scholarly journals Dibenzopyridoimidazocinnolinium cations: a new family of light-up fluorescent DNA probes

2018 ◽  
Vol 5 (12) ◽  
pp. 1916-1927 ◽  
Author(s):  
Pedro Bosch ◽  
David Sucunza ◽  
Francisco Mendicuti ◽  
Alberto Domingo ◽  
Juan J. Vaquero
Keyword(s):  
Dna Binding ◽  
Fluorescence Intensity ◽  
Living Cells ◽  
Dna Probes ◽  
Live Cell ◽  
Binding Ability ◽  
Active Uptake ◽  
New Family ◽  
Cell Staining ◽  
New Compounds

A new family of weakly fluorescent azonia cations with DNA-binding ability by intercalation whose fluorescence intensity increases significantly upon DNA addition is reported. A live-cell staining cells analysis showed the capacity of these new compounds for active uptake and accumulation by living cells.

scholarly journals Activation of the DNA-binding ability of human heat shock transcription factor 1 may involve the transition from an intramolecular to an intermolecular triple-stranded coiled-coil structure.

1994 ◽  
Vol 14 (11) ◽  
pp. 7557-7568 ◽  
Author(s):  
J Zuo ◽  
R Baler ◽  
G Dahl ◽  
R Voellmy
Keyword(s):  
Transcription Factor ◽  
Heat Stress ◽  
Heat Shock ◽  
Dna Binding ◽  
Hydrophobic Interactions ◽  
Coiled Coil ◽  
Heat Shock Transcription Factor ◽  
Single Amino Acid ◽  
Binding Ability ◽  
Heat Shock Element

Heat stress regulation of human heat shock genes is mediated by human heat shock transcription factor hHSF1, which contains three 4-3 hydrophobic repeats (LZ1 to LZ3). In unstressed human cells (37 degrees C), hHSF1 appears to be in an inactive, monomeric state that may be maintained through intramolecular interactions stabilized by transient interaction with hsp70. Heat stress (39 to 42 degrees C) disrupts these interactions, and hHSF1 homotrimerizes and acquires heat shock element DNA-binding ability. hHSF1 expressed in Xenopus oocytes also assumes a monomeric, non-DNA-binding state and is converted to a trimeric, DNA-binding form upon exposure of the oocytes to heat shock (35 to 37 degrees C in this organism). Because endogenous HSF DNA-binding activity is low and anti-hHSF1 antibody does not recognize Xenopus HSF, we employed this system for mapping regions in hHSF1 that are required for the maintenance of the monomeric state. The results of mutagenesis analyses strongly suggest that the inactive hHSF1 monomer is stabilized by hydrophobic interactions involving all three leucine zippers which may form a triple-stranded coiled coil. Trimerization may enable the DNA-binding function of hHSF1 by facilitating cooperative binding of monomeric DNA-binding domains to the heat shock element motif. This view is supported by observations that several different LexA DNA-binding domain-hHSF1 chimeras bind to a LexA-binding site in a heat-regulated fashion, that single amino acid replacements disrupting the integrity of hydrophobic repeats render these chimeras constitutively trimeric and DNA binding, and that LexA itself binds stably to DNA only as a dimer but not as a monomer in our assays.

Luminescent cyclometallated platinum(ii) complexes: highly promising EGFR/DNA probes and dual-targeting anticancer agents

2018 ◽  
Vol 5 (2) ◽  
pp. 413-424 ◽  
Author(s):  
Yang Zhang ◽  
Qun Luo ◽  
Wei Zheng ◽  
Zhaoying Wang ◽  
Yu Lin ◽  
...  
Keyword(s):  
Anticancer Agents ◽  
Platinum Complexes ◽  
Living Cells ◽  
Dna Probes ◽  
High Potential ◽  
Luminescent Probes ◽  
Dual Targeting

Cyclometallated platinum complexes bearing 4-anilinoquinazolines exhibit high potential as luminescent probes for EGFR/DNA in living cells and dual-targeting anticancer agents.

scholarly journals Cloning and characterization of two mouse heat shock factors with distinct inducible and constitutive DNA-binding ability.

1991 ◽  
Vol 5 (10) ◽  
pp. 1902-1911 ◽  
Author(s):  
K D Sarge ◽  
V Zimarino ◽  
K Holm ◽  
C Wu ◽  
R I Morimoto
Keyword(s):  
Heat Shock ◽  
Dna Binding ◽  
Heat Shock Factors ◽  
Binding Ability

scholarly journals Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Linda S. Forero-Quintero ◽  
William Raymond ◽  
Tetsuya Handa ◽  
Matthew N. Saxton ◽  
Tatsuya Morisaki ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Single Molecule ◽  
Computational Models ◽  
Spatial Organization ◽  
Fluorescent Antibody ◽  
Single Gene ◽  
Single Copy ◽  
Living Cells ◽  
Live Cell

AbstractThe carboxyl-terminal domain of RNA polymerase II (RNAP2) is phosphorylated during transcription in eukaryotic cells. While residue-specific phosphorylation has been mapped with exquisite spatial resolution along the 1D genome in a population of fixed cells using immunoprecipitation-based assays, the timing, kinetics, and spatial organization of phosphorylation along a single-copy gene have not yet been measured in living cells. Here, we achieve this by combining multi-color, single-molecule microscopy with fluorescent antibody-based probes that specifically bind to different phosphorylated forms of endogenous RNAP2 in living cells. Applying this methodology to a single-copy HIV-1 reporter gene provides live-cell evidence for heterogeneity in the distribution of RNAP2 along the length of the gene as well as Serine 5 phosphorylated RNAP2 clusters that remain separated in both space and time from nascent mRNA synthesis. Computational models determine that 5 to 40 RNAP2 cluster around the promoter during a typical transcriptional burst, with most phosphorylated at Serine 5 within 6 seconds of arrival and roughly half escaping the promoter in ~1.5 minutes. Taken together, our data provide live-cell support for the notion of efficient transcription clusters that transiently form around promoters and contain high concentrations of RNAP2 phosphorylated at Serine 5.

scholarly journals Improved In Situ Hybridization Efficiency with Locked-Nucleic-Acid-Incorporated DNA Probes

2006 ◽  
Vol 72 (8) ◽  
pp. 5311-5317 ◽  
Author(s):  
Kengo Kubota ◽  
Akiyoshi Ohashi ◽  
Hiroyuki Imachi ◽  
Hideki Harada
Keyword(s):  
In Situ Hybridization ◽  
Nucleic Acid ◽  
Fluorescence Intensity ◽  
Dna Probes ◽  
Locked Nucleic Acid ◽  
Factors Affecting ◽  
Hybridization Efficiency ◽  
Probe Hybridization ◽  
Major Factors

ABSTRACT Low signal intensity due to poor probe hybridization efficiency is one of the major drawbacks of rRNA-targeted in situ hybridization. There are two major factors affecting the hybridization efficiency: probe accessibility and affinity to the targeted rRNA molecules. In this study, we demonstrate remarkable improvement in in situ hybridization efficiency by applying locked-nucleic-acid (LNA)-incorporated oligodeoxynucleotide probes (LNA/DNA probes) without compromising specificity. Fluorescently labeled LNA/DNA probes with two to four LNA substitutions exhibited strong fluorescence intensities equal to or greater than that of probe Eub338, although these probes did not show bright signals when they were synthesized as DNA probes; for example, the fluorescence intensity of probe Eco468 increased by 22-fold after three LNA bases were substituted for DNA bases. Dissociation profiles of the probes revealed that the dissociation temperature was directly related to the number of LNA substitutions and the fluorescence intensity. These results suggest that the introduction of LNA residues in DNA probes will be a useful approach for effectively enhancing probe hybridization efficiency.

Organic/Inorganic Hybrid Silicate Materials for Optical Applications; Highly Fluorinated Hybrid Glasses Doped with (Erbium-ions/CdSe nanoparticles) for Laser Amplifier Material

2004 ◽  
Vol 846 ◽  
Author(s):  
Kyung M. Choi ◽  
John A. Rogers
Keyword(s):  
Fluorescence Intensity ◽  
Nano Particles ◽  
Laser Amplifier ◽  
Inorganic Hybrid ◽  
New Family ◽  
Erbium Ions ◽  
Optical Applications ◽  
Hybrid Silicate ◽  
Chemical Strategy ◽  
Silicate Materials

A new family of organic/inorganic hybrid silicate materials, bridged polysilsesquioxanes, was designed and synthesized through a molecular-level mixing technique. Since hybrid materials in the molecular-composite level, whose domain sizes are in the nanometer-scale, and whose constituents often lose individual identities and thus create new properties, we obtained a set of improved properties from those organically modified glasses. By modifying the Si-O-Si polymeric network, in this study, we produced controllable, porous hybrid glasses for facile and uniform doping of various ions, metals or semiconductor particles. By taking advantage of void volume created in those molecularly modified silicate systems, novel optical materials with designed properties can thus be achieved. Via a chemical strategy, we designed hexylene- or fluoroalkylene-bridged hybrid glasses doped with both Er+3 ions and CdSe nano-particles for the development of new laser amplifier materials. In photoluminescence experiments, a significant enhancement in fluorescence intensity at 1540 nm has been obtained from the fluoroalkylene-bridged glass. The presence of CdSe nano-particles, by virtue of their low phonon energy, also appears to significantly influence the nature of the surrounding environment of Er+3 ions in those modified silicate systems, resulting in the increased fluorescence intensity.

scholarly journals The AP2 domain of APETALA2 defines a large new family of DNA binding proteins in Arabidopsis

1997 ◽  
Vol 94 (13) ◽  
pp. 7076-7081 ◽  
Author(s):  
J. K. Okamuro ◽  
B. Caster ◽  
R. Villarroel ◽  
M. Van Montagu ◽  
K. D. Jofuku
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
New Family ◽  
Ap2 Domain

DNA binding ability and cytotoxicity, cell cycle arrest and apoptosis inducing properties of a benzochromene derivative against K562 human leukemia cells

2021 ◽  
pp. 1-22
Author(s):  
Mina Hanifeh Ahagh ◽  
Gholamreza Dehghan ◽  
Majid Mahdavi ◽  
Mohammad Ali Hosseinpour Feizi ◽  
Reza Teimuri-Mofrad ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Binding ◽  
Cell Cycle Arrest ◽  
Leukemia Cells ◽  
Human Leukemia ◽  
Binding Ability ◽  
Cycle Arrest ◽  
Human Leukemia Cells

Circ-GALNT16 Restrains Colorectal Cancer Progression by Enhancing the SUMOylation of hnRNPK

2021 ◽  
Author(s):  
Chaofan Peng ◽  
Yuqian Tan ◽  
Peng Yang ◽  
Kangpeng Jin ◽  
Chuan Zhang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Dna Binding ◽  
Rna Sequencing ◽  
Cancer Progression ◽  
Molecular Mechanisms ◽  
Transcriptional Level ◽  
Multiple Cancer ◽  
Binding Ability ◽  
Colorectal Cancer Progression

Abstract BackgroundEmerging studies have investigated circRNAs as significant regulation factors in multiple cancer progression. Nevertheless, the biological functions and underlying mechanisms of circRNAs in colorectal cancer progression remain unclear.MethodsA novel circRNA (circ-GALNT16) was identified by microarray and qRT-PCR. A series of phenotype experiments in vitro and vivo were performed to investigate the role of circ-GALNT16 in CRC. FISH, RNA pulldown assay, RIP assay, RNA sequencing, coimmunoprecipitation, and ChIP were constructed to explore the molecular mechanisms of circ-GALNT16 in colorectal cancer.ResultsCirc-GALNT16 was downregulated in colorectal cancer and negatively correlated with poor prognosis. Circ-GALNT16 suppressed the proliferation and metastasis ability of colorectal cancer in vitro and vivo. Mechanistically, circ-GALNT16 could bind to the KH3 domain of heterogeneous nuclear ribonucleoprotein K (hnRNPK), which resulted in the SUMOylation of hnRNPK. Additionally, circ-GALNT16 could enhance the hnRNPK-p53 complex by facilitating the SUMOylation of hnRNPK. Furthermore, RNA sequencing assay identified serpin family E member 1 as the target gene of circ-GALNT16 at the transcriptional level. Rescue assays revealed that circ-GALNT16 regulated the expression of Serpine1 by inhibiting the deSUMOylation of hnRNPK mediated by SUMO specific peptidase 2 and then regulating the sequence-specific DNA binding ability of the hnRNPK-p53 transcriptional complex.ConclusionsCirc-GALNT16 suppressed CRC progression via inhibiting Serpine1 expression through adjusting the sequence-specific DNA binding ability of the SENP2-mediated hnRNPK-p53 transcriptional complex and might work as a biomarker and therapeutic target for CRC.

Abstract 16877: Correlation of Antibody Binding Strength to Complement Fixation

Circulation ◽  
2014 ◽  
Vol 130 (suppl_2) ◽  
Author(s):  
Vishal Y Parikh ◽  
Nancy Reinsmoen ◽  
Jignesh Patel ◽  
Zhe Yu ◽  
Frank Liou ◽  
...  
Keyword(s):  
Fluorescence Intensity ◽  
Heart Transplant ◽  
Binding Assay ◽  
Complement Fixation ◽  
Antibody Binding ◽  
Binding Ability ◽  
Binding Strength ◽  
Desensitization Therapy ◽  
Positive Rate ◽  
Correlation Statistics

Background: In patients (pts) who are highly sensitized, desensitization therapy is commonly applied to reduce antibody (Abs) load and to reduce potential morbidity and mortality following heart transplant (HTx). It is not known as to what level of antibody binding is needed to initiate desensitization therapy. It is believed that high binding Abs may have the ability to fix complement and lead to cytotoxicity. Methods: Between 2011 and 2012 we assessed 13 highly sensitized pts who were noted to have standardized fluorescence intensity (SFI) >100,000 pretransplant. A complement binding assay (C1q binding assay) was then applied to these Abs to assess for a correlation of binding to cytotoxicity. Correlation statistics were used to derive significance between higher antibody binding and capacity to bind complement. Results: There seems to be no correlation between the different binding strength and C1q positivity. However, when evaluating Luminex 1:8 test, there seems to be correlation between class I binding strength with C1q positivity. There was C1q positive rate of 10.8% in SFI 200,000 range. Conclusions: Undiluted antibodies do not correlate to C1q binding ability. However the 1:8 dilution test seems to provide an better prediction of complement binding. 1:8 dilutions should be performed to accurately assess the ability for antibodies to bind complement.

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