Dual DNA binding mode of a turn-on red fluorescent probe thiazole coumarin

Spectroscopic studies on noncovalent binding of nicotinamide-modified BRCA1 (856-871) analogs to calf thymus DNA

Various peptide drugs have entered the market with the development of molecular biology. Peptide drugs are used for treat diseases such as diabetes, breast cancer, and HIV infection. In this study, three nicotinamide-modified peptides were synthesized by modifying the N-terminus of BRCA1 (856-871, Y856R, K862Y, R866W) peptide with three nicotinic acid derivatives using solid-phase peptide synthesis. The results of calf thymus DNA (ctDNA) binding activity indicated that binding constants of BRCA1 (856-871, Y856R, K862Y, R866W) (P0) and three nicotinamide-modified peptides (P1, P2, and P3) to ctDNA were 1.89 × 10³, 2.97 × 10⁴, 7.61 × 10⁴, and 8.09 × 10⁴ L·mol^-1, respectively. The binding affinity of the modified peptides was superior to that of BRCA1 (856-871, Y856R, K862Y, R866W). ΔH^θ < 0 and ΔS^θ < 0 indicated that van der Waals force and hydrogen bond contributed most to peptide-ctDNA binding. Results obtained by Circular dichroism (CD) indicated that peptide binding interaction led to conformational changes in ctDNA. Ultraviolet-visible (UV) spectroscopy, ethidium bromide (EB) competition experiments, DNA melting experiments, and viscosity measurements verified that peptides interacted with ctDNA via groove binding. Ionic strength experiments manifested that electrostatic binding was also involved in peptide-ctDNA binding.

Synergistic Antibacterial Effect and Mechanism of Allicin and an Enterobacter cloacae Bacteriophage

Enterobacter cloacae is a troublesome pathogen causing refractory infections of the lower respiratory tract, urethra and abdominal cavity, endocarditis, osteomyelitis, and neonatal septicemia. It is prone to developing resistance to ordinary antibiotics and has brought a serious problem to clinical treatment. An artful synergistic combination of an antibacterial natural product allicin and a newly isolated bacteriophage, named BD523, was constructed herein. This combination significantly lowered effective dosage of allicin and effectually overcame bacterial drug-resistance. We experimentally evidenced that allicin interacts with bacterial DNA in the groove region by inserting itself into the DNA double helix and, subsequently, disrupts the bacterial DNA by cleaving phosphate diester bonds of deoxynucleotides. Further, BD523 destroys the cell wall and membrane of bacteria by synthesizing lyase proteins, including holin and endolysins. Thus, the synergistic effect of the combination benefits from complementary targeting mechanisms of allicin and BD523. They cooperatively act on bacterial DNA, cell wall, and membrane to improve antibacterial efficiency and avoid drug-resistance. IMPORTANCE Bacterial drug-resistance is a serious problem afflicting pharmacologists all over the world. Many strategies have been developed and practiced to overcome it, but almost no one is satisfactory due to the continual change of bacteria. Combinations of antibiotics and bacteriophages are promising because of the cooperation of 2 bacterial killers with distinct mechanisms. The combination of allicin and an Enterobacter cloacae bacteriophage reported herein can significantly improve the effect of allicin against E. cloacae. Its synergistic effect was even superior to the combination of bacteriophage and neomycin, of which the MIC was significantly lower than allicin. It was ascribed to the complementary antibacterial and the possible resistance-proof mechanism of bacteriophage and allicin. This study provided a pragmatic way to conquer the cunning bacterium, and may offer reference for research and development of new bacterial killers.

Förster Resonance Energy Transfer from Carbon Nanoparticles to a DNA-Bound Compound: A Method to Detect the Nature of Binding

A drug molecule can bind in various orientations to a DNA strand. Nature of the binding decides the functionality and efficacy of the drug. To innovate a new method to detect the nature of binding of a drug to DNA strands, herein we have used the dipole-dipole interaction driven Förster resonance energy transfer (FRET) between carbon nanoparticles (CNPs) and a DNA-bound small molecule, (E)-3-ethyl-2-(4-(pyrrolidin-1-yl)styryl)benzo[d]thiazol-3-ium (EPSBT), which belongs to the hemicyanine family and binds typically to the minor groove of a DNA duplex. EPSBT was designed to obtain appreciable fluorescence quantum yield, which constructed an efficient FRET pair with the synthesized CNPs. The tested compound prefers the thymine nucleobase to bind to the DNA strand. Orientation of its dipole on attachment to the DNA strand and the donor-acceptor distance dictate the FRET efficiency with the CNPs. The results provided a precise estimation of the nature of binding of EPSBT to the DNA backbone and, hence, supposedly will help in deciding the functional efficacy.

DNA Minor Groove-Induced cis-trans Isomerization of a Near-Infrared Fluorescent Probe

The discovery of small molecules that exhibit turn-on far-red or near-infrared (NIR) fluorescence upon DNA binding and understanding how they bind DNA are important for imaging and bioanalytical applications. Here we report the DNA-bound structure and the DNA binding mechanism of quinone cyanine dithiazole (QCy-DT), a recently reported AT-specific turn-on NIR fluorescent probe for double-stranded DNA. The nuclear magnetic resonance (NMR)-derived structure showed minor groove binding but no specific ligand-DNA interactions, consistent with an endothermic and entropy-driven binding mechanism deduced from isothermal titration calorimetry. Minor groove binding is typically fast because it minimally perturbs the DNA structure. However, QCy-DT exhibited unusually slow DNA binding. The cyanine-based probe is capable of cis-trans isomerization due to overlapping methine bridges, with 16 possible slowly interconverting cis/trans isomers. Using NMR, density functional theory, and free energy calculations, we show that the DNA-free and DNA-bound environments of QCy-DT prefer distinctly different isomers, indicating that the origin of the slow kinetics is a cis-trans isomerization and that the minor groove preferentially selects an otherwise unstable cis/trans isomer of QCy-DT. Flux analysis showed the conformational selection pathway to be the dominating DNA binding mechanism at low DNA concentrations, which switches to the induced fit pathway at high DNA concentrations. This report of cis/trans isomerization of a ligand, upon binding the DNA minor groove, expands the prevailing understanding of unique discriminatory powers of the minor groove and has an important bearing on using polymethine cyanine dyes to probe the kinetics of molecular interactions.

Luminescent terpyridine appended geminal bisazide and bistriazoles: multinuclear Pt(II) complexes and AIPE-based DNA detection with the naked eye

We report square planar Pt(ii) complexes as luminescent biosensors for DNA detection in solution. The sensing is attributed to the aggregation induced bright red photoluminescence (AIPE) of the complexes in the presence of DNA that can be seen with the naked eye using only a 360 nm light source. Terpyridine appended luminescent geminal bistriazoles (L1-L4, from geminal bisazide A through azide-alkyne 'click' cycloaddition) with versatile chelating sites were explored for metal coordination and reaction with Pt(dmso)2Cl2 yielding tetranuclear and dinuclear complexes of Pt(ii) with different N∩N ligand environments. Thermally stable gem-bisazide and bistriazoles are hardly reported in the literature and this is the first report of terpyridine appended geminal bisazide and bistriazoles.