Structures and dynamics of a supercoiled DNA

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Abstract
Secondary structures of supercoiled replicative form (RF) phage M13mp7 DNA are investigated by time-resolved fluorescence polarization anisotropy, which monitors the magnitude and uniformity of the torsional rigidity. Tertiary structures are monitored by gel electrophoresis. Seven distinct long-lived structural conformers of this supercoiled DNA are identified: 4 result directly from different replicates of the same standard preparation procedure; 1 results from an alternate preparation; and 2 result from irreversible conversions of such forms to daughter products. These 7 conformers all exhibit either of 2 different, but apparently uniform, torsional rigidities, depending upon the buffer type. Evidently, 2 different secondary structures can prevail in this supercoiled DNA and neither is ordinary B helix. Each conformer also exhibits 1 of 3 basic gel mobilities. The observed dual secondary structures, metastability and hysteresis of this DNA are shown to follow naturally, if the primary function of supercoiling is actually to facilitate remote control of gene activity by site-specific regulatory proteins. A specific model is proposed for gene regulation by protein control of remote junctions between secondary structure domains. The previously inexplicable stimulatory effect of the prmup-1 mutation in the right operator region of the phage .lambda. repressor is rationalized by certain aspects of this model.