SEQUENCE-DEPENDENT EFFECTS OF CPG CYTOSINE METHYLATION - A JOINT H-1-NMR AND P-31-NMR STUDY

The impact of cytosine methylation in the central CpG step of two clos ely related octanucleotide duplexes d(CATCGATG), and d(CTTCGAAG), was examined by H-1-NMR and P-31-NMR experiments, and a quantitative struc tural analysis was performed using the NOE-derived distances, the suga r puckers and the epsilon torsion angles. The two starting oligonucleo tides displayed a B-DNA conformation with, however, significant local structure differences. Although the methylated oligonucleotides retain ed their B-DNA conformation, different structural and thermal stabilit y effects were observed. The magnitude of the methylation effects was to depend on the initial conformation of the CpG site, which is govern ed by the nature of the dinucleotide AT or TT located on the CpG flank s. As an example of sequence dependence, the methylation of CpG entail ed larger conformational variation in d(CATCGATG)(2) than in d(CTTCGAA G)(2). In this study, the H-1 and P-31 chemical-shift parameters averr ed as extremely sensitive probes for detecting subtle conformational c hanges. Finally, our comparative results may aid our understanding of the structural and related biological effects produced by cytosine met hylation in DNA.