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Nucleic Acids Research, 1994, Vol. 22, No. 14 2752-2759
© 1994

STRUCTURAL BIOLOGY

Formation of sheared G:A base pairs in an RNA duplex modelled after ribozymes, as revealed by NMR

Masato Katahira, Mayumi Kanagawa, Hajime Sato, Seiichi Uesugi*, Satoshi Fujii1, Toshiyuki Kohno2 and Tadakazu Maeda2,+

Department of Bioengineering, Faculty of Engineering, Yokohama National University Tokiwadai 156, Hodogaya-ku, Yokohama 240 1Faculty of Pharmaceutical Science, Osaka University Suita, Osaka 565 2Mitsubishi Kasei Institute of Life Sciences Minamiooya 11, Machida-shi, Tokyo 194, Japan

*To whom correspondence should be addressed

Received April 27, 1994. Revised June 9, 1994. Accepted June 9, 1994.

The thermal stability and structure of an RNA duplex, r(GGACGAGUCC)2, the base sequence of which was modelled after both a hammerhead ribozyme and a lead ribozyme, were studied by CD and NMR. We previously demonstrated that the corresponding DNA duplex, d(GGACGAGTCC)2, formed unique ‘sheared’ G:A base pairs, where an amino proton, instead of an imino proton, of G is involved in the hydrogen bonding, and G and A bases are arranged ‘side by side’ instead of ‘head to head’ (Nucleic Acids Res. (1993) 21, 5418 – 5424). CD melting profiles showed that the RNA duplex is thermally more stable than the corresponding DNA duplex. NMR studies revealed that sheared G:A base pairs are formed in the RNA duplex, too, although the overall structure of the RNA is the A form, which differs from the B form taken on by the corresponding DNA. A model building study confirmed that sheared G:A base pairs can be accommodated in the double helical structure of the A form. A difference between the RNA and DNA duplexes in the stacking interaction involving G:A mismatch bases is also suggested. The demonstration that sheared G:A base pairs can be formed not only in DNA but also in RNA suggests thatthis base pairing plays an important role regarding the RNA structure.

+Present address: Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Sagamihara, Kanagawa 228, Japan


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