Sensing lysozyme fibrils by salicylaldimine substituted BODIPY dyes - A correlation with molecular structure

Quick and efficient detection of protein fibrils has enormous impact on the diagnosis and treatment of amyloid related neurological diseases. Among several methods, fluorescence based techniques have garnered most importance in the detection of amyloid fibrils due to its high sensitivity and extreme simplicity. Among other classes of molecular probes, BODIPY derivatives have been employed extensively for the detection of amyloid fibrils. However, there are very few studies on the relationship between the molecular structure of BODIPY dyes and their amyloid sensing activity. Here in a BODIPY based salicylaldimine Schiff base and its corresponding boron complex have been evaluated for their ability to sense amyloid fibrils from hen-egg white lysozyme using steady state and time-resolved spectroscopic techniques. Both dyes show fluorescence enhancement as well as increase in their excited state lifetime upon their binding with lysozyme fibrils. However, the BODIPY derivative which shows more emission enhancement in fibrillar solution has much lower affinity towards amyloid fibrils as compared to other derivative. This contrasting behaviour in the emission enhancement and binding affinity has been explained on the basis of differences in their photophysical properties in water and amyloid fibril originating from the difference in their molecular structure. Such correlation between the amyloid sensitivity and the molecular structure of the probe can open up a new strategy for designing new efficient amyloid probes.

Spectroscopic Characterization of Mitochondrial G-Quadruplexes

Guanine quadruplexes (G4s) are highly polymorphic four-stranded structures formed within guanine-rich DNA and RNA sequences that play a crucial role in biological processes. The recent discovery of the first G4 structures within mitochondrial DNA has led to a small revolution in the field. In particular, the G-rich conserved sequence block II (CSB II) can form different types of G4s that are thought to play a crucial role in replication. In this study, we decipher the most relevant G4 structures that can be formed within CSB II: RNA G4 at the RNA transcript, DNA G4 within the non-transcribed strand and DNA:RNA hybrid between the RNA transcript and the non-transcribed strand. We show that the more abundant, but unexplored, G6AG7 (37%) and G6AG8 (35%) sequences in CSB II yield more stable G4s than the less profuse G5AG7 sequence. Moreover, the existence of a guanine located 1 bp upstream promotes G4 formation. In all cases, parallel G4s are formed, but their topology changes from a less ordered to a highly ordered G4 when adding small amounts of potassium or sodium cations. Circular dichroism was used due to discriminate different conformations and topologies of nucleic acids and was complemented with gel electrophoresis and fluorescence spectroscopy studies.

Beyond amyloid proteins: Thioflavin T in nucleic acid recognition

Thioflavin T (ThT) is a commercially available fluorescent dye that is commonly used in biomedical research for over five decades. It was first reported as an extrinsic fluorescent probe for the detection of amyloid fibrils and related processes and it has also been used extensively for assessing protein binding in fluorescence-based assays. Although the nucleic acid binding of ThT was reported half of a century ago in the 1970s, it was not widely explored until the start of this decade. In recent years, Thioflavin T has become a major tool in the recognition of many types of non-canonical nucleic acid conformations including duplexes, triplexes, and G-quadruplexes. The propensity of ThT binding is more towards base aberrations, bulges, and mismatches highlighting its importance in serving as a diagnostic tool in a variety of ailments/disease conditions. In this review, we cover major advancements in nucleic acid detection/binding by ThT to a variety of nucleic acid structures.

Effect of counter-anions on the aggregation of Thioflavin-T

The aggregation of small molecules in aqueous solution is known to be influenced by the ionic strength of the medium; however, the role played by the identity of salt in the phenomenon of small molecule aggregation is rarely investigated. In the present contribution, we have investigated the effect of counter-anions on the aggregation of a popular cationic amyloid sensing probe, Thioflavin-T (ThT), by taking six different anions, viz. chloride, bromide, acetate, iodide, tetrafluoroborate, and perchlorate. Our results clearly indicate that it is not the ionic strength of the medium which solely controls aggregation of small molecules but distinct ions behave distinctly with regard to the organization. In fact, distinct ion effects play a major role in the salt induced organization of fluorophores. Using detailed steady-state emission, time-resolved emission, and ground-state absorption measurements, the optical properties of salt induced aggregates of ThT have been characterized. We have rationalized our observations on the basis of the theory of matching water affinity, which suggests that the matching free hydration energy is a critical aspect for the formation of contact ion pairs, which eventually results in aggregation. In brief, a larger sized anion, perchlorate, has a lower free energy of hydration and forms a suitable contact ion pair, with a larger organic cation, ThT, having weaker hydration. This contact ion-pair formation subsequently leads to the formation of an aggregate assembly which is found to be emissive in nature. Therefore, it is possible to induce aggregation of ThT by selecting the right counterion with the appropriate size, which may help us to evaluate the false positive signals when high ionic strength and specific counterions are present in the sensing matrix.

Effect of DNA Origami Nanostructures on hIAPP Aggregation

The aggregation of human islet amyloid polypeptide (hIAPP) plays a major role in the pathogenesis of type 2 diabetes mellitus (T2DM), and numerous strategies for controlling hIAPP aggregation have been investigated so far. In particular, several organic and inorganic nanoparticles (NPs) have shown the potential to influence the aggregation of hIAPP and other amyloidogenic proteins and peptides. In addition to conventional NPs, DNA nanostructures are receiving more and more attention from the biomedical field. Therefore, in this work, we investigated the effects of two different DNA origami nanostructures on hIAPP aggregation. To this end, we employed in situ turbidity measurements and ex situ atomic force microscopy (AFM). The turbidity measurements revealed a retarding effect of the DNA nanostructures on hIAPP aggregation, while the AFM results showed the co-aggregation of hIAPP with the DNA origami nanostructures into hybrid peptide–DNA aggregates. We assume that this was caused by strong electrostatic interactions between the negatively charged DNA origami nanostructures and the positively charged peptide. Most intriguingly, the influence of the DNA origami nanostructures on hIAPP aggregation differed from that of genomic double-stranded DNA (dsDNA) and appeared to depend on DNA origami superstructure. DNA origami nanostructures may thus represent a novel route for modulating amyloid aggregation in vivo.

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.

A supramolecule based fluorescence turn-on and ratiometric sensor for ATP in aqueous solution

Considering the biological relevance of adenosine triphosphate (ATP) as an "energy currency" in all organisms and significance of its detection in various diseased conditions, enormous efforts have been made to develop selective and sensitive fluorescent sensors for the detection of ATP. However, these developed sensor probes frequently involve technically challenging and time-consuming synthetic protocols for the production of sensor molecules and often suffer from poor solubility in aqueous medium. Another major disadvantage of these developed sensor systems is their single wavelength based operation which makes their performance susceptible to minute changes in experimental conditions. Herein, we report a fluorescence turn-on ratiometric sensor for the detection of ATP which operates by the dissociation of Thioflavin-T-sulphated-β-cyclodextrin supramolecular assembly by Zn²⁺ followed by ATP induced reassociation of the same. This modulation of the monomer/aggregate equilibrium of the supramolecular assembly followed by subsequent interactions with Zn²⁺ and ATP acts as an optimal scheme for the ratiometric detection of ATP. Overall this supramolecular ensemble based sensing platform provides a simple, sensitive, selective and label free detection approach for ATP in aqueous solution. Importantly, our sensor platform responds to ATP in the biologically complex media of serum samples suggesting its potential for possible applications in real-life scenarios.

Lighting Up the Thioflavin T by Parallel-Stranded TG(GA) n DNA Homoduplexes

Thioflavin T (ThT) was once regarded to be a specific fluorescent probe for the human telomeric G-quadruplex, but more other kinds of DNA were found that can also bind to ThT in recent years. Herein, we focus on G-rich parallel-stranded DNA and utilize fluorescence, absorbance, circular dichroism, and surface plasmon resonance spectroscopy to investigate its interaction with ThT. Pyrene label and molecular modeling are applied to unveil the binding mechanism. We find a new class of non-G-quadruplex G-rich parallel-stranded ( ps) DNA with the sequence of TG(GA) n can bind to ThT and increase the fluorescence with an enhancement ability superior to G-quadruplex. The optimal binding specificity for ThT is conferred by two parts. The first part is composed of two bases TG at the 5' end, which is a critical domain and plays an important role in the formation of the binding site for ThT. The second part is the rest alternative d(GA) bases, which forms the ps homoduplex and cooperates with the TG bases at the 5' end to bind the ThT.

A molecular rotor based ratiometric sensor for basic amino acids

The inevitable importance of basic amino acids, arginine and lysine, in human health and metabolism demands construction of efficient sensor systems for them. However, there are only limited reports on the 'ratiometric' detection of basic amino acids which is further restricted by the use of chemically complex sensor molecules, which impedes their prospect for practical applications. Herein, we report a ratiometric sensor system build on simple mechanism of disassociation of novel emissive Thioflavin-T H-aggregates from heparin surface, when subjected to interaction with basic amino acids. The strong and selective electrostatic and hydrogen bonding interaction of basic amino acids with heparin leads to large alteration in photophysical attributes of heparin bound Thioflavin-T, which forms a highly sensitive sensor platform for detection of basic amino acids in aqueous solution. These selective interactions between basic amino acids and heparin allow our sensor system to discriminate arginine and lysine from other amino acids. This unique mechanism of dissociation of Thioflavin-T aggregates from heparin surface provides ratiometric response on both fluorimetric and colorimetric outputs for detection of arginine and lysine, and thus it holds a significant advantage over other developed sensor systems which are restricted to single wavelength detection. Apart from the sensitivity and selectivity, our system also provides the advantage of simplicity, dual mode of sensing, and more importantly, it employs an inexpensive commercially available probe molecule, which is a significant advantage over other developed sensor systems that uses tedious synthesis protocol for the employed probe in the detection scheme, an impediment for practical applications. Additionally, our sensor system also shows response in complex biological media of serum samples.

Pyrrolic molecular rotors acting as viscosity sensors with high fluorescence contrast

Pyrrolic viscosity sensors exhibit one order of magnitude higher fluorescence contrast compared to that of the conventional phenolic analogues due to the viscosity-sensitive rotation of the rotational pyrrole group.

An ultrafast molecular rotor based ternary complex in a nanocavity: a potential “turn on” fluorescence sensor for the hydrocarbon chain

Formation of a ternary complex by an ultrafast molecular rotor (UMR) with a macrocyclic cavitand has been investigated for the sensitive detection of the alkyl chain of a surfactant.

Polymerase synthesis of DNA labelled with benzylidene cyanoacetamide-based fluorescent molecular rotors: fluorescent light-up probes for DNA-binding proteins

Fluorescent molecular rotors are for the first time used as light-up probes for sensing of DNA–protein interaction.

Dynamics under confinement: torsional dynamics of Auramine O in a nanocavity

Confinement inside the novel anionic sulphobutylether β-cyclodextrin nanocavity significantly slows down the torsional relaxation in Auramine O as compared to native β-CD.

The nature of the different environmental sensitivity of symmetrical and unsymmetrical cyanine dyes: an experimental and theoretical study

Symmetrical and unsymmetrical cyanine dyes are used in different applications due to their different fluorogenic behaviors toward bio-macromolecules and micro-environments. In the present paper, computational studies on these dyes reveal that the potential energy of the electronic excited state is controlled by C-C bond rotational motion, which causes mainly nonradiative deactivation, according to the activation energies for the rotation. The rotations of different C-C bonds in the molecules have quite different rotational activation energies. Symmetrical dyes (Cy) possess an obviously higher rotating energy barrier as well as a larger energy gap compared to unsymmetrical dyes (TO). The C-C bond rotation close to the quinoline moiety of unsymmetrical thiazole orange (TO) allows the dye to possess the lowest energy barrier and also the lowest energy gap. This rotation plays a major role in reducing fluorescence quantum yields and providing a low fluorescent background in the free states of the unsymmetrical cyanine dyes. The results might provide a foundation for the interpretation of the behavior of the dyes and are useful for the future design of new cyanine fluorophores.