EVIDENCE FOR A SEQUENCE-DIRECTED CONFORMATION PERIODICITY IN THE GENOMIC HIGHLY REPETITIVE DNA DETECTABLE WITH SINGLE-STRAND-SPECIFIC CHEMICAL PROBE POTASSIUM-PERMANGANATE

A single-strand-specific chemical probe, potassium permanganate (KMnO4 ), was used to study the sequence-dependent conformation periodicity o f tandem multicopy repetitive DNA sequences HRS60 and GRS (Nicotiana s pecies) at the level of single base pair and dinucleotide step. Local DNA structures, sensitive to KMnO4, revealed periodicity of 182 +/- 2 bp, equal to the length of repeat units. Permanganate-sensitive local structures were mapped in both DNA strands of genomic HRS60 sequences and were found to be linked to d(A)(n) tracts. These adenine tracts ar e located in the proximity of the intrinsically curved domains. Distam ycin A increased reactivity of the DNA but decreased the specificity o f DNA cleavage. Similar conformation periodicity has been detected als o in the 'canrep' family of repeats (Brassica species). All studied re petitive sequences are predominantly located in the constitutive heter ochromatin. We discuss the role of conformation periodicities in relat ion to a structural code for nucleosome phasing at tandem arrays of DN A repeats.