Nucleic acid-binding bis-acridine orange dyes with improved properties for bioimaging and PCR applications.

Understanding the intricate interactions of molecular dyes with nucleic acids is pivotal for advancing medical and biochemical applications. In this work, we present a comprehensive study of the interplay between a novel series of bis-acridine orange (BAO) dyes and double-stranded DNA (dsDNA). These BAO dyes were intentionally designed as two acridine orange units connected by neutral linkers featuring a 2,5-disubstituted thiophene moiety.

Cryostructuring of Polymeric Systems: 67 Properties and Microstructure of Poly(Vinyl Alcohol) Cryogels Formed in the Presence of Phenol or Bis-Phenols Introduced into the Aqueous Polymeric Solutions Prior to Their Freeze-Thaw Processing.

Poly(vinyl alcohol) (PVA) physical cryogels that contained the additives of -, -, and -bis-phenols or phenol were prepared, and their physico-chemical characteristics and macroporous morphology and the solute release dynamics were evaluated. These phenolic additives caused changes in the viscosity of initial PVA solutions before their freeze-thaw processing and facilitated the growth in the rigidity of the resultant cryogels, while their heat endurance decreased. The magnitude of the effects depended on the interposition of phenolic hydroxyls in the molecules of the used additives and was stipulated by their H-bonding with PVA OH-groups.

Towards the development of a DNA automaton: modular RNA-cleaving deoxyribozyme logic gates regulated by miRNAs.

Advancements in DNA computation have unlocked molecular-scale information processing possibilities, utilizing the intrinsic properties of DNA for complex logical operations with transformative applications in biomedicine. DNA computation shows promise in molecular diagnostics, enabling precise and sensitive detection of genetic mutations and disease biomarkers. Moreover, it holds potential for targeted gene regulation, facilitating personalized therapeutic interventions with enhanced efficacy and reduced side effects.

Cryostructuring of Polymeric Systems: 64. Preparation and Properties of Poly(vinyl alcohol)-Based Cryogels Loaded with Antimicrobial Drugs and Assessment of the Potential of Such Gel Materials to Perform as Gel Implants for the Treatment of Infected Wounds.

Physical macroporous poly(vinyl alcohol)-based cryogels formed by the freeze-thaw technique without the use of any foreign cross-linkers are of significant interests for biomedical applications. In the present study, such gel materials loaded with the antimicrobial substances were prepared and their physicochemical properties were evaluated followed by an assessment of their potential to serve as drug carriers that can be used as implants for the treatment of infected wounds. The antibiotic Ceftriaxone and the antimycotic Fluconazole were used as antimicrobial agents.

First-principles studies of substituent effects on squaraine dyes.

Dye molecules that absorb light in the visible region are key components in many applications, including organic photovoltaics, biological fluorescent labeling, super-resolution microscopy, and energy transport. One family of dyes, known as squaraines, has received considerable attention recently due to their favorable electronic and photophysical properties. In addition, these dyes have a strong propensity for aggregation, which results in emergent materials properties, such as exciton delocalization.

Influence of Hydrophobicity on Excitonic Coupling in DNA-Templated Indolenine Squaraine Dye Aggregates.

Control over the strength of excitonic coupling in molecular dye aggregates is a substantial factor for the development of technologies such as light harvesting, optoelectronics, and quantum computing. According to the molecular exciton model, the strength of excitonic coupling is inversely proportional to the distance between dyes. Covalent DNA templating was proved to be a versatile tool to control dye spacing on a subnanometer scale.

Cryostructuring of Polymeric Systems : Application of Deep Neural Networks for the Classification of Structural Features Peculiar to Macroporous Poly(vinyl alcohol) Cryogels Prepared without and with the Additives of Chaotropes or Kosmotropes.

Macroporous poly(vinyl alcohol) cryogels (PVACGs) are physical gels formed via cryogenic processing of polymer solutions. The properties of PVACGs depend on many factors: the characteristics and concentration of PVA, the absence or presence of foreign solutes, and the freezing-thawing conditions. These factors also affect the macroporous morphology of PVACGs, their total porosity, pore size and size distribution, etc.

Cryostructuring of Polymeric Systems. 49. Unexpected "Kosmotropic-Like" Impact of Organic Chaotropes on Freeze⁻Thaw-Induced Gelation of PVA in DMSO.

Urea (URE) and guanidine hydrochloride (GHC) possessing strong chaotropic properties in aqueous media were added to DMSO solutions of poly(vinyl alcohol) (PVA) to be gelled via freeze⁻thaw processing. Unexpectedly, it turned out that in the case of the PVA cryotropic gel formation in DMSO medium, the URE and GHC additives caused the opposite effects to those observed in water, i.e.

Oligomerization of the antimicrobial peptide Protegrin-5 in a membrane-mimicking environment. Structural studies by high-resolution NMR spectroscopy.

Protegrin pore formation is believed to occur in a stepwise fashion that begins with a nonspecific peptide interaction with the negatively charged bacterial cell walls via hydrophobic and positively charged amphipathic surfaces. There are five known nature protegrins (PG1-PG5), and early studies of PG-1 (PDB ID:1PG1) shown that it could form antiparallel dimer in membrane mimicking environment which could be a first step for further oligomeric membrane pore formation. Later, we solved PG-2 (PDB ID:2MUH) and PG-3 (PDB ID:2MZ6) structures in the same environment and for PG-3 observed a strong d NOE effects between residues R18 and F12, V14, and V16.

Oligomeric adiponectin forms and their complexes in the blood of healthy donors and patients with type 2 diabetes mellitus.

Adiponectin (Adn) is a protein that circulates in the blood in several oligomeric forms, namely low-, medium-, and high-molecular-weight forms. Adn may serve as a risk factor for type 2 diabetes mellitus (T2DM). The aims of this work were (1) to produce monoclonal antibodies (MAbs) specific to different Adn oligomeric forms, (2) to design immunoassays suitable for measuring the Adn forms present in human blood, and (3) to investigate the changes in Adn forms that occur in patients with T2DM.

Near-infrared squaraine dyes for fluorescence enhanced surface assay.

Commercially available, near-infrared fluorescent squaraine dyes (Seta-635 and Seta-670) were covalently bound to antibodies and employed insurface enhanced immunoassay. From fluorescence intensity and lifetime changes determined for a surface which had been coated with silver nanoparticles as well as a non-coated glass surface, both labelled compounds exhibited a 15 to 20-fold enhancement of fluorescence on the silver coated surface compared to that achieved on the non-coated surface. In addition, the fluorescence lifetime changes drastically for both labels in the case of silver-coated surfaces.

Seta-633 - a NIR fluorescence lifetime label for low-molecular-weight analytes.

We describe the photophysical properties of Seta-633, a commercially available near-infrared (NIR) dye, and its use as a fluorescent label to study the interaction between low-molecular-weight analytes and proteins using fluorescence lifetime as the readout parameter. In a model assay, we demonstrate that a biotinylated Seta-633 tracer binds to antibiotin with high specificity. Importantly, the lifetime of Seta-633-biotin increases about 1.

Fluorescent probes and labels for biomedical applications.

Fluorescence probes and labels have become indispensable tools for clinical diagnostics, high-throughput screening, and other biomedical applications. We have developed several classes of new squaraine-based red and near-infrared (NIR) probes and labels (SETA and Square series), naphthalimide-based fluorescence lifetime dyes (SeTau series), and cyanine- and squaraine-based quenchers (SQ series). This report discusses the spectral and photophysical properties of these new markers.

Tracing lysozyme-lipid interactions with long-wavelength squaraine dyes.

The applicability of the two newly commercial available squaraine labels Square-670-NHS and Seta-635-NHS to exploring protein-lipid interactions has been evaluated. The labels were conjugated to lysozyme (Lz) (squaraine-lysozyme conjugates below referred to as Square-670-Lz and Seta-635-Lz), a structurally well-characterized small globular protein displaying the ability to interact both, electrostatically and hydrophobically with lipids. The lipid component of the model systems was represented by lipid vesicles composed of zwitterionic lipids egg yolk phosphatidylcholine (PC) and 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine (SOPC), and their mixtures with anionic lipids either beef heart cardiolipin (CL) or 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG), respectively.