DNA interactive property of poly-L-lysine induces apoptosis in MCF-7 cells through DNA interaction.

Poly-L-lysine (PLL) is known to be an encapsulating agent in drug formulation and delivery. PLL also has apoptotic and antiproliferative activities that enable blocking of the tumorigenesis process. However, the dose-selective activities of PLL in exerting apoptosis against cancer are unclear. Therefore, this study has been designed to explore the potential role and dose of PLL in apoptosis, if any. For this, PLL was administered at several doses in cancer cell lines and was found to be more potent against MCF-7 cells. PLL causes mitochondria-mediated apoptotic death through the upregulation of cleaved caspase-3. To investigate the mechanism responsible for this activity, we have analyzed if PLL could have the DNA interactive property or not. For this, molecular docking analysis was carried out to prove whether it has the property to bind with DNA or not. Studies have revealed that PLL is a potent DNA binder and it probably performs such apoptotic activities through the binding of cellular DNA early in an exposure. Simultaneous upregulation of both ROS-mediated stress and also in key protein expressions like Î³-H2AX could also help us to confirm that PLL induces apoptosis through DNA interaction. This finding leads us to believe that PLL could play an interfering role with other chemotherapeutic compounds when used as a drug-coating material as it exerts an apoptotic effect on cancer cells, which should be avoided by using a much lower concentration.

Orientation preferences of hairpin pyrrole-imidazole polyamides toward mCGG site.

Hairpin pyrrole-imidazole (Py-Im) polyamides are promising medium-sized molecules that bind sequence-specifically to the minor groove of B-form DNA. Here, we synthesized a series of hairpin Py-Im polyamides and explored their binding affinities and orientation preferences to methylated DNA with the mCGG target sequence. Thermal denaturation assays revealed that the five hairpin Py-Im polyamides, which were anticipated to recognize mCGG in a forward orientation, bind to nontarget DNA, GGmC, in a reverse orientation. Therefore, we designed five Py-Im polyamides that could recognize mCGG in a reverse orientation. We found that the two Py-Im polyamides containing Im/ß pairs preferentially bound to mCGG in a reverse orientation. The reverse binding Py-Im polyamide successfully inhibited TET1 binding on the methylated DNA. Taken together, this study illustrated the importance of designing reverse binding Py-Im polyamides for the target sequence, mCGG, which paved the way for Py-Im polyamides that can be used with otherwise difficult to access DNA with CG sequences.

Optical DNA Biosensor Based on Square-Planar Ethyl Piperidine Substituted Nickel(II) Salphen Complex for Dengue Virus Detection.

A sensitive and selective optical DNA biosensor was developed for dengue virus detection based on novel square-planar piperidine side chain-functionalized N,N'-bis-4-(hydroxysalicylidene)-phenylenediamine-nickel(II), which was able to intercalate via nucleobase stacking within DNA and be functionalized as an optical DNA hybridization marker. 3-Aminopropyltriethoxysilane (APTS)-modified porous silica nanospheres (PSiNs), was synthesized with a facile mini-emulsion method to act as a high capacity DNA carrier matrix. The Schiff base salphen complexes-labelled probe to target nucleic acid on the PSiNs renders a colour change of the DNA biosensor to a yellow background colour, which could be quantified via a reflectance transduction method. The reflectometric DNA biosensor demonstrated a wide linear response range to target DNA over the concentration range of 1.0 × 10-16-1.0 × 10-10 M (R² = 0.9879) with an ultralow limit of detection (LOD) at 0.2 aM. The optical DNA biosensor response was stable and maintainable at 92.8% of its initial response for up to seven days of storage duration with a response time of 90 min. The reflectance DNA biosensor obtained promising recovery values of close to 100% for the detection of spiked synthetic dengue virus serotypes 2 (DENV-2) DNA concentration in non-invasive human samples, indicating the high accuracy of the proposed DNA analytical method for early diagnosis of all potential infectious diseases or pathological genotypes.

Cyclic ferrocenylnaphthalene diimide derivative as a new class of G-quadruplex DNA binding ligand.

To identify an effective ligand that binds to a G-quadruplex structure but not a double-stranded DNA (dsDNA), a set of biophysical and biochemical experiments were carried out using newly synthesized cyclic ferrocenylnaphthalene diimide (cFNDI, 1) or the non-cyclic derivative (2) with various structures of G-quadruplex DNAs and dsDNA. Compound 1 bound strongly to G-quadruplexes DNAs (106M-1 order) with diminished binding to dsDNA (104M-1 order) in 100mM AcOH-AcOK buffer (pH 5.5) containing 100mM KCl. Interestingly, 1 showed an approximately 50-fold higher selectivity to mixed hybrid-type telomeric G-quadruplex DNA (K=3.4×106M-1 and a 2:1 stoichiometry) than dsDNA (K=7.5×104M-1) did. Furthermore, 1 showed higher thermal stability to G-quadruplex DNAs than it did to dsDNA with a preference for c-kit and c-myc G-quadruplex DNAs over telomeric and thrombin binding aptamers. Additionally, 1 exhibited telomerase inhibitory activity with a half-maximal inhibitory concentration (IC50) of 0.4µM. Compound 2 showed a preference for G-quadruplex; however, the binding affinity magnitude and preference were improved in 1 because the former had a cyclic structure.

Sequence-specific DNA binding by long hairpin pyrrole-imidazole polyamides containing an 8-amino-3,6-dioxaoctanoic acid unit.

With the aim of improving aqueous solubility, we designed and synthesized five N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides capable of recognizing 9-bp sequences. Their DNA-binding affinities and sequence specificities were evaluated by SPR and Bind-n-Seq analyses. The design of polyamide 1 was based on a conventional model, with three consecutive Py or Im rings separated by a ß-alanine to match the curvature and twist of long DNA helices. Polyamides 2 and 3 contained an 8-amino-3,6-dioxaoctanoic acid (AO) unit, which has previously only been used as a linker within linear Py-Im polyamides or between Py-Im hairpin motifs for tandem hairpin. It is demonstrated herein that AO also functions as a linker element that can extend to 2-bp in hairpin motifs. Notably, although the AO-containing unit can fail to bind the expected sequence, polyamide 4, which has two AO units facing each other in a hairpin form, successfully showed the expected motif and a KD value of 16nM was recorded. Polyamide 5, containing a ß-alanine-ß-alanine unit instead of the AO of polyamide 2, was synthesized for comparison. The aqueous solubilities and nuclear localization of three of the polyamides were also examined. The results suggest the possibility of applying the AO unit in the core of Py-Im polyamide compounds.

Novel indole-thiazole and indole-thiazolidinone derivatives as DNA groove binders.

In this study, we report the synthesis of eight novel indole-thiazole and indole-thiazolidinone derivatives, as well as their ability to interact with DNA, analysed through the UV-vis absorption, fluorescence, circular dichroism (CD), viscosity techniques and molecular docking. The ctDNA interaction analysis demonstrated different spectroscopic effects and the affinity constants (Kb) calculated by the UV-vis absorption method were between 2.08 × 105 and 6.99 × 106 M-1, whereas in the fluorescence suppression constants (Ksv) ranged between 0.38 and 0.77 × 104 M-1 and 0.60-7.59 × 104 M-1 using Ethidium Bromide (EB) and 4',6-Diamidino-2-phenylindole (DAPI) as fluorescent probes, respectively. Most derivatives did not alter significantly the secondary structure of the ctDNA according to the CD results. None of the compounds was able to change the relative viscosity of the ctDNA. These results prove that compounds interact with ctDNA via groove binding, which was confirmed by A-T rich oligonucleotide sequence assay with compound JF-252, suggesting the importance of both the phenyl ring coupled to C-4 thiazole ring and the bromo-unsubstituted indole nucleus.

An insight into DNA binding properties of newly designed cationic δ,δ'­diazacarbazoles: Spectroscopy, AFM imaging and living cells staining studies.

Two cationic δ,δ'­diazacarbazoles, 1­Methyl­5H­pyrrolo[3,2­b:4,5­b']dipyridinium iodide (MPDPI) and 1,5­Dimethyl­5H­pyrrolo[3,2­b:4,5­b']dipyridinium iodide (DPDPI), were devised and synthesized. Through characterizations of the interactions between DNA and the two δ,δ'­diazacarbazoles by various spectroscopy means, the strong interactions between the two compounds and double-strand DNA have been observed and the interaction types and mechanisms were explored. UV-Vis and fluorescent data have shown the big changes of DNA in the presence of either of the two compounds, demonstrating that both of the δ,δ'­diazacarbazoles can bind to DNA tightly, and high ionic strength decreased the intercalative interactions. The UV-Vis and fluorescence of dsDNA in the presence of DPDPI showed more profound changes than those in the presence of MPDPI, due to CH3 (in the structure of DPDPI) taking place of H (in the structure of MPDPI) at the position of 5­NH. And the circular dichroism (CD) spectra of CT-DNA and atomic force microscopy (AFM) results indicated more compacted conformation of DNA in the presence of DPDPI than MPDPI, implying that DPDPI has a more significant effect on DNA conformations than MPDPI. Most interestingly, fluorescence enhancement of cationic δ,δ'­diazacarbazoles occurred in the presence of DNA. With ionic strength increasing, the intercalative interactions between δ,δ'­diazacarbazoles and DNA were weakened, but δ,δ'­diazacarbazoles-DNA complexes showed enhanced fluorescence, which indicated that there are other interactions present at high ionic strength. Furthermore, laser confocal fluorescence microscopy results proved that DPDPI was membrane-permeable and stained living cells.