Superhelical Transitions and DNA Regulation

The association of the deoxyribonucleic acid (DNA) with proteins in both prokaryotes and eukaryotes permits non-enzymatic methods of modulating superhelical stresses. Conformational transitions within or relative motions of the nucleosomal particles may modulate stresses on regions of the DNA. The specific activities involved in eukaryotic DNA regulation, and the role of transition-susceptible sites in them, are best studied using animal viruses of known sequence. The regulation of negative superhelicity is known to modulate the initiation of numerous biologically important processes, including transcription, replication, recombination and repair. Theoretical analysis suggests that superhelically driven transitions are expected to occur at less extreme superhelicities in DNA whose tertiary structure is constrained than in unconstrained molecules. DNA within living systems is held in looped structures called topological domains. SV40 has a closed circular genomic DNA. Inside the cell this molecule festoons itself with 24 nucleosomes, forming a structure called the SV40 minichromosome.