Simultaneous binding of minor groove binder and intercalator to dodecamer DNA: importance of relative orientation of donor and acceptor in FRET

Host-assisted delivery of a model drug to genomic DNA: Key information from ultrafast spectroscopy and in silico study

Intended drug delivery to a target without adverse effect is one of the major criteria for its acceptance in real use. Herein, we have made an attempt to explore the delivery efficacy of SDS surfactant in a monomer and micellar stage during the delivery of model drug, Toluidine Blue (TB) from micellar cavity to DNA. Molecular recognition of pre-micellar SDS encapsulated TB with DNA occurs at a rate constant (k1~652 s-1). On the contrary, no significant release of encapsulated TB at micellar concentration was observed within the experimental time frame. This originated from the higher binding affinity of TB towards the nano cavity of SDS at micellar concentration which doesn't allow the delivery of TB from the nano cavity of SDS micelle to DNA. Thus, molecular recognition controls the extent of DNA recognition by TB which in turn modulates the rate of delivery of TB from SDS in a concentration dependent morphology.

Preferential Binding of Thioflavin T to AT-Rich DNA: White Light Emission through Intramolecular Förster Resonance Energy Transfer

Herein we report the effect of different nucleobase pair compositions on the association-induced fluorescence enhancement property of Thioflavin T (ThT), upon binding with 20 base pair long double-stranded DNA (dsDNA). Analysis of binding and decay constants along with the association (K_ass) and dissociation (K_diss) rate constants obtained from the fluctuation in the fluorescence intensity of ThT after binding with different DNA revealed selective affinity of ThT toward AT-rich dsDNA. Molecular docking also substantiates the experimental results. We also observed that addition of orange-emitting ethidium bromide (EtBr) to cyan-emitting ThT-DNA complexes leads to bright white light emission (WLE) through Förster resonance energy transfer. Additionally, the emission of white light is far greater in the case of intra-DNA strands. Besides endorsing the binding insights of ThT to AT-rich dsDNA, the present investigations open a new perspective for realizing promising WLE from two biomarkers without labeling the DNA.

New minor groove covering DNA binding mode of dinuclear Pt(II) complexes with various pyridine-linked bridging ligands and dual anticancer-antiangiogenic activities

New anticancer platinum(II) compounds simultaneously targeting tumor cells and tumor-derived neoangiogenesis, with new DNA interacting mode and large therapeutic window are appealing alternative to improve efficacy of clinical platinum chemotherapeutics. Herein, we describe three novel dinuclear [{Pt(en)Cl}₂(μ-L)]²⁺ complexes with different pyridine-like bridging ligands (L), 4,4'-bipyridine (Pt1), 1,2-bis(4-pyridyl)ethane (Pt2) and 1,2-bis(4-pyridyl)ethene (Pt3), which highly, positively charged aqua derivatives, [{Pt(en)(H₂O)}₂(μ-L)]⁴⁺, interact with the phosphate backbone forming DNA-Pt adducts with an unique and previously undescribed binding mode, called a minor groove covering. The results of this study suggested that the new binding mode of the aqua-Pt(II) complexes with DNA could be attributed to the higher anticancer activities of their chloride analogues. All three compounds, particularly complex [{Pt(en)Cl}₂(μ-4,4'-bipy)]Cl₂·2H₂O (4,4'-bipy is 4,4'-bipyridine) (Pt1), overcame cisplatin resistance in vivo in the zebrafish-mouse melanoma xenograft model, showed much higher therapeutic potential than antiangiogenic drug sunitinib malate, while effectively blocking tumor neovascularization and melanoma cell metastasis. Overall therapeutic profile showed new dinuclear Pt(II) complexes could be novel, effective and safe anticancer agents. Finally, the correlation with the structural characteristics of these complexes can serve as a useful tool for developing new and more effective anticancer drugs.

Study of the Binding Interaction between Wortmannin and Calf Thymus DNA: Multispectroscopic and Molecular Docking Studies

INTRODUCTION

Wortmannin (WTN) is a steroid metabolite that inhibits phosphatidylinositol 3-kinase and other signaling pathways. Structurally, the WTN consists of a cyclopentanophenanthrene-like structure with several oxygen-rich moieties which have the potential to interact with deoxyribonucleic acid (DNA) molecules.

METHODS

We aim to evaluate the WTN and calf thymus DNA (ct-DNA) interaction with molecular docking using the AutoDock 4.2 software. UV and fluorescence spectroscopy and viscosity techniques were performed to confirm the in silico analysis.

RESULTS

Molecular docking showed that the WTN interacted with ct-DNA via hydrogen bonds at guanine-rich sequences. The number of hydrogen bonds between the WTN and DNA was 1-2 bonds (average 1.2) per WTN molecule. The in silico binding constant was 2 × 103 M-1. UV spectroscopy showed that the WTN induced a hyperchromic feature without wavelength shifting. The WTN and DNA interaction led to quenching of DNA-emitted fluorescence. The different concentrations of WTN had no effect on DNA viscosity. Taken together, our results demonstrated WTN interacts with DNA in the nonintercalating mode, which is considered as a new mechanism of action.

CONCLUSION

These results suggest that the WTN may exert its biological effects, at least in part, via interaction with DNA.

Recent Advances in Developing Small Molecules Targeting Nucleic Acid

Nucleic acids participate in a large number of biological processes. However, current approaches for small molecules targeting protein are incompatible with nucleic acids. On the other hand, the lack of crystallization of nucleic acid is the limiting factor for nucleic acid drug design. Because of the improvements in crystallization in recent years, a great many structures of nucleic acids have been reported, providing basic information for nucleic acid drug discovery. This review focuses on the discovery and development of small molecules targeting nucleic acids.

Simultaneous binding of a cyclophane and classical intercalators to DNA: observation of FRET-mediated white light emission

FRET tuning in ternary systems consisting of DNA, an anthracene based cyclophane and a DNA mono-/bis-intercalator is reported.

Structure-based DNA-targeting strategies with small molecule ligands for drug discovery

Nucleic acids are the molecular targets of many clinical anticancer drugs. However, compared with proteins, nucleic acids have traditionally attracted much less attention as drug targets in structure-based drug design, partially because limited structural information of nucleic acids complexed with potential drugs is available. Over the past several years, enormous progresses in nucleic acid crystallization, heavy-atom derivatization, phasing, and structural biology have been made. Many complicated nucleic acid structures have been determined, providing new insights into the molecular functions and interactions of nucleic acids, especially DNAs complexed with small molecule ligands. Thus, opportunities have been created to further discover nucleic acid-targeting drugs for disease treatments. This review focuses on the structure studies of DNAs complexed with small molecule ligands for discovering lead compounds, drug candidates, and/or therapeutics.

Dynamics of light harvesting in ZnO nanoparticles

We have explored light harvesting of the complex of ZnO nanoparticles with the biological probe Oxazine 1 in the near-infrared region using picosecond-time-resolved fluorescence decay studies. We have used ZnO nanoparticles and Oxazine 1 as a model donor and acceptor, respectively, to explore the efficacy of the Förster resonance energy transfer (FRET) in the nanoparticle-dye system. It has been shown that FRET from the states localized near the surface and those in the bulk of the ZnO nanoparticles can be resolved by measuring the resonance efficiency for various wavelengths of the emission spectrum. It has been observed that the states located near the surface for the nanoparticles (contributing to visible emission at lambda approximately 550 nm) can contribute to very high efficiency (>90%) FRET. The efficiency of light harvesting dynamics of the ZnO nanorods has also been explored in this study and they were found to have much less efficiency (approximately 40%) for energy transfer compared to the nanoparticles. The possibility of an electron transfer reaction has been ruled out from the picosecond-resolved fluorescence decay of the acceptor dye at the ZnO surface.

Sequence dependent femtosecond-resolved hydration dynamics in the minor groove of DNA and histone-DNA complexes

Understanding the sequence dependent molecular recognition of DNA is crucial for the rational design of many drugs. Femtosecond resolved studies on the hydration dynamics of the dodecamer duplexes having sequences (CGCGAATTCGCG)2 and (CGCAAATTTGCG)2, and their complexes with the nucleic protein histone 1 (H1) reveal significant correlation of the molecular recognition of the DNA and DNA-protein complexes with the dynamics of hydration. The different molecular recognition of DNA and DNA-protein complexes is also borne out by circular dichroism (CD) and fluorescence detected CD measurements.