Wolters J
Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Germany.
Nucleic Acids Res. 1992 Apr 25;20(8):1843-50. doi: 10.1093/nar/20.8.1843.
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 less than or equal to 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(GCAA)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 purines. 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.
16S 样核糖体RNA中的可变长度发夹结构以四环为主，其程度与核糖体的蛋白质含量相关。与环相邻的碱基对数量（环尖大小）和最近邻组成有助于发夹结构的稳定性。长度可变发夹结构中的平均环尖大小与生物体的嗜热性相关，即在温带环境中，较不稳定的茎结构是可以耐受的，甚至是必要的。最丰富的环家族UUCG、GCAA和CUUG分别在环大小为3、2和7时出现频率最高。大小小于或等于4的短环尖通常更喜欢导致CCC - GGG的最近邻组合。在较长的环尖处发现了环特异性的最末端最近邻：CUC(UUCG)GAG、GUA(GCAA)UAC在环尖大小为5 - 6时出现频率最高，以及GWG(CUUG)CWC。然而，保守发夹结构更喜欢带有额外嘌呤的UUCG和GCAA基序变体。对较小的环家族和单个基序如UUUA、UUUU、CUUGU、UUCGG和UUU进行了优选环尖大小和最近邻组成的研究。突出的六环显示出特定特征。
