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A single nucleotide mismatch in a particular sequence of DNA is considered to play pivotal roles in various central biological processes and is associated with the development of several types of oncogene and genetic diseases. Hence, the identification of particular probes for DNA is of great interest in order to carry out cell imaging, drug delivery, and point of care diagnostic. Herein we report the binding interaction between DNA and tripeptide-functionalized luminescent copper nanoclusters (CuNCs) for recognition of single base pair mismatched (MM) double-stranded (ds) DNA from well-matched (WM) sequences. Isothermal titration calorimetry and UV–vis thermal denaturation established that substitution of a single well-matched GC pair in 20 base pair (bp) DNA with single pyrimidine mismatches; viz. CA, CC, and CT mispair resulted in an enhanced binding affinity of CuNCs to ds DNA. Through fluorescence correlation spectroscopy, we estimated the precise values of the binding interaction at the single-molecule resolution. Analysis of autocorrelation curves, hydrodynamic radius, and association rate constants (K ass) evidently established the higher affinity of CuNCs for the single pair MM dsDNA. The order of binding affinity of CuNCs is found to be CT MM > CA MM > CC MM > WM DNA. Competitive binding studies using Hoechst and ethidium bromide substantiate the groove binding mechanism.

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Herein we report the binding interactions between lysozyme (Lyz) and an anthracycline drug, epirubicin hydrochloride (EPR), through an extensive spectroscopic approach at both ensemble average and single molecular resolution. Our steady-state and time-resolved fluorescence spectroscopy reveals that the drug-induced fluorescence quenching of the protein proceeds through a static quenching mechanism. Isothermal titration calorimetry (ITC) and steady-state experiments reveal almost similar thermodynamic signatures of the drug–protein interactions. The underlying force that plays pivotal roles in the said interaction is hydrophobic in nature, which is enhanced in the presence of a strong electrolyte (NaCl). Circular dichroism (CD) spectra indicate that there is a marginal increase in the secondary structure of the native protein (α-helical content increases from 26.9 to 31.4% in the presence of 100 μM EPR) upon binding with the drug. Fluorescence correlation spectroscopy (FCS) was used to monitor the changes in structure and conformational dynamics of Lyz upon interaction with EPR. The individual association (K ass = 0.33 × 106 ms–1 M–1) and dissociation (K diss = 1.79 ms–1) rate constants and the binding constant (K b = 1.84 × 105 M–1) values, obtained from fluctuations of fluorescence intensity of the EPR-bound protein, have also been estimated. AutoDock results demonstrate that the drug molecule is encapsulated within the hydrophobic pocket of the protein (in close proximity to both Trp62 and Trp108) and resides ∼20 Å apart from the covalently labelled CPM dye. Förster resonance energy transfer (FRET) studies proved that the distance between the donor (CPM) and the acceptor (EPR) is ∼22 Å, which is very similar to that obtained from molecular docking analysis (∼20 Å). The system also shows temperature-dependent reversible FRET, which may be used as a thermal sensor for the temperature-sensitive biological systems.

Targeting mismatched base pairs containing DNA using small molecules and exploring the underlying mechanism involved during the binding interactions is one of the fundamental aspects of drug design. These molecules in turn are used in nucleic acid targeted therapeutics and cancer diagnosis. In this work, we systematically delineate the binding of the anticancer drug, epirubicin hydrochloride (EPR) with 20-mer duplex DNA, having both natural nucleobase pairing and thermodynamically least stable non-Watson−Crick base pairing. From the thermal denaturation studies, we observed that EPR can remarkably enhance the thermal stability of cytosine-cytosine (CC) and cytosine-thymine (CT) mismatched (MM) DNA over other 20-mer duplex DNA. From steady-state fluorescence spectroscopy and isothermal titration calorimetry studies, we concluded that EPR binds strongly with the mismatched duplex DNA through the intercalation binding mode. The interaction of EPR and duplex DNA has also been monitored at a single molecular resolution using fluorescence correlation spectroscopy (FCS). Dynamic quantitates such as diffusion coefficients and hydrodynamic radii obtained from an FCS study along with association and dissociation rate constants estimated from intensity time trace analyses further substantiate the stronger binding affinity of EPR to the thermally less stable mismatched DNA, formed by the most discriminating nucleobase (viz. cytosine). Additionally, we have shown that EPR can be sequestered from nucleic acids using a mixed micellar system of an anionic surfactant and a triblock copolymer. From thermal denaturation studies and circular dichroism spectroscopy, we found that the extent of drug sequestration depends on the binding affinity of EPR to the duplex DNA, and this mixed micellar system can be employed for the removal of excess drug in the case of a drug overdose.

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A one‐step Rh‐catalyzed site‐selective ortho‐C−H alkynylation of perylene as well as naphthalene mono‐ and diimides is reported. A single step regioselective access to ortho‐C−H alkynylated derivatives of these ryleneimides not only increases the step economy of the ortho‐functionalization on these dyes but also provides a quick access route towards highly functionalized dyes that have potential optoelectronic applications. Increased solubility of tetra(triisopropylsilyl)acetylenyl PDIs in organic solvents greatly enhances their utility for further derivatization.

Monitoring the DNA dynamics in solution has great potential to develop new nucleic acid-based sensors and devices. With spectroscopic approaches, both at the ensemble average and single-molecule resolution, this study is directed to differentiate a single nucleotide mismatch (SNM) via a metal ionstabilized mismatched base-pairing (C−Ag + −C/C−Cu 2+ −T) (C = cytosine, T = thymine) and site-selective extrinsic fluorophore, specifically, Thioflavin T (ThT). This is the first approach of its kind where dynamic quantities like molecular diffusion coefficients and diffusion times have been utilized to distinguish the least-stable SNM (CC & CT) formed by the most discriminating nucleobase, specifically, cytosine in a 20-mer duplex DNA. Additionally, this work also quantifies metal ions (Ag + and Cu 2+ ) at lower concentrations using fluorescence correlation spectroscopy. Our results can provide greater molecular-level insights into the mismatch-dependent metal−DNA interactions and also illuminate ThT as a new fluorophore to monitor the dynamics involved in DNA−metal composites.