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biophysical characterization of the strong stabilization of the rna triplex poly(u)?poly(a)poly(u) by 9-o-(ω-amino) alkyl ether berberine analogs强大稳定的生物物理特性rna三聚(u)保利(a)聚(u)九点-(ω-amino)烷基醚小檗碱类似物.pdf

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Biophysical Characterization of the Strong Stabilization of the RNA Triplex poly(U) poly(A) poly(U) by 9-O-(v- N * amino) Alkyl Ether Berberine Analogs 1. 2. 1 2 1 Debipreeta Bhowmik , Suman Das , Maidul Hossain , Lucy Haq , Gopinatha Suresh Kumar * 1 Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India, 2 Department of Chemistry, Jadavpur University, Kolkata, India Abstract Background: Binding of two 9-O-(v-amino) alkyl ether berberine analogs BC1 and BC2 to the RNA triplex poly(U) poly(A) poly(U) was studied by various biophysical techniques. N * Methodology/Principal Findings: Berberine analogs bind to the RNA triplex non-cooperatively. The affinity of binding was remarkably high by about 5 and 15 times, respectively, for BC1 and BC2 compared to berberine. The site size for the binding was around 4.3 for all. Based on ferrocyanide quenching, fluorescence polarization, quantum yield values and viscosity results a strong intercalative binding of BC1 and BC2 to the RNA triplex has been demonstrated. BC1 and BC2 stabilized the Hoogsteen base paired third strand by about 18.1 and 20.5uC compared to a 17.5uC stabilization by berberine. The binding was entropy driven compared to the enthalpy driven binding of berbeine, most likely due to additional contacts within the grooves of the triplex and disruption of the water structure by the alkyl side chain. Conclusions/Significance: Remarkably higher binding affinity and stabilization effect of the RNA triplex by the amino alkyl be
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