methodology provides a straightforward yes/no answer to small molecule DNA binding.

Novel DNA Interacting Molecules with Potentially Two Mode Binding Ability.

The binding study and spectral behavior of novel DNA interacting dyes, bis(vinylpyridinium) benzene derivatives, are reported. Implantation of a extended π-electron moiety into a viologen molecule has lead to the preparation of a series of dicationic dyes with fluorescent properties and potential capability of interacting with DNA by both groove binding and intercalation mode. Drug-DNA interactions were investigated by UV-VIS absorption and fluorescence titration, and circular dichroism measurements. There were no clear isosbestic points in titration data which suggested complex interaction of drugs with DNA. As a tentative explanation of these results, we believe that dye molecules aggregate or intercalate with DNA at lower P/D ratios (DNA to dye concentration) and undergo redistribution in the minor groove at higher P/D ratios. The groove binding mode was supported by presence of induced CD spectra of dyes in the presence of AT sequence containing oligonucleotides. The most pronounced groove binding was observed for the curved m-bis(vinylpyridinium) benzene derivative. Such bimodal behavior may be of great importance for the further application of dyes since DNA sequence selectivity can also serve as valuable tool for the development of base selective DNA probing methods.