scholarly journals Spectroscopic Properties of Two 5′-(4-Dimethylamino)Azobenzene Conjugated G-Quadruplex Forming Oligonucleotides

2020 ◽  
Vol 21 (19) ◽  
pp. 7103
Author(s):  
Concetta Imperatore ◽  
Antonio Varriale ◽  
Elisa Rivieccio ◽  
Angela Pennacchio ◽  
Maria Staiano ◽  
...  

The synthesis of two 5′-end (4-dimethylamino)azobenzene conjugated G-quadruplex forming aptamers, the thrombin binding aptamer (TBA) and the HIV-1 integrase aptamer (T30695), was performed. Their structural behavior was investigated by means of UV, CD, fluorescence spectroscopy, and gel electrophoresis techniques in K+-containing buffers and water-ethanol blends. Particularly, we observed that the presence of the 5′-(4-dimethylamino)azobenzene moiety leads TBA to form multimers instead of the typical monomolecular chair-like G-quadruplex and almost hampers T30695 G-quadruplex monomers to dimerize. Fluorescence studies evidenced that both the conjugated G-quadruplexes possess unique fluorescence features when excited at wavelengths corresponding to the UV absorption of the conjugated moiety. Furthermore, a preliminary investigation of the trans-cis conversion of the dye incorporated at the 5′-end of TBA and T30695 showed that, unlike the free dye, in K+-containing water-ethanol-triethylamine blend the trans-to-cis conversion was almost undetectable by means of a standard UV spectrophotometer.

2020 ◽  
Vol 17 ◽  
Author(s):  
Ahmed Nuri Kursunlu ◽  
Elif Bastug ◽  
Ersin Guler

Background: Chemosensor compounds are useful for sensitive selective detection of cations and anions with fluorophore groups in an attempt to develop the effective selectivity of the sensors. Although familiar fluorescent sensors utilizing inter-molecular interactions with the cations and anions, an extraordinary endeavor was executed the preparation of fluorescent-based sensor compounds. 4,4-difluoro-4- bora-3a,4a-diaza-s-indacene (Bodipy) and its derivatives were firstly used as an agent in the imaging of biomolecules due to their interesting structures, complexation, and fluorogenic properties. Among the fluorescent chemosensors used for cations and anions, Bodipy-based probes stand out owing to the excellent properties such as sharp emission profile, high stability, etc. In this review, we emphasize the Bodipy-based chemosensor compounds, which have been used to image cations and anions in living cells, because of as well as the biocompatibility and spectroscopic properties. Methods: Research and online content related to chemosensor online activity is reviewed. The advances, sensing mechanisms and design strategies of the fluorophore exploiting selective detection of some cation and anions with Bodipy-based chemosensors are explained. It could be claimed that the using of Bodipy-based chemosensors is very important for cations and anions in bio-imaging applications. Results: Molecular sensors or chemosensors are molecules that show a change can be detected when affected by the analyte. They are capable of producing a measurable signal when they are selective for a particular molecule. Molecular and ion recognition that it is important in biological systems such as enzymes, genes, environment, and chemical fields. Due to the toxic properties of many heavy metal ions, it is of great importance to identify these metals due to their harmful effects on living metabolism and the pollution they create in the environment. This process can be performed with analytical methods based on atomic absorption and emission. The fluorescence methods among chemosensor systems have many advantages such as sensitivity, selectivity, low price, simplicity of using the instrument and direct determination in solutions. The fluorescence studies can be applied at nanomolar concentrations. Conclusion: During a few decades, a lot of Bodipy-based chemosensors for the detection of cations & anions have been investigated in bio-imaging applications. For the Bodipy-based fluorescent chemosensors, the Bodipy derivatives were prepared by different ligand groups for the illumination of the photophysical and photochemical properties. The synthesized Bodipy-based chemosensors have remarkable photophysical properties, such as a high quantum yield, strong molar absorption coefficient etc. Moreover, these chemosensors were successfully implemented on living organisms for the detection of analytes.


Sensors ◽  
2021 ◽  
Vol 21 (5) ◽  
pp. 1715
Author(s):  
Nada Elgiddawy ◽  
Shiwei Ren ◽  
Wadih Ghattas ◽  
Waleed M. A. El Rouby ◽  
Ahmed O. El-Gendy ◽  
...  

Designing therapeutic and sensor materials to diagnose and eliminate bacterial infections remains a significant challenge for active theragnostic nanoprobes. In the present work, fluorescent/electroactive poly(3-hexylthiophene) P3HT nanoparticles (NPs) stabilized with quaternary ammonium salts using cetyltrimethylammonium bromide (CTAB), (CTAB-P3HT NPs) were prepared using a simple mini-emulsion method. The morphology, spectroscopic properties and electronic properties of CTAB-P3HT NPs were characterized by DLS, zeta potential, SEM, TEM, UV-vis spectrophotometry, fluorescence spectroscopy and electrochemical impedance spectroscopy (EIS). In an aqueous solution, CTAB-P3HT NPs were revealed to be uniformly sized, highly fluorescent and present a highly positively charged NP surface with good electroactivity. Dual detection was demonstrated as the binding of the bacteria to NPs could be observed by fluorescence quenching as well as by the changes in EIS. Binding of E. coli to CTAB-P3HT NPs was demonstrated and LODs of 5 CFU/mL and 250 CFU/mL were obtained by relying on the fluorescence spectroscopy and EIS, respectively. The antimicrobial activity of CTAB-P3HT NPs on bacteria and fungi was also studied under dark and nutritive conditions. An MIC and an MBC of 2.5 µg/mL were obtained with E. coli and with S. aureus, and of 0.312 µg/mL with C. albicans. Additionally a good biocompatibility toward normal human cells (WI38) was observed, which opens the way to their possible use as a therapeutic agent.


2020 ◽  
Vol 20 (11) ◽  
pp. 6935-6942
Author(s):  
Sang-Wook Chu ◽  
Sung Soo Park ◽  
Chang-Sik Ha

In this study, we have synthesized a light-activated polymer-coated mesoporous silica nanovalve with poly(trans-4-methacryloyloxyazobenzene-co-methylmethacrylic acid-co-vinyltrimethoxysilane) (PMMV) (MSNs/PMMV) for the controlled delivery of guest molecules. The hydrophobicity of azobenzene varies depending on the structure of each isomer. Typically, trans isomers are hydrophobic due to the aromatic ring, but they become more hydrophilic when they are changed to the cis confirmation. Using this concept, we introduced PMMV as a light active nanovalve on the mesoporous silica. To optimize the coating of the light-activated polymer on mesoporous silica, we investigated the conformational change of PMMV in solutions at various pHs. PMMV has a dot-like morphology in acidic solutions under pH 4, but sheet-like morphology in solutions at pH over 4. We investigated the nanovalve behavior of MSNs/PMMV by introducing propidium iodide (PI) as guest molecules. Time-resolved fluorescence spectroscopy showed the excellent light activity of PMMV for open pores. The new PMMV-coated mesoporous silica could be applied in the smart nanovalve system for the controlled delivery of various guest molecules.


2014 ◽  
Vol 106 (2) ◽  
pp. 63a
Author(s):  
Qiaoqiao ruan ◽  
Barbie K. Ganser-Pornillos ◽  
Joseph P. skinner ◽  
Susan Gayda ◽  
Mark Yeager ◽  
...  

Molecules ◽  
2018 ◽  
Vol 23 (8) ◽  
pp. 1874 ◽  
Author(s):  
Martina Tassinari ◽  
Alberto Lena ◽  
Elena Butovskaya ◽  
Valentina Pirota ◽  
Matteo Nadai ◽  
...  

G-quadruplex (G4) nucleic acid structures have been reported to be involved in several human pathologies, including cancer, neurodegenerative disorders and infectious diseases; however, G4 targeting compounds still need implementation in terms of drug-like properties and selectivity in order to reach the clinical use. So far, G4 ligands have been mainly identified through high-throughput screening methods or design of molecules with pre-set features. Here, we describe the development of new heterocyclic ligands through a fragment-based drug discovery (FBDD) approach. The ligands were designed against the major G4 present in the long terminal repeat (LTR) promoter region of the human immunodeficiency virus-1 (HIV-1), the stabilization of which has been shown to suppress viral gene expression and replication. Our method is based on the generation of molecular fragment small libraries, screened against the target to further elaborate them into lead compounds. We screened 150 small molecules, composed by structurally and chemically different fragments, selected from commercially available and in-house compounds; synthetic elaboration yielded several G4 ligands and two final G4 binders, both embedding an amidoxime moiety; one of these two compounds showed preferential binding for the HIV-1 LTR G4. This work presents the discovery of a novel potential pharmacophore and highlights the possibility to apply a fragment-based approach to develop G4 ligands with unexpected chemical features.


2015 ◽  
Vol 43 (18) ◽  
pp. 8884-8897 ◽  
Author(s):  
Elena Tosoni ◽  
Ilaria Frasson ◽  
Matteo Scalabrin ◽  
Rosalba Perrone ◽  
Elena Butovskaya ◽  
...  

Abstract Folding of the LTR promoter into dynamic G-quadruplex conformations has been shown to suppress its transcriptional activity in HIV-1. Here we sought to identify the proteins that control the folding of this region of proviral genome by inducing/stabilizing G-quadruplex structures. The implementation of electrophorethic mobility shift assay and pull-down experiments coupled with mass spectrometric analysis revealed that the cellular protein nucleolin is able to specifically recognize G-quadruplex structures present in the LTR promoter. Nucleolin recognized with high affinity and specificity the majority, but not all the possible G-quadruplexes folded by this sequence. In addition, it displayed greater binding preference towards DNA than RNA G-quadruplexes, thus indicating two levels of selectivity based on the sequence and nature of the target. The interaction translated into stabilization of the LTR G-quadruplexes and increased promoter silencing activity; in contrast, disruption of nucleolin binding in cells by both siRNAs and a nucleolin binding aptamer greatly increased LTR promoter activity. These data indicate that nucleolin possesses a specific and regulated activity toward the HIV-1 LTR promoter, which is mediated by G-quadruplexes. These observations provide new essential insights into viral transcription and a possible low mutagenic target for antiretroviral therapy.


2000 ◽  
Vol 10 (19) ◽  
pp. 2213-2216 ◽  
Author(s):  
Makoto Koizumi ◽  
Keika Akahori ◽  
Toshinori Ohmine ◽  
Shinya Tsutsumi ◽  
Junko Sone ◽  
...  

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