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Nucleic Acids Research, 1988, Vol. 16, No. 12 5673-5684
© 1988

Articles

Fidelity of secondary and tertiary interactions in tRNA

Tim Haselman, Jack E. Chappelear and George E. Fox*

Department of Biochemical and Biophysical Sciences, University of Houston Houston, TX 77004, USA

*To whom correspondence should be addressed

Received December 23, 1987. Revised April 22, 1988. Accepted April 22, 1988.

Contingency table analysis has previously been used to detect sequence correlations in RNAs caused by either secondary or tertiary interactions. An approach known as matrix reduction is developed here as an alternative to the usual Chi square test. This approach is especially sensitive to covariation between equivalent positions and is effective at detecting tertiary interactions that exhibit such covariation. Matrix reduction was also effective at detecting Watson-Crick base-pairs that exhibit a high degree of pairing fidelity. The method was applied to five closely related structural classes of tRNA and a number of tertiary interactions were detected in each class.


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