DNA binding by the antimalarial compound artemisinin

AbstractArtemisinin (ART) is a vital medicinal compound that is used alone or as part of a combination therapy against malaria. ART is thought to function by attaching to heme covalently and alkylating a range of proteins. Using a combination of biophysical methods, we demonstrate that ART is bound by three-way junction and duplex containing DNA molecules. Binding of ART by DNA is first shown for the cocaine-binding DNA aptamer and extensively studied using this DNA molecule. Isothermal titration calorimetry methods show that the binding of ART is both entropically and enthalpically driven at physiological NaCl concentration. Native mass spectrometry methods confirm DNA binding and show that a non-covalent complex is formed. Nuclear magnetic resonance spectroscopy shows that ART binds at the three-way junction of the cocaine-binding aptamer, and that binding results in the folding of the structure-switching variant of this aptamer. This structure-switching ability was exploited using the photochrome aptamer switch assay to demonstrate that ART can be detected using this biosensing assay. This study is the first to demonstrate the DNA binding ability of ART and should lay the foundation for further work to study implications of DNA binding for the antimalarial activity of ART.

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Thermodynamic analysis of cooperative ligand binding by the ATP-binding DNA aptamer indicates a population-shift binding mechanism

Scientific Reports ◽

10.1038/s41598-020-76002-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Sladjana Slavkovic ◽

Yanrui Zhu ◽

Zachary R. Churcher ◽

Aron A. Shoara ◽

Anne E. Johnson ◽

...

Keyword(s):

Ligand Binding ◽

Binding Sites ◽

Dna Aptamer ◽

Titration Calorimetry ◽

Atp Binding ◽

Binding Mechanism ◽

Independent Manner ◽

Ligand Binding Sites ◽

Population Shift ◽

Structure Switching

Abstract The ATP-binding DNA aptamer is often used as a model system for developing new aptamer-based biosensor methods. This aptamer follows a structure-switching binding mechanism and is unusual in that it binds two copies of its ligand. We have used isothermal titration calorimetry methods to study the binding of ATP, ADP, AMP and adenosine to the ATP-binding aptamer. Using both individual and global fitting methods, we show that this aptamer follows a positive cooperative binding mechanism. We have determined the binding affinity and thermodynamics for both ligand-binding sites. By separating the ligand-binding sites by an additional four base pairs, we engineered a variant of this aptamer that binds two adenosine ligands in an independent manner. Together with NMR and thermal stability experiments, these data indicate that the ATP-binding DNA aptamer follows a population-shift binding mechanism that is the source of the positive binding cooperativity by the aptamer.

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Crystal structure of the MBD domain of MBD3 in complex with methylated CG DNA

10.1101/338061 ◽

2018 ◽

Author(s):

Ke Liu ◽

Ming Lei ◽

Bing Gan ◽

Harry Cheng ◽

Yanjun Li ◽

...

Keyword(s):

Dna Binding ◽

Binding Assay ◽

Es Cells ◽

Structural Basis ◽

Titration Calorimetry ◽

Binding Mechanism ◽

Nurd Complex ◽

Binding Ability ◽

Methylated Dna ◽

Normal Expression

ABSTRACTMBD3 is a core subunit of the Mi-2/NuRD complex, and has been previously reported to lack methyl-CpG binding ability. However, recent reports show that MBD3 recognizes both mCG and hmCG DNA with a preference for hmCG, and is required for the normal expression of hmCG marked genes in ES cells. Nevertheless, it is not clear how MBD3 recognizes the methylated DNA. In this study, we carried out structural analysis coupled with isothermal titration calorimetry (ITC) binding assay and mutagenesis studies to address the structural basis for the mCG DNA binding ability of the MBD3 MBD domain. We found that the MBD3 MBD domain prefers binding mCG over hmCG through the conserved arginine fingers, and this MBD domain as well as other mCG binding MBD domains can recognize the mCG duplex without orientation selectivity. Furthermore, we found that the tyrosine-to-phenylalanine substitution at Phe34 of MBD3 is responsible for its weaker mCG DNA binding ability compared to other mCG binding MBD domains. In summary, our study demonstrates that the MBD3 MBD domain is a mCG binder, and also illustrates its binding mechanism to the methylated CG DNA.

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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.

Molecular and Cellular Biology ◽

10.1128/mcb.14.11.7557 ◽

1994 ◽

Vol 14 (11) ◽

pp. 7557-7568 ◽

Cited By ~ 126

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.

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

Genes & Development ◽

10.1101/gad.5.10.1902 ◽

1991 ◽

Vol 5 (10) ◽

pp. 1902-1911 ◽

Cited By ~ 234

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

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

Nucleosides Nucleotides & Nucleic Acids ◽

10.1080/15257770.2021.1937644 ◽

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

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

10.21203/rs.3.rs-501100/v1 ◽

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.

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