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Biophysical Studies on The Interaction of Plant Alkaloids With Polyadenylic Acid Structures

IR@IICB: CSIR-Indian Institute of Chemical Biology, Kolkata

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Title Biophysical Studies on The Interaction of Plant Alkaloids With Polyadenylic Acid Structures
Creator Giri, Prabal
Subject Chemistry
Description A. Physico-chemical properties of the alkaloids Berberine and palmatine are naturally occurring isoquinoline plant alkaloids exhibiting almost similar absorption and weak fluorescence spectra. On the other hand, coralyne, synthetic analogue of berberine, has significantly different absorption and strong fluorescence characteristics. All the three alkaloids are stable in the pH range 2-12. Sanguinarine is a naturally occurring benzophenanthridine plant alkaloid exhibiting pH dependent structural change from positively charged iminium form (pH 1-6.5) to neutral alkanolamine form (pH 8-12) with pKa value of 7.4. B. Physico-chemical properties of polyadenylic acid All eukaryotic mRNA has a polyadenylic acid [poly(A)] tail at their 3’ end that is an important determinant in its maturation, stability and initiation of translation. Poly(A) exists as single strand in neutral and alkaline pH whereas it forms double strand in acidic pH as evidenced from spectroscopic and thermodynamic measurements. C. Interaction of berberine with single and double stranded poly(A) Spectrophotometric studies- Spectrophotometric analysis revealed strong binding of berberine to single stranded (ss) poly(A) with the remarkable hypochromic and bathochromic shift in its absorption spectrum. The binding was of noncooperative manner. On the other hand, the changes in the absorption spectrum for the interaction of berberine with double stranded (ds) poly(A) was very marginal indicating very weak binding. Spectrofluorimetric studies- Spectrofluorimetric analysis also revealed strong binding of berberine to ss poly(A) with appreciable enhancement in its fluorescence spectrum while complexation of berberine to ds poly(A) showed very low enhancement indicating weak binding. The binding stoichiometry evaluated by Job plot was one berberine molecule per two nucleotides of ss poly(A). Spectropolarimetric studies- On increasing concentration of berberine the molar ellipticity of ss poly(A) decreased with the generation of induced CD in 300-400 nm region while complexation with ds poly(A) showed very marginal changes in CD spectrum and no induced CD was generated. Optical and CD melting studies- Both optical and CD melting studies showed the process of non-cooperative denaturation of the berberine-ss poly(A) complex while berberine-ds poly(A) complex showed very negligible changes in the melting profile. Isothermal calorimetric studies- ITC studies of the binding of berberine with ss poly(A) exhibited exothermicity and the main contribution to binding free energy (DGo) came from the enthalpy change whereas the ITC profile showed very negligible heat change for berberine-ds poly(A) complexation and as a result binding parameters could not be calculated. Differential scanning calorimetric studies- DSC thermograms of ss and ds poly(A) showed transitions at 54.8±1.0 °C and 64.8±1.0 °C respectively. A stabilization of 10.4 °C was observed at the saturating D/P in berberine-ss poly(A) complexation whereas with berberine-ds poly(A) complexation very marginal change in DSC thermogram noticed. Viscometric studies- The relative specific viscosity of berberine-ss poly(A) complex increased with increasing D/P indicating partial intercalation mode of binding while there was no such change for berberine-ds poly(A) complexation, which was indicative of very weak external binding.
Date 2008
Type Thesis
Format application/pdf
Identifier http://www.eprints.iicb.res.in/693/1/Binder1.pdf
Giri, Prabal (2008) Biophysical Studies on The Interaction of Plant Alkaloids With Polyadenylic Acid Structures. PhD thesis, Jadavpur University.
Relation http://www.eprints.iicb.res.in/693/