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Nucleic Acids Research, 1995, Vol. 23, No. 13 2427-2433
© 1995

CHEMISTRY

X-ray crystal struture of a dimethylene sulfone-bridged ribonucleotide dimer in a single-stranded state

Birgitte Hyrup+, Clemens Richert§, Thomas Schulte-Herbrüggen1, Steven A. Benner and Martin Egli*

Department of Chemistry, Swiss Federal Institute of Technology CH-8092 Zürich, Switzerland 1Laboratory of Physical chemistry, Swiss Federal INstitute of Technology CH-8092 Zürich, Switzerland

*To whom corespondence should be addressed

Received April 6, 1995. Accepted May 22, 1995.

A crystal structure has been solved for an analog of the r(ApU) rlbodinucleotlde, n(Aso2U), where a bridging non-ionic dimethylene surf one linker replaces the phosphodiester linking group found in natural RNA. Crystals of the single-stranded state of r(Aso2U) were obtained from water at 50°C. In these crystals, one hydrogen bond is formed between bases from different strands and base stacking occurs in intermolecular ‘homo-A’ and ‘homo-U’ stacks. Similar to typical oligoribonucleotides, the ribose rings adopt N-type conformations and dihedral angles x are In the anti range. The all-trans rotamer of the CH2-SO2-CH2-CH2 ridge was found, which leads to a large adenine-uracil distance. Qualitative analysis of a NOESY spectrum of the ASO2U part in r(Uso2Cso2Aso2U) dissolved in a dimethylsurfoxide-D2O mixture Indicates that the conformation observed in the crystal is also populated In solution. Comparison with the structure of r(GsO2C),which has been crystallized In the Watson-Crick paired state, shows that a rotation around {zeta} by +112° leads from the observed, single-stranded state to a conformation that is compatible with formation of a duplex. A concerted trans/gauche flip of {alpha} and {gamma} then yields the standard conformer of A-type RNA helices. From the observed structure of r(Gso2C) and other oligonucleotjdes it is anticipated that this flip will also revert the ribose pucker from C2;-exo to C3'-endo.

+Permanent address:University of copenhegen, The H.Cørsted Institute, UNiversitesparken 5,2100, USA

§present address:Department of Chemistry, Tufs University, Medford, MA 02155, USA


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