DNA is known to be a flexible polymer with a number of conformations available to it. In recent years proteins have been found which interact with the Z form and the A form of DNA, so that alternative conformations and transitions between conformations are likely to have a role in the expression of DNA function. However, since alternative DNA conformations are most likely present in small amounts in the genome and are unstable under normal solution conditions, it is necessary to use synthetic model polynucleotides to study conformational transitions in DNA. Our laboratory has done necessary groundwork by synthesizing polymers that exist stably under mild conditions in five different specific conformations: the low and high salt Z forms, the regular and alternating A forms, and the alternating B form. Although other conformations of DNA may exist in a cell, it seems likely that if alternative DNA structures are physiologically important, at least one of the above structures will be among them. I propose to pursue several complementary lines of research: 1) Physical characterization. This will involve investigation of the relative stability of the various conformations as a function of environmental parameters (temperature, specific ion binding, kinetics, etc.); 2) Chemical characterization. Comparison will be made of the reactivities of the various conformations toward alkylating agents, and the behavior of the model polynucleotides toward intercalating drugs will be explored; 3) Biological characterization. A search will be conducted for proteins which bind specifically to the non-standard conformations. Additionally, our laboratory is continuing work begun on the sequence dependence of the B-Z transition. To understand the structural features that are important in stabilizing the Z form we are synthesizing defined sequence, alternating purine- pyrimidine polymers and determining the effect of sequence and base composition on the B-Z transition. Within the next few years we expect to be able to predict the conditions under which any given sequence will be in the Z conformation.
