TAILIEUCHUNG - Báo cáo khoa học: Netropsin interactions in the minor groove of d(GGCCAATTGG) studied by a combination of resolution enhancement and ab initio calculations

The structure of the complex between the minor groove binder netropsin and d(GGCCAATTGG) was determined via single-crystal X-ray tech-niques. The structure was refined to completion , result-ing in a residual R-factor of (including 68 water molecules). Using crystal engineering and cryocooling techniques, the resolution could be enhanced to A ˚ , resulting in an unambiguous determination of the drug conformation and orientation. | ềFEBS Journal Netropsin interactions in the minor groove of d GGCCAATTGG studied by a combination of resolution enhancement and ab initio calculations Kristof Van Hecke1 Pham Cam Nam2 Minh Tho Nguyen2 and Luc Van Meervelt1 1 Biomolecular Architecture Chemistry Department Heverlee Belgium 2 Quantum Chemistry Chemistry Department Heverlee Belgium Keywords B-DNA double helix base triplets minor groove binder netropsin quantum chemical calculations The structure of the complex between the minor groove binder netropsin and d GGCCAATTGG was determined via single-crystal X-ray techniques. The structure was refined to completion using resulting in a residual R-factor of including 68 water molecules . Using Correspondence L. Van Meervelt Biomolecular Architecture Chemistry Department Celestijnenlaan 200F B-3001 Leuven Heverlee Belgium Fax 32 16 327990 Tel 32 16 327609 E-mail crystal engineering and cryocooling techniques the resolution could be enhanced to A resulting in an unambiguous determination of the drug conformation and orientation. As previously noticed bifurcated hydrogen bonds are formed between the amide nitrogen atoms of the drug and the N3 and O2 atoms of A and T base pairs respectively clearly cataloging the structure to class I. As the bulky NH2 group on guanine was believed to prevent binding of the drug in the minor groove the detailed nature of several of the amidinium and guanidinium end contacts were further inves- Note A web page is available at http research bma tigated by ab initio quantum chemical methods. Received 7 April2005 revised 12 May 2005 accepted 16 May 2005 doi The naturally occurring antiviral and antitumor drug netropsin Nt Fig. 1 from Streptomyces netropsis has a binding preference for stretches of AT-rich over GC sequences in the minor groove of double helical B-DNA 1 2 . Hence it contributes to

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