An oligonucleotide probe incorporating the chromophore of green fluorescent protein is useful for the detection of HER-2 mRNA breast cancer marker

Modular access to nucleobase GFP-surrogates: pH-responsive smart probes for ratiometric nucleic acid diagnostics

We have utilized a modular on-strand aldol approach to synthesize chalcone-based fluorescent molecular rotors (FMRs) bearing phenolic oxygen donors that mimic the natural tyrosine (Tyr66) chromophore 4-hydroxybenzylidene-imidazolinone (HBI) within green fluorescent proteins (GFPs). Leveraging the FMRs' propensity to undergo non-radiative decay via twisted intramolecular charge transfer upon excitation within certain microenvironments, we have addressed the longstanding issues of poor brightness (ε max × Φ fl) and weak turn-on responses for GFP-surrogates within nucleic acids. To demonstrate its potential and lay the groundwork for future applications, these FMRs were incorporated into NarI12 and TBA15 oligonucleotides with canonical (A, C, T, G) or locked nucleic acids (LNAs) (TL, AL) as flanking bases. The resulting duplexes and G-quadruplexes (GQs) were studied using fluorescence spectroscopy, molecular dynamics simulations, and quantum mechanical calculations, yielding a comprehensive understanding of their structural and photophysical properties in DNA, DNA : RNA, and GQ contexts. Electron-rich chalcones favor neutral phenol excitation (ROH) to afford both phenol (ROH*) and phenolate (RO-*) emission, with the latter generated through an intermolecular excited-state proton transfer process, while electron-deficient chalcones serve as ratiometric excitation indicators, due to their photoacidity. The surrogates display strong turn-on responses (up to 154-fold) in a GQ → duplex topology switch with flanked LNAs, giving Φ fl up to 0.58 and molar brightness ∼ 15 000 cm-1 M-1 in the duplex. By synergizing the NA sequence and probe, we achieve a switchable ON-to-OFF photoinduced electron transfer, resulting in a 134-fold turn-on emission response to pH. Our findings are the first to optimize the performance of GFP-surrogates as internal nucleobase replacements and suggest multiple ways in which they may be useful tools for NA diagnostics.

Chimeric GFP-uracil based molecular rotor fluorophores

Uracil has been modified at the 5-position to derive a small library of nucleobase-chromophores which were inspired by green fluorescent protein (GFP). The key steps in the syntheses were Erlenmeyer azlactone synthesis followed by amination by use of hexamethyl disilazane (HMDS) to produce the imidazolinone derivatives. The uracil analogues displayed emission in the green region of visible spectrum and exhibited microenvironmental sensitivity exemplified by polarity-based solvatochromism and viscosity-dependent emission enhancement. Solid-state quantum yields of approximately 0.2 and solvent dependent emission wavelengths beyond 500 nm were observed. Select analogues were incorporated into peptide nucleic acid (PNA) strands which upon duplex formation with DNA showed good response ranging from a turn-off of fluorescence in presence of an opposing mismatched residue to a greater than 3-fold turn-on of fluorescence upon binding to fully complementary DNA strand.

DNA Oligonucleotides as Antivirals and Vaccine Constituents against SARS Coronaviruses: A Prospective Tool for Immune System Tuning

The SARS-CoV-2 pandemic has demonstrated the need to create highly effective antivirals and vaccines against various RNA viruses, including SARS coronaviruses. This paper provides a short review of innovative strategies in the development of antivirals and vaccines against SARS coronaviruses, with a focus on antisense antivirals, oligonucleotide adjuvants in vaccines, and oligonucleotide vaccines. Well-developed viral genomic databases create new opportunities for the development of innovative vaccines and antivirals using a post-genomic platform. The most effective vaccines against SARS coronaviruses are those able to form highly effective memory cells for both humoral and cellular immunity. The most effective antivirals need to efficiently stop viral replication without side effects. Oligonucleotide antivirals and vaccines can resist the rapidly changing genomic sequences of SARS coronaviruses using conserved regions of their genomes to generate a long-term immune response. Oligonucleotides have been used as excellent adjuvants for decades, and increasing data show that oligonucleotides could serve as antisense antivirals and antigens in vaccine formulations, becoming a prospective tool for immune system tuning.

Post-genomic platform for development of oligonucleotide vaccines against RNA viruses: diamond cuts diamond

The coronavirus pandemic has starkly demonstrated the need to create highly effective vaccines against various viral diseases. The emerging new platforms for vaccine creation (adenovirus vectors and mRNA vaccines) have shown their worth in the fight against the prevention of coronavirus infection. However, adenovirus vectors and mRNA vaccines have a serious disadvantage: as a rule, only the S protein of the coronavirus is presented as an antigen. This tactic for preventing infection allows the ever-mutating virus to escape quickly from the immunity protection provided by such vaccines. Today, viral genomic databases are well-developed, which makes it possible to create new vaccines on a fundamentally new post-genomic platform. In addition, the technology for the synthesis of nucleic acids is currently experiencing an upsurge in demand in various fields of molecular biology. The accumulated experience suggests that the unique genomic sequences of viruses can act as antigens that trigger powerful humoral and cellular immunity. To achieve this effect, the following conditions must be created: the structure of the nucleic acid must be single-stranded, have a permanent 3D nanostructure, and have a unique sequence absent in the vaccinated organism. Oligonucleotide vaccines are able to resist the rapidly changing genomic sequences of RNA viruses by using conserved regions of their genomes to generate a long-term immune response, acting according to the adage that a diamond cuts a diamond. In addition, oligonucleotide vaccines will not contribute to antibody-dependent enhanced infection, since the nucleic acid of the coronavirus is inside the viral particle. It is obvious that new epidemics and pandemics caused by RNA viruses will continue to arise periodically in the human population. The creation of new, safe, and effective platforms for the production of vaccines that can flexibly change and adapt to new subtypes of viruses is very urgent and at this moment should be considered as a strategically necessary task.

Ultrasonic assisted synthesis of styrylpyridinium dyes: Optical properties and DFT calculations

The ultrasonic technique has received considerable attention in several fields; in particular, it gained rapid momentum in organic synthesis due to the larger reaction rates, milder reaction conditions, and better yields. We report herein a facile synthesis of a series of styrylpyridinium based dyes under ultrasonic irradiation. Within short reaction time (15 min) under ultrasonic irradiation, compared to normal laboratory conditions, (4-16 h), we can achieve good to excellent yields. The reaction time is shortened because ultrasound can accelerate the generation of the nucleophile of the pyridinium salt and subsequently a nucleophilic addition of an aldehyde followed by dehydration affords the styrylpyridinium dye, (Knoevenagel condensation). The photophysical properties of all compounds are comprehensively investigated in different solvents. All the compounds exhibit negative solvatochromism both in absorption and fluorescence emission spectra. Such behavior is due to the higher dipole moment of these molecules at the ground state. DFT calculations were performed to understand the electronic structure of the molecules. Our results show the high efficacy of sonochemistry over other methods for preparation of styrylpyridinium dyes.

Altered Response to Total Body Irradiation of C57BL/6-Tg (CAG-EGFP) Mice

Application of green fluorescent protein (GFP) in a variety of biosystems as a unique bioindicator or biomarker has revolutionized biological research and made groundbreaking achievements, while increasing evidence has shown alterations in biological properties and physiological functions of the cells and animals overexpressing transgenic GFP. In this work, response to total body irradiation (TBI) was comparatively studied in GFP transgenic C57BL/6-Tg (CAG-EGFP) mice and C57BL/6 N wild type mice. It was demonstrated that GFP transgenic mice were more sensitive to radiation-induced bone marrow death, and no adaptive response could be induced. In the nucleated bone marrow cells of GFP transgenic mice exposed to a middle dose, there was a significant increase in both the percentage of cells expressing pro-apoptotic gene Bax and apoptotic cell death. While in wild type cells, lower expression of pro-apoptotic gene Bax and higher expression of anti-apoptotic gene Bcl-2, and significant lower induction of apoptosis were observed compared to GFP transgenic cells. Results suggest that presence of GFP could alter response to TBI at whole body, cellular and molecular levels in mice. These findings indicate that there could be a major influence on the interpretation of the results obtained in GFP transgenic mice.

Synthesis of 2'-Deoxyuridine Modified with a 3,5-Difluoro-4-Methoxybenzylidene Imidazolinone Derivative for Incorporation into Oligonucleotide Probes for Detection of HER2 Breast Cancer Marker

Nucleoside intercalator conjugates (NICs) describe an innovative methodology developed in our research group for preparation of fluorescence turn-on DNA hybridization probes targeting specific mRNA sequences (e.g., breast cancer markers). In this methodology, we conjugate a non-fluorescent intercalator to the base of a nucleic acid (e.g., uracil) via a flexible spacer. This modified monomer can be incorporated into oligonucleotides by solid-phase synthesis and a large fluorescence enhancement is observed when the modified oligonucleotide is hybridized with its complementary strand due to intercalation of the fluorophore between the two strands. 5-(6-p-Methoxybenzylidene imidazolinone-1-hexene)-2'-deoxyuridine (dU^MBI ) is a synthetic monomer to which 4-methoxybenzylidene imidazolinone (MBI), the fluorescent chromophore of green fluorescent protein (GFP), has been conjugated via a flexible spacer. The detection of human epidermal growth factor receptor 2 (HER2) mRNA by this probe has already been established by our group. The fluorescent intensity of the single-strand DNA can be considered as negligible due to the free rotation of the fluorophore. Upon hybridization, however, the flexible spacer allows for the intercalation of the fluorophore between the hybridized strands, giving rise to enhanced fluorescence and indicating the presence of target mRNA. 3,5-Difluoro-4-methoxybenzylidene (DFMBI) has enhanced photophysical properties compared to MBI fluorophore. This protocol describes a simple, reliable, efficient, and general method for the synthesis of improved derivative dU^DFMBI as a monomer of fluorescent turn-on DNA hybridization probe with application for detection of HER2 mRNA. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Synthesis of 5-[(6)-3,5-difluoro-4-methoxybenzylidene imidazolinone-1-hexene]-2'-deoxyuridine.