Interaction of bis-aryl functionalized molecules with nucleosides and nucleic acids

Abstract

A series of novel molecules with a cyclen (1,4,7,10-tetraazacyclododecane) moiety appended on and bearing different aromatic fragments in the structures were synthesized and characterized. The binding activities of these compounds towards DNA were systematically studied by spectroscopic, viscometric and gel electrophoresis methods. The results suggest that the stacking interaction plays an important role in improving the DNA binding ability of the compounds. The binding modes of the compounds towards DNA are also affected by the sizes of the aromatic rings. The binding interaction between binaphthyl compound 1b and several nucleosides was studied by fluorescence titration. Stacking interaction and hydrophobic interaction play the key role in such non-selective binding process.stacking and hydrophobic interactions, DNA binding, aromatic compounds, nucleosides, oligonucleotides

mtDNA-Specific Ultrasensitive Near-Infrared Fluorescent Probe Enables the Differentiation of Healthy and Apoptotic Cells

“…Furthermore, the intensity at 277 nm was enhanced (Figure c,e), and the intensity at 246 nm was reduced (Figure c,d) with increasing concentrations of YON (0 to 120.0 μM). These results further confirmed that YON could strongly bind to DNA through interacting with the minor grooves, resulting in negligible damage to the DNA. , …”

“…These results further confirmed that YON could strongly bind to DNA through interacting with the minor grooves, resulting in negligible damage to the DNA. 24,25 To explain the fluorescence response mechanism, the HOMO and LUMO energy changes and conformational changes of YON before and after binding to mtDNA were simulated using Gaussian 16. Figure 3a,b indicated that the energy of the HOMO and the LUMO and the energy gap (ΔE) were lower for YON, when bound with mtDNA.…”

“…Fluorescent organic small molecules as probes with an easily adjustable structure can specifically bind to DNA and emit various fluorescence signals. Numerous studies have shown that fluorescent probes can interact with DNA through electrostatic interaction, intercalative binding, and groove association to realize specific and highly sensitive detection for DNA. − In addition, near-infrared fluorescent probes can avoid endogenous fluorescence interference from the organism, resulting in minimal cell damage and exhibiting enhanced tissue penetration ability. These properties provide the possibility of ultrasensitive, specific, and minimal damage monitoring of mtDNA in vivo.…”

“…These properties provide the possibility of ultrasensitive, specific, and minimal damage monitoring of mtDNA in vivo. Up to now, a variety of DNA-related near-infrared fluorescent probes have been reported. − For example, a near-infrared fluorescent switch-on probe, quinone cyanine dithiazole, was reported that could recognize AT-rich DNA through minor groove binding . Recently, three benzothiazole-based NIR probes were designed for the specific recognition of G-quadruplex DNA in mitochondria .…”

Synthesis, DNA binding and cleavage studies of the copper(II) complexes of PNA-cyclen conjugates

“…Many cyclen complexes were used as chemical nucleases in DNA recognition and cleavage [17][18][19]. Among all the artificial nucleases, transition metal complexes have been studied extensively due to their diversity in structure and reactivity [20,21].…”