Study by optical spectroscopy and molecular dynamics of the interaction of acridine-spermine conjugate with DNA

Investigation on the interaction of Safranin T with anionic polyelectrolytes by spectrophotometric method

Understanding the role played by chemical additives such as NaCl salt, acid and Cetylpyridinium Chloride (CPC) surfactant on the interaction between dye and polyelectrolyte contributes to optimization of processes using polyelectrolytes in the removal of dye from aqueous solution. Herein we focus in the interaction between Safranin T, a cationic dye, with two anionic polyelectrolytes, poly(ammonium acrylate) and poly(acrylic acid) using spectrophotometric method and conductivity measurement. In aqueous solution, each of anionic polyelectrolytes forms a complex with the dye and induces a metachromasy indicated by the blue shift of the absorbance of the dye. The stoichiometry of complexes evaluated by the molar ratio method are 1:1 for Safranin T poly(ammonium acrylate) and 2:1 in the case of Safranin T poly(acrylic acid). The effect of additives on the stability of complexes has been studied by varying concentrations of the salt and the surfactant and pH of the solution. The thermodynamic parameters of interaction ΔG, ΔH and ΔS at different temperatures were evaluated to determine the stability constant of the complexes.

In silico studies toward understanding the interactions of DNA base pairs with protonated linear/cyclic diamines

Protonated amino groups are ubiquitous in nature and important in the fields of chemistry and biology. In search of efficient polyamine analogues, we have performed DFT calculations on the interactions of some simple cyclic and constrained protonated diamines with the DNA base pairs and compared the results with those obtained for the corresponding interactions involving linear diamines, which mimic biogenic polyamines such as spermine. The interactions are mainly governed by the strong hydrogen bonding between the ligand and the DNA base pairs. The DFT calculations suggest that the major-groove N7 interaction (GC base pair) with linear diamine is energetically more favored than other possible interactions, as reported with spermine. The cyclic diamines exhibited better interactions with the N7 site of the AT and GC base pairs of DNA than the linear diamines. The net atomic charges calculated for the protonated amine hydrogens were higher for the cyclic systems than for the linear diamines, inducing better binding affinity with the DNA base pairs. The stable conformers of cyclic diamines were predicted using the MP2/aug-cc-pVDZ level of theory. The positions of the protonated diamine groups in these cyclic systems are crucial for effective binding with the DNA base pairs. The DFT-calculated results show that diequatorial (ee) 1,2-cyclohexadiamine (CHDA) is a promising candidate as a polyamine analogue for biogenic polyamines. Molecular dynamics simulations were performed using explicit water molecules for the interaction of representative ligands with the DNA base pairs to examine the influence of solvent molecules on such interactions.

A novel CUG(exp)·MBNL1 inhibitor with therapeutic potential for myotonic dystrophy type 1

Myotonic dystrophy type 1 (DM1) is caused by an expanded CUG repeat (CUG(exp)) that sequesters muscleblind-like 1 protein (MBNL1), a protein that regulates alternative splicing. CUG(exp) RNA is a validated drug target for this currently untreatable disease. Herein, we develop a bioactive small molecule (1) that targets CUG(exp) RNA and is able to inhibit the CUG(exp)·MBNL1 interaction in cells that model DM1. The core of this small molecule is based on ligand 2, which was previously reported to be active in an in vitro assay. A polyamine-derivative side chain was conjugated to this core to make it aqueous-soluble and cell-penetrable. In a DM1 cell model this conjugate was found to disperse CUG(exp) ribonuclear foci, release MBNL1, and partially reverse the mis-splicing of the insulin receptor pre-mRNA. Direct evidence for ribonuclear foci dispersion by this ligand was obtained in a live DM1 cell model using time-lapse confocal microscopy.

Identification of ligands for the Tau exon 10 splicing regulatory element RNA by using dynamic combinatorial chemistry

We describe the use of dynamic combinatorial chemistry (DCC) to identify ligands for the stem-loop structure located at the exon 10-5'-intron junction of Tau pre-mRNA, which is involved in the onset of several tauopathies including frontotemporal dementia with Parkinsonism linked to chromosome 17 (FTDP-17). A series of ligands that combine the small aminoglycoside neamine and heteroaromatic moieties (azaquinolone and two acridines) have been identified by using DCC. These compounds effectively bind the stem-loop RNA target (the concentration required for 50% RNA response (EC(50)): 2-58 μM), as determined by fluorescence titration experiments. Importantly, most of them are able to stabilize both the wild-type and the +3 and +14 mutated sequences associated with the development of FTDP-17 without producing a significant change in the overall structure of the RNA (as analyzed by circular dichroism (CD) spectroscopy), which is a key factor for recognition by the splicing regulatory machinery. A good correlation has been found between the affinity of the ligands for the target and their ability to stabilize the RNA secondary structure.

Accurate measurements of protein interactions in cells via improved spatial image cross-correlation spectroscopy

The sensitive detection of protein interactions in living cells is an important first step toward understanding each of the multitude of cellular processes that are regulated by such interactions. Spatial image cross-correlation spectroscopy (ICCS) is one method used to measure protein-protein interactions from the analysis of two-channel fluorescence microscopy images. In spatial ICCS, cross-correlation of fluctuations in fluorescence intensity recorded as images from two independent wavelength detection channels in a fluorescence microscope is used to determine the average number of interacting particles in the imaged region. Even in situations where the particle number density is relatively high, ICCS provides an accurate measure of molecular interactions. However, it was shown previously that the method suffers from relatively high detection limits of interacting particles (approximately 20%) and can be perturbed by heterogeneous spatial distributions of the fluorescent particles within the images. Here, we demonstrate new approaches to circumvent some of the limitations of ICCS. Spatial scrambling of pixel blocks within fluorescence images was investigated as a way of extending the detection of spatial ICCS to measure lower interaction fractions as well as colocalization within cells. We also show that 'mean-intensity-padding' of regions of interest within fluorescence images is a feasible method of applying ICCS to arbitrarily selected areas of the cell with boundaries or edge morphologies that would be impossible to analyze with conventional ICCS. Using these newly developed strategies we were able to measure the fraction of actin that interacts with alpha-actinin in the leading edge of a migrating cell.