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Photochemical demonstration of stacked protonated cytosine base pairs in a novel dna secondary structure



Photochemical demonstration of stacked protonated cytosine base pairs in a novel dna secondary structure



Biochemistry 24(7): 1676-1683



The secondary structure of the alternating polydeoxynucleotide sequence poly[d(C-T)] was studied as a function of pH by UV absorbance and circular dichrosim [CD] spectroscopy and by the analysis of UV-induced photoproducts. As the pH was lowered, poly[d(CT)] underwent a conformational transition that was characterized by changes in the long-wavelength region (280-320 nm) of the CD spectrum. These changes have previously been interpreted as evidence for the formation of a core of stacked, protonated C.cntdot.C+ base pairs in a double-helical complex of poly[d(C-T)], with the thymidyl residues being looped out into the solvent. Poly[d(C-T)] was labeled with [U-14C]cytosine and [methyl-3H]thymine and irradiated at pH values both above and below the conformational transition point (monitored by CD spectroscopy). The distribution of radioactivity in uracil < > uracil dimers, uracil < > thymine dimers (the deamination products of cytosine < > cytosine and cytosine < > thymine dimers, respectively) and thymine < > thymine dimers was then determined. As the pH was decreased, an increase in the yield of uracil < > uracil dimers and a decrease in the yield of uracil < > thymine dimers, which occurred concomitantly with the change in the CD spectrum was found. These changes were interpreted as evidence that a stacked C.cntdot.C+base-paired structure was indeed formed by alternate cytosine bases in poly[d(C-T)] at acid pH, with the thymidyl residues being individually looped out of the structure. The dose-dependent kinetics of photoproduct formation and a loss of the long-wavelength CD band of the irradiated poly[d(C-T)] self-complex indicated that the structure was destabilized during irradiation, due to dimerization of the looped-out thymines. A new range of conformations is accessible to DNA.

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Accession: 006110030

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