Biomaterial Database

Spectroscopic Properties of Two 5'-(4-Dimethylamino)Azobenzene Conjugated G-Quadruplex Forming Oligonucleotides. 2020

Concetta Imperatore, and Antonio Varriale, and Elisa Rivieccio, and Angela Pennacchio, and Maria Staiano, and Sabato D'Auria, and Marcello Casertano, and Carlo Altucci, and Mohammadhassan Valadan, and Manjot Singh, and Marialuisa Menna, and Michela Varra

Department of Pharmacy, School of Medicine, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy.

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.

UI	MeSH Term	Description	Entries
D009841	Oligonucleotides	Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)	Oligonucleotide
D001391	Azo Compounds	Organic chemicals where aryl or alkyl groups are joined by two nitrogen atoms through a double bond (R-N	Azo Dye,Azo Dyes,Compounds, Azo,Dye, Azo,Dyes, Azo
D013057	Spectrum Analysis	The measurement of the amplitude of the components of a complex waveform throughout the frequency range of the waveform. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)	Spectroscopy,Analysis, Spectrum,Spectrometry
D052157	Aptamers, Nucleotide	Nucleotide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.	DNA Aptamer,DNA Aptamers,RNA Aptamers,Rna Aptamer,Nucleotide Aptamers,Oligonucleotide Ligands, DNA,Oligonucleotide Ligands, RNA,Aptamer, DNA,Aptamer, Rna,Aptamers, DNA,Aptamers, RNA,DNA Oligonucleotide Ligands,RNA Oligonucleotide Ligands
D054856	G-Quadruplexes	Higher-order DNA and RNA structures formed from guanine-rich sequences. They are formed around a core of at least 2 stacked tetrads of hydrogen-bonded GUANINE bases. They can be formed from one two or four separate strands of DNA (or RNA) and can display a wide variety of topologies, which are a consequence of various combinations of strand direction, length, and sequence. (From Nucleic Acids Res. 2006;34(19):5402-15)	DNA G-Quadruplexes,DNA, Quadruplex,G-Quadruplexes, DNA,G-Quadruplexes, RNA,Guanine-Quadruplexes,Guanine-Quartets,Guanine-Tetrads,Quadruplex DNA,RNA, G-Quadruplexes,Tetraplex DNA,DNA G Quadruplexes,DNA, Tetraplex,G Quadruplexes,G Quadruplexes, DNA,G Quadruplexes, RNA,G-Quadruplexes RNA,G-Quadruplexes RNAs,Guanine Quadruplexes,Guanine Quartets,Guanine Tetrads,Guanine-Quartet,Guanine-Tetrad,RNA G-Quadruplexes,RNA, G Quadruplexes,RNAs, G-Quadruplexes