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UNWINDING THE DOUBLE HELIX: USING DIFFERENTIAL MECHANICS TO PROBE CONFORMATIONAL CHANGES IN 200 DNA signal sequences, several of which are very close together, including both known poly-adenylation sites. As a second example, a search of all known E. coli sequences finds more than 100 locations having the sequence associated with LexA binding. Analysis of which of these sites are destabilized could suggest whether some might be promoters for previously unrecognized SOSregulated genes. The transition behavior of stressed DNA molecules can be complicated by several additional factors. First, there are other types of transitions possible for specific sequences within a DNA molecule. For example, sequences in which a purine (A or G) alternates with a pyrimidine (C or T) along each strand can adopt a left- handed helical structure. Transitions to this and to other alternative conformations also can be driven by imposed superhelicity. So the equilibrium experienced by a stressed molecule actually involves competition among several types of transitions, not just strand separation. Because these other conformations usually are possible only at a small number of short sites having the correct sequence, their analysis is combinatorially simpler than the treatment of strand separation. The theoretical methods described here are currently being extended to include the possible occurrence of other types of transitions. The second complication arises from the structural restraints on DNA in cells. There the DNA is not free to twist and writhe to minimize its energy, but instead is wound around basic proteins to form a chromatin fiber. This drastically alters the types of deformations the molecule can undergo. While it is not clear precisely how this constraint interacts with superhelicity, conformational transitions are expected to be driven by less extreme deformations in restrained molecules than in unrestrained ones (Benham, 1987). The approach outlined here has great promise for finding biologically important correlates of regulation and for illuminating specific mechanisms of function. REFERENCES Benham, C.J., 1987, ''The influence of tertiary structural restraints on conformational transitions in superhelical DNA," Nucleic Acids Res. 15, 9985-9995. Benham, C.J., 1990, "Theoretical analysis of heteropolymeric transitions in superhelical DNA molecules of specified sequence," J. Chem. Phys. 92, 6294-6305.
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