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Protonated Structures of Naturally Occurring Deoxyribonucleic Acids and Their Interaction With Berberine

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Title Protonated Structures of Naturally Occurring Deoxyribonucleic Acids and Their Interaction With Berberine
 
Creator Bhadra, Kakali
Kumar, G Suresh
Das, Suman
Islam, Md. Maidul
Maiti, Motilal
 
Subject Chemistry
 
Description Protonation-induced conformational changes in natural DNAs of diverse base composition under the influence of low
pH, low temperature, and low ionic strength have been studied using various spectroscopic techniques. At pH 3.40, 10 mM [Na+], and at 5 �C, all natural DNAs irrespective of base composition adopted an unusual and stable conformation remarkably different from the canonical B-form conformation. This protonated conformation has been characterized to have unique absorption and circular dichroic spectral characteristics and exhibited cooperative thermal melting profiles with decreased thermal melting temperatures compared to their respective B-form counterparts. The nature of this protonated structure was further investigated by monitoring the interaction of the plant alkaloid, berberine that was previously shown from our laboratory to differentially bind to B-form and HL-form of poly[d(G–C)] [Bioorg. Med. Chem. 2003, 11, 4861]. Binding of berberine to protonated conformation of natural DNAs resulted in intrinsic circular dichroic changes as well as generation of induced circular dichroic bands for the bound berberine molecule with opposite signs and magnitude compared with B-form structures. Nevertheless, the binding of the alkaloid to both the B and protonated forms was non-linear and non-cooperative as revealed from Scatchard plots derived from spectrophotometric
titration data. Steady state fluorescence studies on the other hand showed remarkable increase of the rather weak intrinsic fluorescence of berberine on binding to the protonated structure compared to the B-form structure. Taken together, these results suggest that berberine can detect the formation of significant population of HL-form structures under the influence of protonation
irrespective of heterogeneous base compositions in natural DNAs.
 
Date 2005
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://www.eprints.iicb.res.in/341/1/BIOORGANIC_%26_MEDICINAL_CHEMISTRY_13(16)4851%2D4863_;2005[37].pdf
Bhadra, Kakali and Kumar, G Suresh and Das, Suman and Islam, Md. Maidul and Maiti, Motilal (2005) Protonated Structures of Naturally Occurring Deoxyribonucleic Acids and Their Interaction With Berberine. Bioorganic & Medicinal Chemistry, 13 (16). pp. 4851-4863.
 
Relation http://dx.doi.org/10.1016/j.bmc.2005.05.010
http://www.eprints.iicb.res.in/341/