scholarly journals Disassembly of Dimeric Cyanine Dye Supramolecular Assembly by Tetramolecular G-quadruplex Dependence on Linker Length and Layers of G-quartet

Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 2015 ◽  
Author(s):  
Lijia Yu ◽  
Yansong Zhang ◽  
Chunguang Ding ◽  
Xiaodong Shi
Keyword(s):  
Supramolecular Assembly ◽  
Cyanine Dyes ◽  
Binding Mode ◽  
Cyanine Dye ◽  
Linker Length ◽  
Disassembly Process ◽  
1H Nmr Titration ◽  
Repeat Units ◽  
G Quadruplex ◽  
Photochemical Properties

Cyanine dyes have been widely applied in various biological systems owing to their specific photochemical properties. Assembly and disassembly process of cyanine dyes were constructed and regulated by special biomolecules. In this paper, dimeric cyanine dyes with different repeat units (oligo-oxyethylene) in linker (TC-Pn) (n = 3–6) were found to form H-aggregates or mixture aggregates in PBS. These aggregates could be disassembled into dimer and/or monomer by (TGnT) tetramolecular G-quadruplexes (n = 3–6, 8), which were affected by the linker length of dimeric cyanine dyes and layers of G-quartets. The 1H-NMR titration results suggest that the binding mode of dimeric cyanine dye with TGnT might be on both ends—stacking like a clip. This binding mode could clearly explain that matching structures between dimeric cyanine dyes and TGnT quadruplexes could regulate the disassembly properties of aggregates. These results could provide clues for the development of highly specific G-quadruplex probes.

Targeting of parallel c-myc G-quadruplex by dimeric cyanine dye supramolecular assembly: dependence on the linker length

The Analyst ◽  
2015 ◽  
Vol 140 (5) ◽  
pp. 1637-1646 ◽  
Author(s):  
Lijia Yu ◽  
Qianfan Yang ◽  
Junfeng Xiang ◽  
Hongxia Sun ◽  
Lixia Wang ◽  
...  
Keyword(s):  
Supramolecular Assembly ◽  
Cyanine Dyes ◽  
Cyanine Dye ◽  
Linker Length ◽  
G Quadruplex

The recognizing ability of parallel c-myc G-quadruplex by dimeric cyanine dyes depends on their linker length.

scholarly journals Albumin-chaperoned cyanine dye yields superbright NIR-II fluorophore with enhanced pharmacokinetics

2019 ◽  
Vol 5 (9) ◽  
pp. eaaw0672 ◽  
Author(s):  
Rui Tian ◽  
Qiao Zeng ◽  
Shoujun Zhu ◽  
Joseph Lau ◽  
Swati Chandra ◽  
...  
Keyword(s):  
High Performance ◽  
Tumor Imaging ◽  
Supramolecular Assembly ◽  
Cyanine Dyes ◽  
Circulation Time ◽  
Cyanine Dye ◽  
Tissue Imaging ◽  
Quantum Yields ◽  
Scattering Coefficients ◽  
Targeting Ability

NIR-II fluorescence imaging greatly reduces scattering coefficients for nearly all tissue types at long wavelengths, benefiting deep tissue imaging. However, most of the NIR-II fluorophores suffer from low quantum yields and/or short circulation time that limit the quality of NIR-II imaging. Here, we engineered a supramolecular assembly of protein complex with lodged cyanine dyes to produce a brilliant NIR-II fluorophore, providing a NIR-II quantum yield of 21.2% with prolonged circulation time. Computational modeling revealed the mechanism for fluorescence enhancement and identified key parameters governing albumin complex for NIR-II fluorophores. Our complex afforded high-resolution microvessel imaging, with a 3-hour imaging window compared to 2 min for free dye alone. Furthermore, the complexation strategy was applied to an antibody-derived assembly, offering high-contrast tumor imaging without affecting the targeting ability of the antibody. This study provides a facile strategy for producing high-performance NIR-II fluorophores by chaperoning cyanine dyes with functional proteins.

scholarly journals A dual-site simultaneous binding mode in the interaction between parallel-stranded G-quadruplex [d(TGGGGT)] 4 and cyanine dye 2,2′-diethyl-9-methyl-selenacarbocyanine bromide

2012 ◽  
Vol 41 (4) ◽  
pp. 2709-2722 ◽  
Author(s):  
Wei Gai ◽  
Qianfan Yang ◽  
Junfeng Xiang ◽  
Wei Jiang ◽  
Qian Li ◽  
...  
Keyword(s):  
Binding Mode ◽  
Cyanine Dye ◽  
G Quadruplex ◽  
Dual Site

Recognizing parallel-stranded G-quadruplex by cyanine dye dimer based on dual-site binding mode

2015 ◽  
Vol 26 (6) ◽  
pp. 705-708 ◽  
Author(s):  
Li-Jia Yu ◽  
Wei Gai ◽  
Qian-Fan Yang ◽  
Jun-Feng Xiang ◽  
Hong-Xia Sun ◽  
...  
Keyword(s):  
Binding Mode ◽  
Cyanine Dye ◽  
G Quadruplex ◽  
Dual Site ◽  
Site Binding

A cyanine dye supramolecular FRET switch driven by G-quadruplex to monitor mitophagy

2021 ◽  
pp. 109429
Author(s):  
Xiaomeng Guo ◽  
Dawei Yang ◽  
Ranran Sun ◽  
Qian Li ◽  
Hongyan Du ◽  
...  
Keyword(s):  
Cyanine Dye ◽  
G Quadruplex

scholarly journals G-Quadruplexes and Their Ligands: Biophysical Methods to Unravel G-Quadruplex/Ligand Interactions

2021 ◽  
Vol 14 (8) ◽  
pp. 769
Author(s):  
Tiago Santos ◽  
Gilmar F. Salgado ◽  
Eurico J. Cabrita ◽  
Carla Cruz
Keyword(s):  
High Throughput ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Binding Mode ◽  
Titration Calorimetry ◽  
Apparent Affinity ◽  
G Quadruplex ◽  
Ligand Interactions ◽  
Types Of Information ◽  
Fluorescent Intercalator Displacement

Progress in the design of G-quadruplex (G4) binding ligands relies on the availability of approaches that assess the binding mode and nature of the interactions between G4 forming sequences and their putative ligands. The experimental approaches used to characterize G4/ligand interactions can be categorized into structure-based methods (circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography), affinity and apparent affinity-based methods (surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and mass spectrometry (MS)), and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting, G4-fluorescent intercalator displacement assay (G4-FID), affinity chromatography and microarrays. Each method has unique advantages and drawbacks, which makes it essential to select the ideal strategies for the biological question being addressed. The structural- and affinity and apparent affinity-based methods are in several cases complex and/or time-consuming and can be combined with fast and cheap high-throughput approaches to improve the design and development of new potential G4 ligands. In recent years, the joint use of these techniques permitted the discovery of a huge number of G4 ligands investigated for diagnostic and therapeutic purposes. Overall, this review article highlights in detail the most commonly used approaches to characterize the G4/ligand interactions, as well as the applications and types of information that can be obtained from the use of each technique.

scholarly journals Novel Trimethine Cyanine Dye as Potential Amyloid Marker

2018 ◽  
Keyword(s):  
Absorption Spectra ◽  
Electrostatic Interactions ◽  
Amyloid Fibrils ◽  
Binding Mode ◽  
Docking Studies ◽  
Cyanine Dye ◽  
Dye Absorption ◽  
Self Association ◽  
A Chain ◽  
Log Normal

The applicability of the novel cyanine dye AK 3-1 to the detection and characterization of pathogenic protein aggregates, amyloid fibrils, was tested using the absorption spectroscopy technique. In an organic solvent dimethyl sulfoxide (DMSO), absorption spectra of AK3-1 exhibits vibrational structure with the relative intensity of 0-0 sub-band being higher than that for the 0-1 sub-band. In an aqueous phase the dye absorption band undergoes hypsochromic shift relative to DMSO due to H-aggregation of the dye. The interaction of AK3-1 with the native and fibrillar insulin was followed by the decrease of monomer band and the enhancement of H-dimer band. To evaluate the relative contributions of the monomeric and aggregated forms, the absorption spectra of the protein-bound dye were deconvoluted using the asymmetric log-normal (LN) function. The analysis of the set of fitting parameters provides evidence for the protein-induced AK3-1 self-association into the head-to-head dimers, with the magnitude of this effect being much more pronounced for fibrillar protein form. The molecular docking studies showed that the AK3-1 monomer tends to associate with the specific arrangement of side chains in the β-sheet formed by L17 leucine residues (of the insulin B-chain), located on the dry steric zipper interface of the fibril, while the dye dimers form stable complexes with the amyloid groove formed by the residues Q15 and E17 of the A-chain, and located on the wet interface of the fibril. The latter binding site is more easily accessible and is additionally stabilized by the electrostatic interactions between the positively charged dye and the E17 residue. This binding mode seems to be prevailing over that for the AK3-1 monomers. Based on the results obtained, AK3-1 may be recommended as a prospective amyloid marker complementary to the classical amyloid reporters Thioflavin T and Congo Red.

scholarly journals Visible-Light Photoswitching of G-Quadruplex Ligand Binding Mode Allows Reversible Control of G-Tetrad Structure

2020 ◽  
Author(s):  
Michael O'Hagan ◽  
Javier Ramos Soriano ◽  
Susanta Haldar ◽  
Juan Carlos Morales ◽  
Adrian Mulholland ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Visible Light ◽  
Uv Light ◽  
Binding Mode ◽  
High Energy ◽  
Light Sources ◽  
Biologically Relevant ◽  
G Quadruplex ◽  
Potential Applications ◽  
Robust Regulation

<div><p>Photoresponsive ligands for G-quadruplex oligonucleotides (G4) offer exciting opportunities for the reversible regulation of these assemblies with potential applications in biological chemistry and responsive nanotechnology. However, achieving the robust regulation of G4 ligand activity with low-energy visible light sources that are easily accessible and compatible with biological systems remains a significant challenge to realizing these applications. Herein, we report the G4-binding properties of a photoresponsive dithienylethene (DTE). We demonstrate the first example of G4-specific acceleration of the photoswitching kinetics of a small molecule and the visible-light mediated switching of the G4 ligand binding mode in physiologically-relevant conditions, which in turn allows control over the G4 tetrad structure of telomeric G4 in potassium buffer. The process is fully reversible and avoids the need for high-energy UV light. This affords an efficient, practical and biologically-relevant means of control that may be applied in the generation of new responsive G4/ligand supramolecular systems.</p></div><br>

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