Nucleic Acids Research, 1992, Vol. 20, No. 8 1843-1850
© 1992
SURVEY AND SUMMARY |
The nature of preferred hairpin structures in 16S-like rRNA variable regions
Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel OlshausenstraBe 40, D-2300 Kiel 1, Germany
Received November 14, 1991. Revised March 5, 1992. Accepted March 5, 1992.
Variable length hairpins in 16S-like rRNA show a predominance for tetra-loops, its degree correlates with the protein content of the ribosome. The number of base-pairs adjacent to the loop (the tip size) and the nearest neighbor composition contribute to the stability of hairpin structures. The average tip size in length variable hairpins correlates with the thermophilicity of the organism, i.e. in temperate environments less stable stem structures are tolerated or even necessary. The most abundant loop families UUCG, GCAA, and CUUG occur most frequently at loop sizes 3, 2, and 7, respectively. Short tips of size 
4 generally prefer nearest-neighbor combinations that result in CCC—GGG. Loop-specific tipmost nearest neighbors are revealed at longer tips: CUC(UUCG)GAG, GUA(GC-AA)UAC with a maximum at tip sizes 5–6, and GWG(CUUG)CWC. Conserved hairpins, however, prefer variants of the UUCG and GCAA motifs with additional purlnes. Minor loop families and single motifs such as UUUA, UUUU, CUUGU, UUCGG, and UUU are investigated for preferable tip sizes and nearest-neighbor composition. Specific features are revealed for prominent hexa-loops.
*Present address: HarmsstraBe 34, D-2300 Kiel 1, Germany