scholarly journals A Personal Journey across Fluorescent Sensing and Logic Associated with Polymers of Various Kinds

Polymers ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 1351 ◽  
Author(s):  
Chao-Yi Yao ◽  
Seiichi Uchiyama ◽  
A. Prasanna de Silva
Keyword(s):  
Phase Separation ◽  
Metal Ion ◽  
Chemical Species ◽  
Polymer Science ◽  
Molecular Sensing ◽  
Fluorescent Sensing ◽  
Molecular Logic ◽  
Fluorescent Molecular Sensing ◽  
Molecular Scale ◽  
Identification Tags

Our experiences concerning fluorescent molecular sensing and logic devices and their intersections with polymer science are the foci of this brief review. Proton-, metal ion- and polarity-responsive cases of these devices are placed in polymeric micro- or nano-environments, some of which involve phase separation. This leads to mapping of chemical species on the nanoscale. These devices also take advantage of thermal properties of some polymers in water in order to reincarnate themselves as thermometers. When the phase separation leads to particles, the latter can be labelled with identification tags based on molecular logic. Such particles also give rise to reusable sensors, although molecular-scale resolution is sacrificed in the process. Polymeric nano-environments also help to organize rather complex molecular logic systems from their simple components. Overall, our little experiences suggest that researchers in sensing and logic would benefit if they assimilate polymer concepts.

scholarly journals A multicolor and ratiometric fluorescent sensing platform for metal ions based on arene–metal-ion contact

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Anna Kanegae ◽  
Yusuke Takata ◽  
Ippei Takashima ◽  
Shohei Uchinomiya ◽  
Ryosuke Kawagoe ◽  
...  
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Near Infrared ◽  
Molecular Design ◽  
Theoretical Calculations ◽  
Probe Design ◽  
One Pot ◽  
Fluorescent Sensing ◽  
Sensing Platform ◽  
Ratiometric Detection

AbstractDespite continuous and active development of fluorescent metal-ion probes, their molecular design for ratiometric detection is restricted by the limited choice of available sensing mechanisms. Here we present a multicolor and ratiometric fluorescent sensing platform for metal ions based on the interaction between the metal ion and the aromatic ring of a fluorophore (arene–metal-ion, AM, coordination). Our molecular design provided the probes possessing a 1,9-bis(2′-pyridyl)-2,5,8-triazanonane as a flexible metal ion binding unit attached to a tricyclic fluorophore. This architecture allows to sense various metal ions, such as Zn(II), Cu(II), Cd(II), Ag(I), and Hg(II) with emission red-shifts. We showed that this probe design is applicable to a series of tricyclic fluorophores, which allow ratiometric detection of the metal ions from the blue to the near-infrared wavelengths. X-ray crystallography and theoretical calculations indicate that the coordinated metal ion has van der Waals contact with the fluorophore, perturbing the dye’s electronic structure and ring conformation to induce the emission red-shift. A set of the probes was useful for the differential sensing of eight metal ions in a one-pot single titration via principal component analysis. We also demonstrate that a xanthene fluorophore is applicable to the ratiometric imaging of metal ions under live-cell conditions.

Matter, energy and information network of a graphene-peptide-based fluorescent sensing system for molecular logic computing, detection and imaging of cancer stem cell marker CD133 in cells and tumor tissues

The Analyst ◽  
2019 ◽  
Vol 144 (6) ◽  
pp. 1881-1891 ◽  
Author(s):  
Fu Rui Zhang ◽  
Jiao Yang Lu ◽  
Qing Feng Yao ◽  
Qiu Yan Zhu ◽  
Xin Xing Zhang ◽  
...  
Keyword(s):  
Stem Cell Marker ◽  
Information Network ◽  
Cancer Stem Cell Marker ◽  
Cell Marker ◽  
Fluorescent Sensing ◽  
Sensing System ◽  
Molecular Logic ◽  
Tumor Tissues ◽  
Logic Operations ◽  
Matter Energy

A graphene-peptide-based fluorescent sensing system for molecular logic operations, sensing and imaging of CD133.

scholarly journals Amorphous Mixtures of Ice and C60 Fullerene

2020 ◽  
Author(s):  
Siriney Halukeerthi ◽  
Jacob J. Shephard ◽  
Sukhpreet Talewar ◽  
John S. O. Evans ◽  
Alexander Rosu-Finsen ◽  
...  
Keyword(s):  
Phase Separation ◽  
Percolation Threshold ◽  
Thermal Desorption ◽  
Crystallization Temperature ◽  
Space Exploration ◽  
Chemical Species ◽  
C60 Fullerene ◽  
Volume Percent ◽  
Water Desorption ◽  
Amorphous Ice

Carbon and ice make up a substantial proportion of our Universe. Recent space exploration has shown that these two chemical species often coexist including on comets, asteroids and in the interstellar medium. Here we prepare mixtures of C<sub>60</sub> fullerene and H<sub>2</sub>O by vapor co-deposition at 90 K with molar C<sub>60</sub>:H<sub>2</sub>O ratios ranging from 1:1254 to 1:5. The C<sub>60</sub> percolation threshold is found between the 1:132 and 1:48 samples, corresponding to a transition from matrix-isolated C<sub>60</sub> molecules to percolating C<sub>60</sub> domains that confine the H<sub>2</sub>O. Below this threshold, the crystallization and thermal desorption properties of H<sub>2</sub>O are not significantly affected by the C<sub>60</sub>, whereas the crystallization temperature of H<sub>2</sub>O is shifted towards higher temperatures for the C<sub>60</sub>-rich samples. These C<sub>60</sub>-rich samples also display exotherms corresponding to the crystallization of C<sub>60</sub> as the two components undergo phase separation. More than 60 volume percent C<sub>60</sub> is required to significantly affect the desorption properties of H<sub>2</sub>O. A thick blanket of C<sub>60</sub> on top of pure amorphous ice is found to display large cracks due to water desorption. These findings may help understand the recently observed unusual surface features and the H<sub>2</sub>O weather cycle on the 67P/Churyumov–Gerasimenko comet.

scholarly journals HP1 proteins compact DNA into mechanically and positionally stable phase separated domains

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Madeline M Keenen ◽  
David Brown ◽  
Lucy D Brennan ◽  
Roman Renger ◽  
Harrison Khoo ◽  
...  
Keyword(s):  
Phase Separation ◽  
Single Molecule ◽  
Genome Organization ◽  
Stable Phase ◽  
Dna Molecules ◽  
Weakly Bound ◽  
Dna Compaction ◽  
Polymer Properties ◽  
Molecular Scale ◽  
Hp1 Proteins

In mammals, HP1-mediated heterochromatin forms positionally and mechanically stable genomic domains even though the component HP1 paralogs, HP1α, HP1β, and HP1γ, display rapid on-off dynamics. Here, we investigate whether phase-separation by HP1 proteins can explain these biological observations. Using bulk and single-molecule methods, we show that, within phase-separated HP1α-DNA condensates, HP1α acts as a dynamic liquid, while compacted DNA molecules are constrained in local territories. These condensates are resistant to large forces yet can be readily dissolved by HP1β. Finally, we find that differences in each HP1 paralog’s DNA compaction and phase-separation properties arise from their respective disordered regions. Our findings suggest a generalizable model for genome organization in which a pool of weakly bound proteins collectively capitalize on the polymer properties of DNA to produce self-organizing domains that are simultaneously resistant to large forces at the mesoscale and susceptible to competition at the molecular scale.

scholarly journals Zinc and Copper Ions Differentially Regulate Prion-Like Phase Separation Dynamics of Pan-Virus Nucleocapsid Biomolecular Condensates

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1179 ◽  
Author(s):  
Anne Monette ◽  
Andrew J. Mouland
Keyword(s):  
Phase Separation ◽  
Metal Ion ◽  
Rna Binding ◽  
Copper Ions ◽  
Virus Assembly ◽  
Neurological Diseases ◽  
Meta Analysis ◽  
Metal Homeostasis ◽  
Virus Infections ◽  
As Stress

Liquid-liquid phase separation (LLPS) is a rapidly growing research focus due to numerous demonstrations that many cellular proteins phase-separate to form biomolecular condensates (BMCs) that nucleate membraneless organelles (MLOs). A growing repertoire of mechanisms supporting BMC formation, composition, dynamics, and functions are becoming elucidated. BMCs are now appreciated as required for several steps of gene regulation, while their deregulation promotes pathological aggregates, such as stress granules (SGs) and insoluble irreversible plaques that are hallmarks of neurodegenerative diseases. Treatment of BMC-related diseases will greatly benefit from identification of therapeutics preventing pathological aggregates while sparing BMCs required for cellular functions. Numerous viruses that block SG assembly also utilize or engineer BMCs for their replication. While BMC formation first depends on prion-like disordered protein domains (PrLDs), metal ion-controlled RNA-binding domains (RBDs) also orchestrate their formation. Virus replication and viral genomic RNA (vRNA) packaging dynamics involving nucleocapsid (NC) proteins and their orthologs rely on Zinc (Zn) availability, while virus morphology and infectivity are negatively influenced by excess Copper (Cu). While virus infections modify physiological metal homeostasis towards an increased copper to zinc ratio (Cu/Zn), how and why they do this remains elusive. Following our recent finding that pan-retroviruses employ Zn for NC-mediated LLPS for virus assembly, we present a pan-virus bioinformatics and literature meta-analysis study identifying metal-based mechanisms linking virus-induced BMCs to neurodegenerative disease processes. We discover that conserved degree and placement of PrLDs juxtaposing metal-regulated RBDs are associated with disease-causing prion-like proteins and are common features of viral proteins responsible for virus capsid assembly and structure. Virus infections both modulate gene expression of metalloproteins and interfere with metal homeostasis, representing an additional virus strategy impeding physiological and cellular antiviral responses. Our analyses reveal that metal-coordinated virus NC protein PrLDs initiate LLPS that nucleate pan-virus assembly and contribute to their persistence as cell-free infectious aerosol droplets. Virus aerosol droplets and insoluble neurological disease aggregates should be eliminated by physiological or environmental metals that outcompete PrLD-bound metals. While environmental metals can control virus spreading via aerosol droplets, therapeutic interference with metals or metalloproteins represent additional attractive avenues against pan-virus infection and virus-exacerbated neurological diseases.

Evaluation of metal ion sensing behaviour of fluorescent probe along with its precursors: PET-CHEF mechanism, molecular logic gate behaviour and DFT studies

2019 ◽  
Vol 95 (1-2) ◽  
pp. 79-89 ◽  
Author(s):  
Chitra Varadaraju ◽  
Mosae Selvakumar Paulraj ◽  
G. Tamilselvan ◽  
I. V. Muthu Vijayan Enoch ◽  
V. Srinivasadesikan ◽  
...  
Keyword(s):  
Fluorescent Probe ◽  
Metal Ion ◽  
Logic Gate ◽  
Dft Studies ◽  
Molecular Logic Gate ◽  
Ion Sensing ◽  
Molecular Logic ◽  
Metal Ion Sensing

Target-triggered cascade recycling amplification for label-free detection of microRNA and molecular logic operations

2016 ◽  
Vol 52 (2) ◽  
pp. 402-405 ◽  
Author(s):  
Sai Bi ◽  
Jiayan Ye ◽  
Ying Dong ◽  
Haoting Li ◽  
Wei Cao
Keyword(s):  
Logic Gates ◽  
Logic Circuits ◽  
Label Free ◽  
Chemiluminescence Detection ◽  
Molecular Logic ◽  
Label Free Detection ◽  
Molecular Scale ◽  
Ultrahigh Sensitivity ◽  
Recycling Amplification ◽  
Logic Operations

A cascade recycling amplification (CRA) that implements cascade logic circuits with feedback amplification function is developed for label-free chemiluminescence detection of microRNA-122 with an ultrahigh sensitivity of 0.82 fM and excellent specificity, which is applied to construct a series of molecular-scale two-input logic gates by using microRNAs as inputs and CRA products as outputs.

Synthesis, characterization, theoretical investigations and fluorescent sensing behavior of oligomeric azine-based Fe3+Chemosensors

2021 ◽  
pp. 095400832110556
Author(s):  
Subramani Manigandan ◽  
Athianna Muthusamy ◽  
Raju Nandhakumar ◽  
Charles Immanuel David ◽  
Siddeswaran Anand
Keyword(s):  
Electrical Conductivity ◽  
Metal Ion ◽  
Fluorescent Sensing ◽  
Electrical Studies ◽  
Imine Nitrogen ◽  
Basic Set ◽  
Theoretical Investigations ◽  
Different Temperatures ◽  
Density Values ◽  
High Dielectric

Three azine oligomeric esters were synthesized, characterized by IR, UV, 1H, 13C{1H} and GPC technique, and applied to chemosensor application. The sensitivity response of the oligomers towards the metal ion was evaluated for a metal ion series. The results have shown selective and sensitive “turn off” fluorescence response towards Fe3+ ion in DMF/H2O (1:1, pH: 7.4, fluorophore: 5 μM) solution. The binding stoichiometry and binding constant of the fluorophores were calculated using the Stern–Volmer equation and Benesi–Hildebrand plots, respectively. The quenching of fluorophores on the addition of Fe3+ ion indicates the capability of fluorophore towards quantitative analysis of Fe3+. The dimer of oligomers was theoretically studied using DFT, B3LYP/6-311G level basic set to support and explain the quenching mechanism of LMCT, PET process and to explain the DC, AC electrical studies results. The electrical conductivity measurements of solid-state, I2 doped and undoped oligomers were carried out and the conductivity gradually increases with increase in iodine vapor contact time of oligomers. The electrical conductivity was related with band gap and charge density values of imine nitrogen obtained by Huckel calculations. The dielectric measurements at different temperatures and frequencies were made by two probe method. Among the oligomers, EBHAP has recorded a high dielectric constant at the low applied frequency of 50 Hz at 373 K due to loosely attached π bonds resulting good polarization.

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