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Nunn, Christine M., Garman, Elspeth and Neidle, Stephen (1997) Crystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin. Biochemistry, 36 (16). pp. 4792-4799. ISSN 0006-2960
The crystal structure of netropsin bound to the decamer d(CGCAATTGCG) has been determined at 2.4 Å resolution. This is the first example of a crystal structure of netropsin bound to decamer DNA. The central eight bases of each DNA single-strand base pair with a self-complementary strand to form an octamer B-DNA duplex. These duplexes lie end to end within the unit cell. The terminal 5‘-C and G-3‘ bases are unpaired and interact with the neighboring duplexes via interactions within both the major and minor groove to form base triplet interactions of the type C+−G·C and G*(G·C), respectively. The triplet interaction of the type C+−G·C is known to exist within triplex DNA with the C+ base oriented parallel with the Watson−Crick guanine base to which it hydrogen bonds. The netropsin molecule lies within the minor groove of the octamer duplex and assumes a class I type position, with bifurcated hydrogen-bonding interactions from the amide groups of the netropsin to the A·T base pairs of the minor groove. The netropsin molecule fits within a five base pair long minor groove site by bending of the flexible amidinium group at one end of the drug.
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