Crystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin

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

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Abstract / Description

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.

Item Type:	Article
Uncontrolled Keywords:	netropsin, antibiotics, crystal structure, DNA, deoxyribonucleic acid
Subjects:	600 Technology > 610 Medicine & health
Department:	School of Human Sciences
Depositing User:	Christine Nunn
Date Deposited:	03 Aug 2015 09:05
Last Modified:	25 Jun 2020 15:47
URI:	https://repository.londonmet.ac.uk/id/eprint/728

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