RNA 的历史与未来

核酶的发现使得人们有理由相信生命起源于RNA ,通过试管演化实验获得的各种各样的催化性RNA 更使人们 对地球历史早期的RNA 世界有了越来越多的了解。同时,随着RNA 结构和功能上非凡的多样性的日益被揭示,RNA 在未来的临床应用研究中所具有的巨大潜力也正逐渐显现出来。

稳定的RNA 发夹结构在人类88 个mRNA 编码区中的分布

　以UNCG, GNRA , CUU G (N = A , U , C 或G; R = G或A) 为端环能够形成稳定的、保 守的发夹结构. 它们具有特殊的结构特征, 并在体内发挥着重要的生物学功能. 这些稳定的发夹 广泛分布于体内rRNA , 催化RNA 和非编码mRNA 中. 但对人类88 个编码区mRNA 二级结构的 研究当中, 却没有发现C(UUCG) G发夹. 而且, 与rRNA 不同, 这些编码区mRNA 四环序列的 分布没有明显的偏好性.

RNA A_6膨胀环的动力学特征

通过对RNA A6膨胀环在水溶液中的动力学模拟发现,在A6膨胀环中,环区构象主要以非堆积构象为主,环区具有较大的构象柔性,膨胀环区链的构象波动对已形成的RNA分子弯折的影响不大,弯折角只是在小范围内变动,提示作为全局结构,带大尺寸膨胀环的RNA分子仍然具有一定的刚性,柔性主要表现在膨胀环区域.

Recent advance in the study of ribosomal model.

With the technological developments of cryoelectron microscope, X-ray diffraction and the growing data available on various components of ribosome, some marvelously intricate structural models of the Escherichia coli 70S ribosome have been reconstructed. The picture of the ribosomal model are detailed, including the placement of the mRNA, the arrangement of the A-site and P-site tRNAs and the peptidyltransferase within the interface gap as well as the path of nascent polypeptide chain, which results in a better understanding of the structure and function of ribosome as well as the translational process.

Additional angles to calculate the deformation of RNA helices induced by bulge loops

Bulges are common features of folded RNA structures. The RNA axial kinking caused by bulges has been confirmed by many experiments. Usually, a kinking angle zeta and a bending angle theta are used to describe the kinking and twisting of RNA molecules containing bulges. Here, we present two additional angles (twist angle zeta(1), twist angle zeta(2)) to describe the deformation of RNA helices induced by bulge loops because only two angles (a kinking angle zeta and a bending angle theta) are not enough to define the deformation of RNA induced by bulges. (C) 2002 Elsevier Science B.V. All rights reserved.

Dynamics of RNA with A6 bulge loop

In order to understand the behavior of RNAs with large bulges In solution, molecular dynamics was performed on the RNA molecule in water with A6 bulge. The result of simulation showed that nonstacked conformation Is the main conformation in large bulges, and the backbone of large bulge is of great conformational flexibility, but bulges-induced bends are relatively rigid. The fluctuation in bulge has little influence on the bend angle of RNAs.

Stable RNA hairpins in 88 coding regions of human mRNA

RNA hairpins containing UNCG, GNRA, CUUG (N = A, U, C or G, R = G or A) loops are unusually thermodynamic stable and conserved structures. The structural features of these hairpin loops are very special, and they play very important roles in vivo. They are prevalent in rRNA, catalytic RNA and non-coding mRNA. However, the 5' C(UUCG)G 3' hairpin is not found in the folding structure of 88 human mRNA coding regions. It is also different from rRNA in that there is no preference for certain sequences among tetraloops in these 88 mRNA folding structures.

Statistical correlation between protein secondary structure and messenger RNA stem-loop structure

Anew integrated sequence-structure database, called IADE (Integrated ASTRAL-DSSP-EMBL), incorporating matching mRNA sequence, amino acid sequence, and protein secondary structural data, is constructed. It includes 648 protein domains. Based on the IADE database, we studied the relation between RNA stem-loop frequencies and protein secondary structure. It was found that the alpha-helices and beta-strands on proteins tend to be preferably "coded" by mRNA stem region, while the coils on proteins tend to be preferably "coded" by mRNA loop region. These tendencies are more obvious if we observe the structural words (SWs). An SW is defined by a four-amino-acid-fragment that shows the pronounced secondary structural (alpha-helix or beta-strand) propensity. It is demonstrated that the deduced correlation between protein and mRNA structure can hardly be explained as the stochastic fluctuation effect. (C) 2003 Wiley Periodicals, Inc.

Cardioviral RNA structure logo analysis: entropy, correlations, and prediction

In recent years, there has been an increased number of sequenced RNAs leading to the development of new RNA databases. Thus, predicting RNA structure from multiple alignments is an important issue to understand its function. Since RNA secondary structures are often conserved in evolution, developing methods to identify covariate sites in an alignment can be essential for discovering structural elements. Structure Logo is a technique established on the basis of entropy and mutual information measured to analyze RNA sequences from an alignment. We proposed an efficient Structure Logo approach to analyze conservations and correlations in a set of Cardioviral RNA sequences. The entropy and mutual information content were measured to examine the conservations and correlations, respectively. The conserved secondary structure motifs were predicted on the basis of the conservation and correlation analyses. Our predictive motifs were similar to the ones observed in the viral RNA structure database, and the correlations between bases also corresponded to the secondary structure in the database.

Influence of ground anchors on topographic amplification at slope crests

One feature of earthquake loading in regions containing sloping ground is a marked increase in accelerations at the crests of slopes. Many field cases exist where such increased accelerations were measured. The observed increase in the amount and severity of observed building damage near the edge of cliff-type topographies has been attributed to the topographic amplification. To counter this, it has been shown that anchoring the soil mass responsible for this to the rest of the stable soil mass can reduce the amount of topographic amplification. In this study, dynamic centrifuge modelling will be used to identify the region affected by topographic amplification in a model slope. The soil accelerations recorded will be compared to those measured in a comparable model treated by anchors. In addition, the tension measured in the anchors will be examined in order to better understand how the anchors are transferring the loads and mitigating these amplifications. © 2010 Taylor & Francis Group, London.