Stereochemistry of RNA cleavage by the Tetrahymena ribozyme and evidence that the chemical step is not rate-limiting

The intervening sequence of the ribosomal RNA precursor of Tetrahymena is a catalytic RNA molecule, or ribozyme. Acting as a sequence-specific endoribonuclease, it cleaves single-stranded RNA substrates with concomitant addition of guanosine. The chemistry of the reaction has now been studied by introduction of a single phosphorothioate in the substrate RNA at the cleavage site. Kinetic studies show no significant effect of this substitution on kcat (rate constant) or Km (Michaelis constant), providing evidence that some step other than the chemical step is rate-limiting. Product analysis reveals that the reaction proceeds with inversion of configuration at phosphorus, consistent with an in-line, SN2 (P) mechanism. Thus, the ribozyme reaction is in the same mechanistic category as the individual displacement reactions catalyzed by protein nucleotidyltransferases, phosphotransferases, and nucleases.     

Role of the protein moiety of ribonuclease P, a ribonucleoprotein enzyme

The Bacillus subtilis ribonuclease P consists of a protein and an RNA. At high ionic strength the reaction is protein-independent; the RNA alone is capable of cleaving precursor transfer RNA, but the turnover is slow. Kinetic analyses show that high salt concentrations facilitate substrate binding in the absence of the protein, probably by decreasing the repulsion between the polyanionic enzyme and substrate RNAs, and also slow product release and enzyme turnover. It is proposed that the ribonuclease P protein, which is small and basic, provides a local pool of counter-ions that facilitates substrate binding without interfering with rapid product release.     

Transition state stabilization by a catalytic RNA

The hairpin ribozyme catalyzes sequence-specific cleavage of RNA through transesterification of the scissile phosphate. Vanadate has previously been used as a transition state mimic of protein enzymes that catalyze the same reaction. Comparison of the 2.2 angstrom resolution structure of a vanadate-hairpin ribozyme complex with structures of precursor and product complexes reveals a rigid active site that makes more hydrogen bonds to the transition state than to the precursor or product. Because of the paucity of RNA functional groups capable of general acid-base or electrostatic catalysis, transition state stabilization is likely to be an important catalytic strategy for ribozymes.     

基于SmarTeam的汽车产品配置器开发

为探讨和解决汽车制造企业大批量定制的问题,在阐述了SmarTeam模块和功能的基础上,分析了汽车行业对产品配置器的需求,构建了汽车产品配置器的结构框架;针对系统的底层平台层、配置系统逻辑层和产品配置器表现层三部分进行研究,设计了汽车产品配置的体系结构;以汽车制动总成为实例,确立了产品配置器的运行过程,为汽车产品实现面向大规模定制奠定了基础。     

赖氨酸铜稳定常数的测定及优化计算

采用pH电位滴定法测定了铜离子与赖氨酸配合物在离子强度为0．1mol／L（NaCl）、温度为25℃时的pH值变化,用半整数作图法得出配合物的稳定常数为：1gK;=10．6,1gK：=8．5,1gK,=2．1。并运用量子化学密度泛函理论对产物的几何构型进行了优化,同时计算得到了热分解反应的标准热力学量变。     

青海省马铃薯卷叶病毒的RT-PCR法检测

根据马铃薯卷叶病毒（PLRV）外壳蛋白基因的保守序列设计了一对寡聚核苷酸引物,从田间自然感染PLRV的马铃薯病株中提取病毒总RNA,用反转录-聚合酶链式反应扩增出符合设计大小240bp的特异性产物,而对照没有任何扩增产物。建立了快速、准确检验PLRV的分子检测方法,为青海省马铃薯生产中卷叶病毒的检测和防治提供了有效手段。     

多位点生物杀虫毒素BtA形成的HPLC分析

 基于多位点生物杀虫毒素理论和生物耦合技术，研制生物杀虫毒素BtA，为新生物农药的开发提供了一种新思路、新方法和新手段。将苏云金芽孢杆菌（B.t.）晶体进行酶解改造，形成带末端氨基的原毒素；将阿维菌素的羟基进行激活、衍生化，形成带羧基的阿维菌素衍生物（Abamectin-COONa）；再利用氨基-羧基偶联剂（EDC）进行两种生物毒素的生物耦合。利用反相液相色谱（HPLC）检测不同反应时间的BtA生物耦合体系，以确定生物耦合反应的发生；通过反应底物两两组合的分析比较，识别生物耦合产物BtA生成的色谱特征，分析生物耦合产物---多位点生物杀虫毒素BtA的产生过程。     

RNA as an RNA polymerase: net elongation of an RNA primer catalyzed by the Tetrahymena ribozyme

A catalytic RNA (ribozyme) derived from an intervening sequence (IVS) RNA of Tetrahymena thermophila will catalyze an RNA polymerization reaction in which pentacytidylic acid (C5) is extended by the successive addition of mononucleotides derived from a guanylyl-(3',5')-nucleotide (GpN). Cytidines or uridines are added to C5 to generate chain lengths of 10 to 11 nucleotides, with longer products being generated at greatly reduced efficiency. The reaction is analogous to that catalyzed by a replicase with C5 acting as the primer, GpNs as the nucleoside triphosphates, and a sequence in the ribozyme providing a template. The demonstration that an RNA enzyme can catalyze net elongation of an RNA primer supports theories of prebiotic RNA self-replication.     

Probing high-barrier pathways of surface reactions by scanning tunneling microscopy

The ability of scanning tunneling microscopy to probe the pathways of thermally activated high-barrier surface processes is frequently limited by competing low-barrier processes that can confuse measurement of the true initial and final configuration. We introduce an approach to circumvent this difficulty by driving the surface process with nanosecond laser heating. The method is applied to determine the pathway of recombinative desorption in the H/Si(001) system. The observed configuration of dangling bonds after laser heating reveals that the desorbed hydrogen molecules are not formed on single dimers, but rather from neighboring silicon dimers via an interdimer reaction pathway.     

中华大蟾蜍皮肤galectin-3cDNA分子多样性及氨基酸变异分析

以中华大蟾蜍Bzfo gargarizans皮肤总核糖核酸(RNA)反转录第1链互补脱氧核糖核酸(cDNA)为模板,以聚合酶链式反应(PCR)扩增出galec tin-3基因片段并通过TA克隆将其插入到pGM-T载体,通过DNA测序确定该基因片段序列,然后利用美国国家生物技术信息中心(NCBI)中ORF finder查找基因的全长开放阅读框(ORF).筛选到9个编码galectin-3的cDNA序列,其中2个序列编码N-端截短型galectin-3(galectin-3C).Clustal X2.0多序列比对和DnaSP4.0分析cDNA序列的多样性.结果发现:中华大蟾蜍alectin-3C区域具有高密度的单核苷酸多态性(SNP),频率为每20 bp为1个单核苷酸多态性.推导的氨基酸序列比对显示这9个基因在N端和糖识别结构域(CRD)有较高同源性,包括磷酸化位点、糖基结合位点和相关基序,而在串联重复区则存在较大差异.galectin-3基因及其编码蛋白的多样性很可能赋予中华大蟾蜍很强的环境适应能力.     

中华大蟾蜍皮肤galectin-3 cDNA分子多样性及氨基酸变异分析

 以中华大蟾蜍Bufo gargarizans皮肤总核糖核酸（RNA）反转录第1链互补脱氧核糖核酸（cDNA）为模板,以聚合酶链式反应（PCR）扩增出galectin-3基因片段并通过TA克隆将其插入到pGM-T载体,通过DNA测序确定该基因片段序列,然后利用美国国家生物技术信息中心（NCBI）中ORF finder查找基因的全长开放阅读框（ORF）。筛选到9个编码galectin-3的cDNA序列,其中2个序列编码N-端截短型galectin-3（galectin-3C）。Clustal X2.0多序列比对和DnaSP 4.0分析cDNA序列的多样性。结果发现：中华大蟾蜍galectin-3C区域具有高密度的单核苷酸多态性（SNP）,频率为每20 bp为1个单核苷酸多态性。推导的氨基酸序列比对显示这9个基因在N端和糖识别结构域（CRD）有较高同源性,包括磷酸化位点、糖基结合位点和相关基序,而在串联重复区则存在较大差异。galectin-3基因及其编码蛋白的多样性很可能赋予中华大蟾蜍很强的环境适应能力。图3表1参24     

狂犬病病毒SRV9株N、P、G和L蛋白基因的克隆及表达载体构建

以狂犬病病毒RNA为模板,采用RT-PCR方法克隆获取N、P、G及L蛋白编码基因核苷酸序列,应用定向克隆技术,构建真核表达载体 pcDNA3.1-N、pcDNA3.1-P、pcDNA3.1-G及pcDNA3.1-L.经测序鉴定证实获取的N、P、G及L蛋白区全长核苷酸序列与文献报道的一致,并成功构建了其真核表达载体.     

南芥菜花叶病毒分子生物学快速检测方法的研究

根据南芥菜花叶病毒(Arabis mosaic Nepovirus)CP基因序列,设计并合成了特异性RT-PCR检测引物,对南芥菜花叶病毒和非南芥菜花叶病毒的感病植物组织进行了PCR扩增反应。结果,南芥菜花叶病毒的感病植物组织的PCR产物均出现364bp的特异性扩增条带,而非南芥菜花叶病毒均未出现扩增条带,证明这对引物具有南芥菜花叶病毒鉴定特异性。将提取的南芥菜花叶病毒总RNA做梯度稀释,测定该检测体系的敏感度,结果表明,此体系最低可检出南芥菜花叶病毒提取的RNA模板浓度为150pg/μL。     

Reversible unfolding of single RNA molecules by mechanical force

Here we use mechanical force to induce the unfolding and refolding of single RNA molecules: a simple RNA hairpin, a molecule containing a three-helix junction, and the P5abc domain of the Tetrahymena thermophila ribozyme. All three molecules (P5abc only in the absence of Mg2+) can be mechanically unfolded at equilibrium, and when kept at constant force within a critical force range, are bi-stable and hop between folded and unfolded states. We determine the force-dependent equilibrium constants for folding/unfolding these single RNA molecules and the positions of their transition states along the reaction coordinate.     

河南省马铃薯Y病毒的分子检测与鉴定

利用RT-PCR技术对郑州市和信阳市的马铃薯Y病毒(potato virus Y,PVY)进行了鉴定。依据PVY p1基因序列设计合成1对引物,以带毒的马铃薯叶片总RNA为模板,RT-PCR扩增得到0.58kb的目的DNA片段,而健康对照无此片段。对PCR产物进行序列测定,Blast分析表明,该DNA序列与PVY N:O株系p1基因序列相似性可达99%,证明所得DNA片段确为PVY p1基因,从而建立了PVY的RT-PCR检测方法。在此基础上,从节省检测时间、优化反应程序及反应体系等方面进行了改进。     

An RNA processing activity that debranches RNA lariats

The excised introns of pre-messenger RNA's (pre-mRNA's) and intron-containing splicing intermediates are in a lariat configuration in which the 5' end of the intron is covalently joined by a 2',5'-phosphodiester bond to a specific adenosine residue near the 3' end of the intron. A 2',5'-phosphodiesterase activity in HeLa cell extracts has been detected that debranches RNA lariats, converting them to linear RNA molecules by specific cleavage of the 2',5'-phosphodiester bond. This lariat debranching activity is distinct from previously reported 2',5'-phosphodiesterases with regard to its biochemical and substrate requirements as well as its stringent cleavage specificity. The debranching activity is observed only if the RNA lariats generated during in vitro processing are deproteinized and added back to the extract. These results suggest that during the normal in vitro splicing reaction the 2',5'-phosphodiester bond of RNA lariats is protected from cleavage by the lariat debranching activity.     

D-alanine in the frog skin peptide dermorphin is derived from L-alanine in the precursor

A D-alanine-containing peptide termed dermorphin, with potent opiate-like activity, has been isolated from skin of the frog Phyllomedusa sauvagei. Complementary DNA (cDNA) libraries were constructed from frog skin messenger RNA and screened with a mixture of oligonucleotides that contained the codons complementary to five amino acids of dermorphin. Clones were detected with inserts coding for different dermorphin precursors. The predicted amino acid sequences of these precursors contained homologous repeats of 35 amino acids that included one copy of the heptapeptide dermorphin. In these cloned cDNAs, the alanine codon GCG occurred at the position where D-alanine is present in the end product. This suggests the existence of a novel post-translational reaction for the conversion of an L-amino acid to its D-isomer.