Conversions of the left-handed form and the protonated form of DNA back to the bound right-handed form by sanguinarine and ethidium: A comparative study

Interaction of Isoquinoline Alkaloids with Polymorphic DNA Structures

“…pH Measurements were conducted on an Cyberscan 2100 high-precision bench pH-meter with an accuracy of > AE 0.001 units (Eutech Instruments Pte Ltd., Singapore). For coralyne -DNA interaction studies, citrate/phosphate buffer containing 8% EtOH was used, as reported in [62] 6 ]Cl 3 kept stirred at 20 AE 0.58 as described in [26] [27]. An equilibrium time of 40 min was allowed after initiating the B-to-Z conformational transition.…”

“…The B-to-H L transition was initiated by slowly adding the B form polymer stock soln. to 10 mm CP buffer, pH 3.4, kept stirred and maintained at 10 AE 0.58 as described in [26] [27]. Generally, the structural transition from B to H L form followed very fast kinetics and was found to be completed in ca.…”

“…The absorbance of the Z-DNA UV spectrum (curve 2) showed decrease in the absorbance at 295-nm region compared to the B form. The H L form of poly[d(G-C)] at pH 3.4 has a Hoogsteen base-paired structure [27], and is distinctly different from the right-handed B-DNA and left-handed Z-DNA structures [26] [36]. Fig.…”

“…For example, several intercalating molecules have now been characterized to convert the left-handed Z-form conformation to the bound B form. Ethidium [32] [33], actinomycin D [39], daunomycin [34], sanguinarine [26] [36], aristololactam b-d-glucoside [40], and several others cooperatively convert the Z-form structure back to bound B-form conformation. The binding of small molecules, however, to other polymorphic forms of DNA is still poorly studied [37] [41].…”

“…Chen had reported that pyrene strongly binds to the DNA at acidic pH [31]. Our laboratory had shown that sangunarine and ethidium converted the H L -form structure of poly[d(G-C)] and poly[d(Gme5 C)] cooperatively to bound B form [26], while the alkaloid aristololactam b-d-glucoside strongly bound the H L -form structures of these polymers [38]. These different binding characteristics of the small molecules to the above-mentioned polymorphic forms prompted the investigation of the interaction of isoquinoline alkaloids with these structures.…”