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Nucleic Acids Research, 1988, Vol. 16, No. 11 5013-5030
© 1988

Articles

Bulge-out structures in the single-stranded trimer AUA and in the duplex (CUGGUGCGG).(CCGCCCAG). A model-building and NMR study

Yvonne Th. van den Hoogen, Aart A. van Beuzekom, Erik de Vroom, Gijs A. van der Marel, Jacques H. van Boom and Cornelis Altona

Gorlaeus Laboratories, Leiden University PO Box 9502, 2300 RA Leiden, The Netherlands

Received April 14, 1988. Accepted May 6, 1988.

Model-building studies were carried out on the trimer AUA. Bulge-out structures which allow incorporation into a continuous RNA helix were generated and energy-minimized. All geometrical features obtained by previous NMR studies on purine-pyrimidine-purine sequences are accounted for in these models. One of the models was used to fit into a double helical fragment. Only minor changes were necessary to construct a central bulge-out in an otherwise intact duplex.

NMR and model-building studies were performed on the duplex (CUGGUGCGG)·(CCGCCCAG) which contains an unpaired uridine residue. NOE data, chemical-shift profiles and imino-proton resonances provided evidence that the extra U is bulged out of the duplex. The relatively small dispersion in 31P chemical shifts (~0.7 ppm) indicate the absence of t/g or g/t combinations for the phosphodiester angles {zeta}/{alpha}. An energy-minimized model of the duplex, which fits the present collection of data, is presented.


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