Association of novel monomethine cyanine dyes with bacteriophage MS2: A fluorescence study

Photonics of Some Monomethine Cyanine Dyes in Solutions and in Complexes with Biomolecules

In search of new probes for biomolecules, the spectral fluorescent study of four monomethine cyanine dyes (MCD), both unsymmetrical and symmetrical, has been carried out in different organic solvents, in aqueous buffer solutions, and in the presence of DNA and HSA. The complexation of MCD with biomacromolecules leads to a steep growth of the fluorescence intensity. Complexes of MCD with dsDNA and HSA of various types were modeled in silico by molecular docking. Experiments on thermal dissociation of dsDNA in the presence of MCD showed the formation of intercalative complexes of MCD with DNA. Quenching of intrinsic fluorescence of HSA by MCD occurred with rate constants much higher than the diffusion limit, that is, in dye-HSA complexes. Effective constants of MCD complexation with the biomacromolecules were estimated. MCD 1 has the best characteristics as a possible fluorescent probe for dsDNA and can serve as a sensitive and selective probe for dsDNA in the presence of HSA. Photochemical properties of MCD complexed with DNA have been also studied. An increase in the quantum yield of the triplet states of MCD in complexes with DNA has been found, which may be important for using these dyes as potential candidates in photodynamic therapy.

Advance on Engineering of Bacteriophages by Synthetic Biology

Since bacteriophages (phages) were firstly reported at the beginning of the 20th century, the study on them experiences booming-fading-emerging with discovery and overuse of antibiotics. Although they are the hotspots for therapy of antibiotic-resistant strains nowadays, natural phage applications encounter some challenges such as limited host range and bacterial resistance to phages. Synthetic biology, one of the most dramatic directions in the recent 20-years study of microbiology, has generated numerous methods and tools and has contributed a lot to understanding phage evolution, engineering modification, and controlling phage-bacteria interactions. In order to better modify and apply phages by using synthetic biology techniques in the future, in this review, we comprehensively introduce various strategies on engineering or modification of phage genome and rebooting of recombinant phages, summarize the recent researches and potential directions of phage synthetic biology, and outline the current application of engineered phages in practice.

Estimation of Nanoparticle's Surface Electrostatic Potential in Solution Using Acid-Base Molecular Probes. III. Experimental Hydrophobicity/Hydrophilicity and Charge Distribution of MS2 Virus Surface

MS2 bacteriophage is often used as a model for evaluating pathogenic viruses' behavior in aqueous solution. However, the questions of the virus surface's hydrophilic/hydrophobic balance, the charge distribution, and the binding mechanism are open. Using the dynamic light scattering method and laser Doppler electrophoresis, the hydrodynamic diameter and the ζ-potential of the virus particles were measured at their concentration of 5 × 10¹¹ particles per mL and ionic strength 0.03 M. The values were found to be 30 nm and -29 or -34 mV (by Smoluchowski or Ohshima approximations), respectively. The MS2 bacteriophage surface was also investigated using a series of acid-base indicator dyes of various charge type, size, and structure. Their spectral and acid-base properties (pK_a) are very sensitive to the microenvironment in aqueous solution, including containing nanoparticles. The electrostatic potential of the surface Ψ was estimated using the common formula: Ψ = 59 × (pK_aⁱ - pK_a) in mV at 25 °C. The Ψ values were -50 and +10 mV, respectively, which indicate the "mosaic" way of the charge distribution on the surface. These data are in good agreement with the obtained ζ-potential values and provide even more information about the virus surface. It was found that the surface of the MS2 virus is hydrophilic in solution in contrast to the commonly accepted hypothesis of the hydrophobicity of virus particles. No hydrophobic interactions between various molecular probes and the capsid were observed.

Molecular Docking of Cyanine and Squarylium Dyes with NSP15 Endoribonuclease of the SARS-CoV-2 Coronavirus

The ongoing spread of the COVID-19 coronavirus infection requires us to find new tools and methods for detecting and studying the infection and preventing morbidity (new analytical procedures and tests). With the aim of developing probes for the detection of SARS-CoV-2 coronavirus by modeling in silico (molecular docking), the noncovalent binding of cyanine and squarylium dyes with different molecular charges and different types of heterocyclic residues and substituents (42 compounds in total) with different variants of the NSP15 endoribonuclease of the SARS-CoV-2 coronavirus (COVID-19) of the original (wild) type and mutant types is studied. The interaction energies and spatial configurations of the dye molecules in complexes with NSP15 are determined. Some dyes with negative values of the total energy of the complex E_tot are promising for further practical study as probes for coronavirus.

Polymethine Dyes as Probes for Detecting the SARS-COV-2 Coronavirus: In silico Molecular Docking Study

The noncovalent interaction between various polymethine dyes (45 compounds in total) and a spike protein (S), one of the main structural component of the SARS-CoV-2 coronavirus, is studied in silico (molecular docking) to develop effective probes to detect the virus. The interaction energies and the spatial configurations of the complexes of the dye molecules with S are found. We showed that cationic polymethine dyes and neutral squarylium dyes do not form stable complexes with S. Some anionic dyes having negative total energies E_tot may be recommended for practical research.

RNA-targeting low-molecular-weight fluorophores for nucleoli staining: synthesis, in silico modelling and cellular imaging

Herein we present our work on the synthesis, investigation of the photophysical properties, interactions with nucleic acids, molecular docking, and imaging application of three carbocyanine dyes.