Effects of 5 cytosine methylation on the B-Z transition in DNA restriction fragments and recombinant plasmids.
Alternating (dC-dG)n regions in DNA restriction fragments and recombinant plasmids were methylated at the 5 position of the cytosine residues by the HhaI methylase. Methylation lowers the concentration of NaCl or MgCl2 necessary to cause the B-Z conformational transition in these sequences. Ionic strengths higher than physiological conditions are required to form the Z conformation when the methylated (dC-dG)n tract is contiguous with regions that do not form Z structures, in contrast to the results with the DNA polymer poly(m5dC-dG) . poly(m5dC-dG). In supercoiled plasmids containing (dC-dG)n sequences, methylation reduces the number of negative supercoils necessary to stabilize the Z conformation. Calculations of the observed free energy contributions of the B-Z junction and cytosine methylation suggest that two junctions offset the favorable effect of methylation on the Z conformation in (dC-dG)n sequences (about 29 base-pairs in length). Studies with individual methylated topoisomers demonstrate that increasing Na+ concentration up to approximately 0.2 M inhibits the formation of the Z conformation in the (m5dC-dG)n region of supercoiled plasmids. The results suggest that methylation may serve as a triggering mechanism for Z DNA formation in supercoiled DNAs.
D003596:Cytosine / Q000378:metabolism*; D004262:DNA Restriction Enzymes / Q000378:metabolism; D004274:DNA, Recombinant / Q000378:metabolism*; D004587:Electrophoresis, Agar Gel; D008274:Magnesium / Q000494:pharmacology; D015636:Magnesium Chloride; D008745:Methylation; D009690:Nucleic Acid Conformation; D009994:Osmolar Concentration; D010957:Plasmids; D012965:Sodium Chloride / Q000494:pharmacology; D013816:Thermodynamics
D004274:DNA, Recombinant; D015636:Magnesium Chloride; D012965:Sodium Chloride; D003596:Cytosine; D004262:DNA Restriction Enzymes; D008274:Magnesium