New Water‐Soluble Cationic Poly(<i>p</i>‐phenylenevinylene) Derivative: the Interaction with DNA and Selective Fluorescence Enhancement Induced by ssDNA

Zhang, Wenjun; Xu, Li; Qin, Jingui; Yang, Chuluo

doi:10.1002/marc.201200696

Cited by 8 publications

(2 citation statements)

References 41 publications

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“…Hydrogen-bond interactions are likely the main force dictating DNA sequence reading by proteins [14]. The hydrophobic bases are more exposed in single-stranded DNA than in dsDNA, leading to more hydrophobic interactions [15,16]. We examined how these interactions affect the binding of protein and DNA by analysing the distribution of these interactions throughout the hTLR9 ECD-CpG ODN complex.…”

Section: Resultsmentioning

confidence: 99%

Toll-like receptor 9 interaction with CpG ODN – An in silico analysis approach

Zhou¹,

Pan

et al. 2013

Theor Biol Med Model

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BackgroundToll-like receptor 9 (TLR9) recognises unmethylated CpG DNA and activates a signalling cascade, leading to the production of inflammatory cytokines such as TNF-α, IL-1, IL-6 and IL-12 via the adaptor protein MyD88. However, the specific sequence and structural requirements of the CpG DNA for the recognition of and binding to TLR9 are unknown. Moreover, the 3D structures of TLR9 and the TLR9-ODN complex have not been determined. In this study, we propose a reliable model of the interaction of the TLR9 ECD with CpG ODN using bioinformatics tools.ResultsThe three-dimensional structures of two TLR9 ECD-CpG ODN complexes were constructed using a homology modelling and docking strategy. Based on the models of these complexes, the TLR9 ECD-CpG ODN interaction patterns were calculated. The results showed that the interface between the human TLR9 and the CpG ODN molecule is geometrically complementary. The computed molecular interactions indicated that LRR11 is the main region of TLR9 that binds to CpG ODN and that five positively charged residues within LRR11 are involved in the binding of the TLR9 ECD to the CpG ODN. Observations in the close-up view of these interactions indicated that these five positively charged residues contribute differently to the binding region within the TLR9 ECD-CpG ODN complex. 337Arg and 338Lys reside in the binding sites of ODN, forming hydrogen bonds and direct contacts with the CpG ODN, whereas 347Lys, 348Arg, and 353His do not directly contact the CpG ODN. These results are in agreement with previously reported experimental data.ConclusionIn this study, we present two structural models for the human and mouse TLR9 ECD in a complex with CpG ODN. Some features predicted by this model are consistent with previously reported experimental data. This complex model may lead to a better understanding of the function of TLR9 and its interaction with CpG ODN and will improve our understanding of TLR9-ligand interaction in general.

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Section: Resultsmentioning

confidence: 99%

Toll-like receptor 9 interaction with CpG ODN – An in silico analysis approach

Zhou¹,

Pan

et al. 2013

Theor Biol Med Model

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“…The intensity was increased at 70% water content, after which it decreased sharply up to 90% water content. The emission peak is dominated by the effect of intramolecular charge transfer and the conformation of the polymer chain, whereas the emission intensity is mainly contributed to by the synergistic effect of polymer aggregates and the viscosity of the mixture solvent [36,85,86]. Polymers tend to form aggregates in water because of interchain hydrophobic interactions.…”

Section: Emission Properties Of Polymers 1-5 In the Solid State (Film And Powdered)mentioning

confidence: 99%

Poly(Pyridinium Salt)s Containing 2,7-Diamino-9,9′-Dioctylfluorene Moieties with Various Organic Counterions Exhibiting Both Lyotropic Liquid-Crystalline and Light-Emitting Properties

Bhowmik

Koh

et al. 2021

Molecules

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A series of poly(pyridinium salt)s-fluorene main-chain ionic polymers with various organic counterions were synthesized by using ring-transmutation polymerization and metathesis reactions. Their chemical structures were characterized by Fourier Transform Infrared (FTIR), proton (1H), and fluorine 19 (19F) nuclear magnetic resonance (NMR) spectrometers. These polymers showed a number-average molecular weight (Mns) between 96.5 and 107.8 kg/mol and polydispersity index (PDI) in the range of 1.12–1.88. They exhibited fully-grown lyotropic phases in polar protic and aprotic solvents at different critical concentrations. Small-angle X-ray scattering for one polymer example indicates lyotropic structure formation for 60–80% solvent fraction. A lyotropic smectic phase contains 10 nm polymer platelets connected by tie molecules. The structure also incorporates a square packing motif within platelets. Thermal properties of polymers were affected by the size of counterions as determined by differential scanning calorimetry and thermogravimetric analysis measurements. Their ultraviolet-visible (UV-Vis) absorption spectra in different organic solvents were essentially identical, indicating that the closely spaced π-π* transitions occurred in their conjugated polymer structures. In contrast, the emission spectra of polymers exhibited a positive solvatochromism on changing the polarity of solvents. They emitted green lights in both polar and nonpolar organic solvents and showed blue light in the film-states, but their λem peaks were dependent on the size of the counterions. They formed aggregates in polar aprotic and protic solvents with the addition of water (v/v, 0%–90%), and their λem peaks were blue shifted.

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Strong Fluorescence of Poly(N-vinylpyrrolidone) and Its Oxidized Hydrolyzate

Song

Lin

Zhu

et al. 2014

Macromol. Rapid Commun.

129

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Discovering fluorescence of existing compounds, which are generally regarded as non-fluorescent, is of important academic and technical significance. This article reports the fluorescence of common compounds containing pyrrolidone ring(s) and their oxidized hydrolyzates. Poly(N-vinylpyrrolidone) (PVP), polymerized from a very weak fluorescent monomer N-vinyl-2-pyrrolidone (NVP), exhibits strong intrinsic fluorescence. Moreover, the fluorescence of its "hydrolyzate" is dramatically enhanced by about 1000 times. The "hydrolyzate" of N-methyl-pyrrolidone (NMP) also exhibits significantly enhanced fluorescence. By studying the chemical structures and fluorescence of the hydrolyzates, the enhanced fluorescence is attributed to the formation of secondary amine oxide. The much stronger fluorescence of the polymers compared to the corresponding small molecular compounds is ascribed to the "aggregation-induced emission" (AIE) effect of the luminophores. PVP and its oxidized hydrolyzate also show some phenomena different to the common AIE effect. The fluorescence of PVP and its oxidized hydrolyzate shows stimuli response to metal ions and pH values. This study introduces novel fluorescent materials for various potential applications.

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New Water‐Soluble Cationic Poly(p‐phenylenevinylene) Derivative: the Interaction with DNA and Selective Fluorescence Enhancement Induced by ssDNA

Cited by 8 publications

References 41 publications

Toll-like receptor 9 interaction with CpG ODN – An in silico analysis approach

Toll-like receptor 9 interaction with CpG ODN – An in silico analysis approach

Poly(Pyridinium Salt)s Containing 2,7-Diamino-9,9′-Dioctylfluorene Moieties with Various Organic Counterions Exhibiting Both Lyotropic Liquid-Crystalline and Light-Emitting Properties

Strong Fluorescence of Poly(N-vinylpyrrolidone) and Its Oxidized Hydrolyzate

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