Gutell R R, Cannone J J, Shang Z, Du Y, Serra M J
Institute for Cellular and Molecular Biology, University of Texas, 2500 Speedway, Austin, TX, 78712-1095, USA.
J Mol Biol. 2000 Dec 1;304(3):335-54. doi: 10.1006/jmbi.2000.4172.
In 1985 an analysis of the Escherichia coli 16 S rRNA covariation-based structure model revealed a strong bias for unpaired adenosines. The same analysis revealed that the majority of the G, C, and U bases were paired. These biases are (now) consistent with the high percentage of unpaired adenosine nucleotides in several structure motifs. An analysis of a larger set of bacterial comparative 16 S and 23 S rRNA structure models has substantiated this initial finding and revealed new biases in the distribution of adenosine nucleotides in loop regions. The majority of the adenosine nucleotides are unpaired, while the majority of the G, C, and U bases are paired in the covariation-based structure model. The unpaired adenosine nucleotides predominate in the middle and at the 3' end of loops, and are the second most frequent nucleotide type at the 5' end of loops (G is the most common nucleotide). There are additional biases for unpaired adenosine nucleotides at the 3' end of loops and adjacent to a G at the 5' end of the helix. The most prevalent consecutive nucleotides are GG, GA, AG, and AA. A total of 70 % of the GG sequences are within helices, while more than 70 % of the AA sequences are unpaired. Nearly 50 % of the GA sequences are unpaired, and approximately one-third of the AG sequences are within helices while another third are at the 3' loop.5' helix junction. Unpaired positions with an adenosine nucleotide in more than 50 % of the sequences at the 3' end of 16 S and 23 S rRNA loops were identified and arranged into the A-motif categories XAZ, AAZ, XAG, AAG, and AAG:U, where G or Z is paired, G:U is a base-pair, and X is not an A and Z is not a G in more than 50 % of the sequences. These sequence motifs were associated with several structural motifs, such as adenosine platforms, E and E-like loops, A:A and A:G pairings at the end of helices, G:A tandem base-pairs, GNRA tetraloop hairpins, and U-turns.
1985年，一项基于大肠杆菌16S rRNA共变的结构模型分析显示，未配对的腺苷存在强烈偏好。同样的分析表明，大多数的鸟嘌呤（G）、胞嘧啶（C）和尿嘧啶（U）碱基是配对的。这些偏好（现在）与几个结构基序中未配对腺苷核苷酸的高比例一致。对一组更大的细菌比较16S和23S rRNA结构模型的分析证实了这一初步发现，并揭示了环区域中腺苷核苷酸分布的新偏好。在基于共变的结构模型中，大多数腺苷核苷酸是未配对的，而大多数的G、C和U碱基是配对的。未配对的腺苷核苷酸在环的中部和3'端占主导地位，并且是环5'端第二常见的核苷酸类型（G是最常见的核苷酸）。在环的3'端以及与螺旋5'端的G相邻处，未配对的腺苷核苷酸还有其他偏好。最普遍的连续核苷酸是GG、GA、AG和AA。总共70%的GG序列在螺旋内，而超过70%的AA序列是未配对的。近50%的GA序列是未配对的，大约三分之一的AG序列在螺旋内，另有三分之一在3'环-5'螺旋连接处。在16S和23S rRNA环的3'端，超过50%的序列中具有腺苷核苷酸的未配对位置被识别出来，并被归类为A基序类别XAZ、AAZ、XAG、AAG和AAG:U（其中G或Z是配对的，G:U是碱基对，并且在超过50%的序列中，X不是A且Z不是G）。这些序列基序与几个结构基序相关，如腺苷平台、E和E样环、螺旋末端的A:A和A:G配对、G:A串联碱基对、GNRA四环发夹和U型转弯。
