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- Article; binding affinity; binding site; circular dichroism; concentration response; controlled study; drug binding; drug specificity; Human immunodeficiency virus 1; measurement; melting point; molecular model; nonhuman; priority journal; protein footprinting; RNA structure; structure analysis; temperature measurement; ultraviolet spectrophotometry; virus strain; dimer; framycetin; nucleotide; pancreatic ribonuclease; virus RNA (1)
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Full-Text Articles in Chemistry
Footprinting, Circular Dichroism And Uv Melting Studies On Neomycin B Binding To The Packaging Region Of Human Immunodeficiency Virus Type-1 Rna, Mark P. Mcpike, Julie M. Sullivan, Jerry Goodisman, James C. Dabrowiak
Footprinting, Circular Dichroism And Uv Melting Studies On Neomycin B Binding To The Packaging Region Of Human Immunodeficiency Virus Type-1 Rna, Mark P. Mcpike, Julie M. Sullivan, Jerry Goodisman, James C. Dabrowiak
Chemistry - All Scholarship
We have studied the binding of neomycin to a 171mer RNA (Ψ-RNA) from the packaging region of the LAI strain of human immunodeficiency virus type-1, HIV-1 (LAI). The RNase I footprinting studies reveal that the primary binding site for the drug is in stem-loop 1, which contains the dimer initiation site of HIV-1. Loading this site with neomycin causes a structural change in the RNA, allowing nucleotides in the neighboring stem-loop 2 to participate in the drug site. Drug binding to secondary sites induces structural changes in other stem-loops of the RNA. Footprinting plots, showing cutting at a site as …
Footprinting And Circular Dichroism Studies On Paromomycin Binding To The Packaging Region Of Human Immunodeficiency Virus Type-1, Mark P. Mcpike, Jerry Goodisman, James C. Dabrowiak
Footprinting And Circular Dichroism Studies On Paromomycin Binding To The Packaging Region Of Human Immunodeficiency Virus Type-1, Mark P. Mcpike, Jerry Goodisman, James C. Dabrowiak
Chemistry - All Scholarship
We have studied the interaction of the aminoglycoside drug, paromomycin, with a 171-mer from the packaging region of HIV-1 (ψ-RNA), using quantitative footprinting and circular dichroism spectroscopy. The footprinting autoradiographic data were obtained by cutting end-labeled RNA with RNase I or RNase T1 in the presence of varying paromomycin concentrations. Scanning the autoradiograms produced footprinting plots showing cleavage intensities for specific sites on the ψ-RNA as functions of drug concentration. Footprinting plots showing binding were analyzed using a two-state model to give apparent binding constants for specific sites of the ψ-RNA. These plots show that the highest-affinity paromomycin binding site …