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Nucleic Acids Research, 1983, Vol. 11, No. 9 2801-2814
© 1983

CHEMISTRY

Molecular structure of deoxyadenjlyl–3'–methylphosphonate–5'thymldine dlhydrate, (d-ApT-2H2O), a dinudeodde monophosphate with neutral pbosphodiester backbone. An X-ray crystal study*

K.K. Chacko§,, K. Lindner, W Saenger+, and P.S. Miller

Abteilung Chemie, Max-Planck-Institut f{euro}r experimentdle Medizin Hernann-Rein-Str. 3, D-3400 Göttingen, FRG Division of Biophysics, School of Hygiene and Public Health, The Johns Hopkins University Baltimore, MD 21205, USA

Received March 24, 1983. Accepted March 12, 1983.

dAPT, a modified deoxyribose dinucleoaide phosphate with an uncharged methylphosphonate group, crystallizes as dihy-drate in space group P2.2.2, a = 9.629(3), b = 20.884(6) and c = 14.173 (4)Å Z = 4. The structure has been determined using 2176 X-ray diffractometer reflections and refined to a final R of 0.105. Torsion angles about P-0(5') and P-0(3') bonds are –91.8° and 117-8°. The former is in the normal (–)gauche range while the latter is eclipsed. Bases are oriented anti, the sugar of adenosine is puckered T3 (C(2')endo) whereas that of thymidine displays puckering disorder with-major and minor occupancy sites. Major site is a half-chair 2T (C(2' )endo-C(1')exo) and minor site an envelope 3kT2 (C(31 )endo). Adenine and thymine bases of symmetry related molecules form reversed Hoogsteen type base pairs, water molecules are disordered in the crystal lattice.

§Present address: Department of Crystallography and Biophysics, Umversity of Madras, Madras 600 025, India

+Present address: Institut fur Knstallographie, Freie UniversitAt Berlin, Takustr. 6, D-1000 Berim 33, FRG

*Dedicated to Professor Dr.Friedrich Cramer on the occasion of his 60th birthday


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