Binding mechanism of the anticancerogenic metalloporphyrin Cu(II)TOEPyP(4) to DNA in vitro

Pumilio is an RNA-binding protein originally identified in Drosophila, with a Puf domain made up of eight Puf repeats, three helix bundles arranged in a rainbow architecture, where each repeat recognizes a single base of the RNA-binding sequence. The eight-base recognition sequence can therefore be modified simply via mutation of the repeat that recognizes the base to be changed and this is understood in detail via high-resolution crystal structures. The binding mechanism is also altered in a variety of homologues from different species, with bases flipped out from the binding site to regenerate a consensus sequence. Thus Pumilios can be designed with bespoke RNA recognition sequences and can be fused to nucleases, split GFP, etc. as tools in vitro and in cells.

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In vitro investigation of the interaction between the hepatitis C virus drug sofosbuvir and human serum albumin through 1H NMR, molecular docking, and spectroscopic analyses

New Journal of Chemistry ◽

10.1039/c5nj02003d ◽

2016 ◽

Vol 40 (3) ◽

pp. 2530-2540 ◽

Cited By ~ 24

Author(s):

Hongqin Yang ◽

Yanmei Huang ◽

Di Wu ◽

Jin Yan ◽

Jiawei He ◽

...

Keyword(s):

Molecular Docking ◽

Hepatitis C Virus ◽

Hepatitis C ◽

Human Serum Albumin ◽

Binding Mechanism ◽

Quantitative Investigation ◽

Qualitative And Quantitative ◽

Spectroscopic Analyses ◽

In Vitro Investigation

The qualitative and quantitative investigation of sofosbuvir and HSA interaction provides a convictive explanation for its binding mechanism.

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Protective effect of baicalein on DNA oxidative damage and its binding mechanism with DNA: An in vitro and molecular docking study

Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy ◽

10.1016/j.saa.2021.119605 ◽

2021 ◽

Vol 253 ◽

pp. 119605

Author(s):

Rui Wang ◽

Jian Li ◽

De-Bao Niu ◽

Fei-Yue Xu ◽

Xin-An Zeng

Keyword(s):

Molecular Docking ◽

Oxidative Damage ◽

Protective Effect ◽

Docking Study ◽

Binding Mechanism ◽

Molecular Docking Study ◽

Dna Oxidative Damage

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Transglomerular cationic macromolecular flux is mediated by a convection-binding mechanism

AJP Renal Physiology ◽

10.1152/ajprenal.1989.256.5.f882 ◽

1989 ◽

Vol 256 (5) ◽

pp. F882-F893

Author(s):

C. I. Whiteside ◽

C. J. Lumsden

Keyword(s):

Molecular Size ◽

Protamine Sulfate ◽

Solute Flux ◽

Computer Assisted ◽

Binding Mechanism ◽

Multiple Indicator Dilution ◽

Glomerular Polyanion ◽

Anesthetized Dogs ◽

Multiple Indicator

Glomerular polyanion function was explored using charged and neutral [3H]dextrans in the multiple indicator-dilution experiment. Anesthetized dogs received an intrarenal bolus of 125I-labeled albumin (plasma reference), [14C]inulin (glomerular reference) and [3H]dextran (test solute), followed by rapid serial sampling of the renal venous and urine outflows. Reduced urinary recovery of cationic diethylaminoethyl dextrans (DEAE) [3H]dextrans [19.0– to 31.5–A Stokes-Einstein radius (SER)], compared with neutral [3H]dextran indicated intrarenal binding reversed by excess unlabeled cationic dextran. Tubular microperfusion with cationic [3H]dextran confirmed a pretubular binding site (presumed glomerular). The application of a computer-assisted mathematical model of convective flux plus reversible binding revealed that binding affinity increased with molecular size. In vitro high-affinity binding of the same cationic [3H]dextrans to isolated rat glomeruli was also found to increase with molecular size and was inhibited by protamine sulfate. Intrarenal polycation perfusion with protamine sulfate (1.0–3.8 mg/g kidney) or lysozyme (1.1–2.2 mg/g body wt) resulted in intraglomerular binding of anionic [3H]dextran without increased proteinuria or altered glomerular permselectivity to neutral [3H]dextrans less than or equal to 33.0–A SER. Hence, transglomerular cationic solute flux is mediated by a convection-binding mechanism that creates an effective polyvalent barrier.

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