Structural study of the DNA fragment d(CGCTGGCCACCG) and a preliminary crystallographic study of the self-complementary DNA sequence d(CGGTGGCCACCG)

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Chen, Mei
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This thesis is aimed at elucidating the structures of two DNA fragments, d(CGCTGGCCACCG) (referred to as 'mismatched' DNA hereafter) and d(CGGTGGCCACCG). The fragment d(CGCTGGCCACCG), if duplexed, contains two C-C mismatches which are the least efficiently repaired mismatches and are considered a critical structural element in the development of fragile X syndrome. The fragment d(CGGTGGCCACCG) which is self-complementary contains the sequence GTG/CAC which frequently occurs in regulatory regions and is related to DNA-protein recognition. Small crystals of the DNA fragment d(CGCTGGCCACCG) have been obtained. The effect of individual crystallizing agents on the conformation of the 'mismatched' DNA fragment has been studied and discussed in detail. There is evidence that in the crystallizing solutions the 'mismatched' DNA forms a hairpin structure possibly with the first and the last four bases in the stem in B-DNA helical form and the central four bases in the loop which are partially stacked. Under the same crystallizing condition, the self-complementary DNA is duplexed and its helical type is B-form. Based on the crystallizing experiments, structural studies, and an extensive search of the literature, some suggestions regarding additional crystallizing conditions for the 'mismatched' DNA are made. Two kinds of crystals of the self-complementary DNA sequence d(CGGTGGCCACCG) have been crystallized using $\rm BaCl\sb2$ and $\rm ZnCl\sb2$ as salt, respectively. (Abstract shortened by UMI.)