Alternative base pairing between 5′- and 3′-terminal sequences of small subunit RNA may provide the basis of a conformational switch of the small ribosomal subunit + (original) (raw)

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Institut fur Biologie III der Universität Freiburg, Schänzle-StraBe 1

D-7800 Freiburg, FRG

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Institut fur Biologie III der Universität Freiburg, Schänzle-StraBe 1

D-7800 Freiburg, FRG

Search for other works by this author on:

Institut fur Biologie III der Universität Freiburg, Schänzle-StraBe 1

D-7800 Freiburg, FRG

Search for other works by this author on:

• This articles is dedicated to the memory of H.G. Wittmann

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Hans Kossel, Brigitte Hoch, Patric Zeltz, Alternative base pairing between 5′- and 3′-terminal sequences of small subunit RNA may provide the basis of a conformational switch of the small ribosomal subunit , Nucleic Acids Research, Volume 18, Issue 14, 25 July 1990, Pages 4083–4088, https://doi.org/10.1093/nar/18.14.4083
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Abstract

The compiled sequences of small subunit ribosomal RNAs have been screened for base complementary between 5′- and 3′-terminal regions. Highly conserved complementary sequences are found which allow formation of a helix between the two ends of 5 or 6 base pairs. This helix is composed of sequences from the loop region of the first 5′-terminal stem and from sequences immediately distal to the last stem (the Me 2 A-stem) of the 3′- terminus and therefore allows a coaxial stacking with either of these two flanking stems. Formation of the 5′uo;/3′-helical arrangement is, however, only possible at the cost of dissolving the ‘pseudo-knot’ helix between the 5′-terminal region and the internal region of small subunit RNA. It is postulated that the mutually exclusive conformational states are in dynamic equilibrium and that they correlate with distinct functional states of the small ribosomal subunit. The ’pseudo-knot‘ containing conformation with the 3'-terminal sequences more exposed is likely to represent the initiating state, whereas the 5′/3′ terminal paired ‘closed’ conformation may represent the elongating state in which interaction with fortuitous ribosomal binding sequences of mRNAs is avoided.

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• This articles is dedicated to the memory of H.G. Wittmann

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