Construction of a ribozyme-expression system that effectively transports ribozymes to the cytoplasm.

In our previous studies, it was demonstrated that the activity of a ribozyme in vivo was governed by several parameters, which include a high level-expression of ribozyme, the intracellular stability of the ribozyme and colocalization of the ribozyme with its target RNA in the same cellular compartment. To generate ribozymes with significant activity in vivo, we have developed a ribozyme-expression system based on a human tRNA(Val) promoter. Our tRNA-embedded ribozymes produced by our ribozyme-expression system remain relatively stable in cultured cells with half-lives longer than 30 min. Moreover, tRNA-ribozymes with a cloverleaf structure were efficiently exported from the nucleus to the cytoplasm, where they would effectively cleave target RNAs. In the present study, we investigated the relationship between the secondary structure of the tRNA-ribozymes and the transport efficacy of them in mammalian cells by using a screening system in vivo. Furthermore, we also investigated the mechanism of the export of tRNA-embedded ribozymes both in mammalian cells and in Xenopus oocytes.     

作用于HBV（adr亚型）RNA的tRNA—包埋锤头状核酶的研究

设计了针对ＨＢＶ（ａｄｒ亚型）ＲＮＡ的二个锤头状核酶（ＲＳ３和ＲＣ２）,并将其插入ｔＲＮＡ反密码环中（ＲｔＳ３和ＲｔＣ２）,以增加其稳定性。实验表明,虽然插入ｔＲＮＡ中的核酶与裸露核酶相比,催化活性有所下降,但在胎牛血清和ＨｅｐＧ２细胞抽提液中的稳定性却明显提高。因此,ｔＲＮＡ－包埋核酶有可能提高在体内的抗病毒能力。     

tRNA-包埋核酶在HepG2细胞中的抗HBV活性

已知 ｔ Ｒ Ｎ Ａ 包埋核酶比裸露核酶在胎牛血清和 Ｈｅｐ Ｇ２ 细胞抽提液中有较高的稳定性 构建了 ｈ Ｃ Ｍ Ｖ 启动子驱动下的抗 Ｈ Ｂ Ｖ（ａｄｒ 亚型）的 ｔ Ｒ Ｎ Ａ 包埋核酶基因质粒,与携带 Ｈ Ｂ Ｖ 基因的ｐ１２Ⅱ质粒共转染 Ｈｅｐ Ｇ２ 细胞,用 Ｇ４１８ 筛选抗性细胞 分析稳定表达细胞中的 Ｈ Ｂ Ｖ Ｒ Ｎ Ａ, Ｈ Ｂ Ｖ 抗原合成和新生 Ｄ Ｎ Ａ 合成,表明ｔ Ｒ Ｎ Ａ 包埋核酶比裸露核酶有较高的抑制 Ｈ Ｂ Ｖ 活性．ｔ Ｒ Ｎ Ａ 包埋核酶和裸露核酶分别使靶 Ｒ Ｎ Ａ 减少 ８２％ ～８７％ 和 ７５％ ～８１％ ,抗原减少 ７３％ ～８０％ 和７０％ ～７４％ 以及新生 Ｄ Ｎ Ａ 减少 ７４％ ～７６％ 和 ６７％ ～７１％ 结果指出,核酶,特别是 ｔ Ｒ Ｎ Ａ 包埋核酶,对 Ｈｅｐ Ｇ２ 细胞中 Ｈ Ｂ Ｖ 表达和复制有明显抑制作用,可能作为 Ｈ Ｂ Ｖ 基因治疗的手段之一      

Modified binary hammerhead ribozymes with high catalytic activity

A series of binary hammerhead ribozymes was designed and assessed in terms of cleavage activity and nuclease resistance. Enhanced nuclease resistance of binary ribozymes was achieved by incorporation of Z-modified nucleotides at the selective positions along with addition of 3'-3-linked thymidine cap. These modified binary ribozymes efficiently cleave 190-nucleotides long MDR1 mRNA fragment and display catalytic activity much higher then respective full-length analogs.     

The ordered processing of intervening sequences in 23S rRNA of Rhodobacter sphaeroides requires RNase J

The essential processing of ribosomal rRNA precursors requires concerted and sequential cleavages by different endo- and exoribonucleases. Despite long lasting investigations of these processes the exact order of steps remained elusive. Many bacteria perform additional rRNA processing steps by removing intervening sequences within the 23S rRNA. This leads to disintegration of the 23S rRNA and discontinuously assembled fragments within the ribosomes. The maturation of these fragments also requires successive cleavage events by different RNases. Our study reveals that the 5'-to-3' exoribonuclease RNase J is responsible for the final 5'-end maturation of all three 23S rRNA fragments in the α-proteobacterium Rhodobacter sphaeroides. Additionally the results show that 5'- and 3'-processing steps are closely coupled: mature 5'-ends are a strict prerequisite for the final 3'-trimming of the 23S rRNA fragments.     

Binary hammerhead ribozymes with improved catalytic activity

A new design of binary hammerhead ribozymes displaying high catalytic activity and nucleolytic stability is described. These catalytic structures consist of two partially complementary oligoribonucleotides, capable of assembling into the hammerhead-like structure without tetraloop II on binding to the RNA target. A series of these binary ribozymes targeting the translation initiation region of multiple drug resistance gene mdr1 mRNA was synthesized and assessed in terms of catalytic activity under single and multiple reaction turnover conditions. Enhanced nuclease resistance of the binary ribozymes was achieved by incorporation of 2'-modified nucleotides at selected positions, along with addition of a 3'-3'-linked thymidine cap. The new binary ribozymes exhibit higher RNA cleavage activity than their full-length analogs because of faster dissociation of cleavage products. Furthermore, an excess of one of the ribozyme strands provides the possibility to unfold structured regions of the target RNA and facilitate productive complex formation.     

Directing the outcome of deoxyribozyme selections to favor native 3'-5' RNA ligation

Previous experiments have identified numerous RNA ligase deoxyribozymes, each of which can synthesize either 2',5'-branched RNA, linear 2'-5'-linked RNA, or linear 3'-5'-linked RNA. These products may be formed by reaction of a 2'-hydroxyl or 3'-hydroxyl of one RNA substrate with the 5'-triphosphate of a second RNA substrate. Here the inherent propensities for nucleophilic reactivity of specific hydroxyl groups were assessed using RNA substrates related to the natural sequences of spliceosome substrates and group II introns. With the spliceosome substrates, nearly half of the selected deoxyribozymes mediate a ligation reaction involving the natural branch-point adenosine as the nucleophile. In contrast, mostly linear RNA is obtained with the group II intron substrates. Because the two sets of substrates differ at only three nucleotides, we conclude that the location of the newly created ligation junction in DNA-catalyzed branch formation depends sensitively on the RNA substrate sequences. During the experiment that led primarily to branched RNA, we abruptly altered the selection strategy to demand that the deoxyribozymes create linear 3'-5' linkages by introducing an additional selection step involving the 3'-5'-selective 8-17 deoxyribozyme. Although no 3'-5' linkages (相似文献   

Efficient substrate cleavage catalyzed by hammerhead ribozymes derivatized with selenium for X-ray crystallography

Because oxygen and selenium are in the same group (Family VI) in the periodic table, the site-specific mutagenesis at the atomic level by replacing RNA oxygen with selenium can provide insights on the structure and function of catalytic RNAs. We report here the first Se-derivatized ribozymes transcribed with all nucleoside 5'-(alpha-P-seleno)triphosphates (NTPalphaSe, including A, C, G, and U). We found that T7 RNA polymerase recognizes NTPalphaSe Sp diastereomers as well as the natural NTPs, whereas NTPalphaSe Rp diastereomers are neither substrates nor inhibitors. We also demonstrated the catalytic activity of these Se-derivatized hammerhead ribozymes by cleaving the RNA substrate, and we found that these phosphoroselenoate ribozymes can be as active as the native one. These hammerhead ribozymes site-specifically mutagenized by selenium reveal the close relationship between the catalytic activities and the replaced oxygen atoms, which provides insight on the participation of oxygen in catalysis or intramolecular interaction. This demonstrates a convenient strategy for the mechanistic study of functional RNAs. In addition, the active ribozymes site-specifically derivatized by selenium will allow for convenient MAD phasing in X-ray crystal structure studies.     

The efficiency of strand invasion by Escherichia coli RecA is dependent upon the length and polarity of ssDNA tails

RecA protein is essential for homologous recombination and the repair of DNA double-strand breaks in Escherichia coli. The protein binds DNA to form nucleoprotein filaments that promote joint molecule formation and strand exchange in vitro. RecA polymerises on ssDNA in the 5'-3' direction and catalyses strand exchange and branch migration with a 5'-3' polarity. It has been reported previously, using D-loop assays, in which ssDNA (containing a heterologous block at one end) invades supercoiled duplex DNA that 3'-homologous ends are reactive, whereas 5'-ends are inactive. This polarity bias was thought to be due to the polarity of RecA filament formation, which results in the 3'-ends being coated in RecA, whereas 5'-ends remain naked. Using a range of duplex substrates containing ssDNA tails of various lengths and polarities, we now demonstrate that when no heterologous block is imposed, 5'-ends are just as reactive as 3'-ends. Moreover, using short-tailed substrates, we find that 5'-ends form more stable D-loops than 3'-ends. This bias may be a consequence of the instability of short 3'-joints. With more physiological substrates containing long ssDNA tails, we find that RecA shows no intrinsic preference for 5' or 3'-ends and that both form D-loop complexes with high efficiency.     

The effects of tetrachlorobiphenyls on the electron transfer reaction of isolated rat liver mitochondria

A comparative study was made of the effects of several symmetrical tetrachlorobiphenyls (TCBs) on the electron transfer from succinate to oxygen of rat liver mitochondria, and some differences in effects caused by the different chlorine positions of the biphenyl ring were clarified. TCBs used in this study included 2,3,2',3'-, 2,4,2',4'-, 2,5,2',5'-, 2,6,2',6'-, and 3,4,3',4'-TCBs. The inhibitory actions of 2,3,2',3'-, 2,4,2',4'-, and 2,5,2',5'-TCBs on succinate oxidase were potent, while those caused by 2,6,2',6'- and 3,4,3',4'-TCBs were significantly weak. The inhibition sites of 2,3,2',3'-, 2,4,2',4'-, and 2,5,2',5'-TCBs in succinate oxidase were succinate dehydrogenase and cytochrome b-c segment of the electron transport chain. In the cytochrome b-c segment, these TCBs acted on myxothiazol-sensitive site rather than antimycin-sensitive site. Cytochrome c oxidase was hardly affected by TCBs. These results indicate that 2,3,2',3'-, 2,4,2',4'-, and 2,5,2',5'-TCBs severely depress the electron transfer with succinate as the substrate, which secondarily reduces the synthesis of ATP. The relationship between the activity and chemical structure of TCBs is also discussed.     

Nucleic acid crystallography: current progress

Fifty years after the publication of the DNA double helix model by Watson and Crick, new nucleic acid structures keep emerging at an ever-increasing rate. The past three years have brought a flurry of new oligonucleotide structures, including those of a Hoogsteen-paired DNA duplex, Holliday junctions, DNA-drug complexes, quadruplexes, a host of RNA motifs and various nucleic acid analogues. Major advances were also made in terms of the structure and function of catalytic RNAs. These range from improved models of the phosphodiester cleavage reactions catalyzed by the hairpin and hepatitis delta virus ribozymes to the visualization of a complete active site of a group I self-splicing intron with bound 5'- and 3'-exons. These triumphs are complemented by a refined understanding of cation-nucleic-acid interactions and new routes to the generation of derivatives for phasing of DNA and RNA structures.     

Inhibition of protein synthesis by the cordycepin analog of (2'-5')ppp(Ap)nA, (2'-5')ppp(3'dAp)n3'dA, in intact mammalian cells

The introduction of the cordycepin analog of (2'-5')An, (2'-5')ppp(3'dAp)n3'dA [referred to as (2'-5')p33'dAn], into mouse L929 cells and cultured human fibroblasts resulted in a dose-dependent inhibition of protein synthesis which was comparable to the inhibition observed by (2'-5')ppp(Ap)nA [referred to as (2'-5')p3An]. The inhibition of protein synthesis by (2'-5')p33'dAn was much more persistent than that of the naturally occurring (2'-5')p3An following prolonged incubation of cells. Furthermore, the (2'-5')p3An was cytotoxic to mammalian cells in culture, whereas the (2'-5')p33'dAn was not.     

Immobilized RNA switches for the analysis of complex chemical and biological mixtures

A prototype biosensor array has been assembled from engineered RNA molecular switches that undergo ribozyme-mediated self-cleavage when triggered by specific effectors. Each type of switch is prepared with a 5'-thiotriphosphate moiety that permits immobilization on gold to form individually addressable pixels. The ribozymes comprising each pixel become active only when presented with their corresponding effector, such that each type of switch serves as a specific analyte sensor. An addressed array created with seven different RNA switches was used to report the status of targets in complex mixtures containing metal ion, enzyme cofactor, metabolite, and drug analytes. The RNA switch array also was used to determine the phenotypes of Escherichia coli strains for adenylate cyclase function by detecting naturally produced 3',5'- cyclic adenosine monophosphate (cAMP) in bacterial culture media.     

抗水稻条纹叶枯病毒核酶的设计,克隆及体外活性测定

为探索控制水稻条纹叶枯病毒（Ｒｉｃｅｓｔｒｉｐｅｖｉｒｕｓ,ＲＳＶ）设计合成了特异切割该病毒ＲＮＡ保守区及编码病害特异性蛋白（ＤｉｓｅａｓｅＳｐｅｃｉｆｉｃＰｒｏｔｅｉｎ,ＤＳＰ）基因的核酶,核酶基因的长度均为４０个碱基,用化学合成方法合成其正链及与其３＇－末端互补的１５个碱基引物,用ＴａｇＤＮＡ多聚酶合成其互补链。双链ＤＮＡ直接插入克隆载体ＰＧＥＭ３ｚｆ（＋）的Ｓｍａｌ位点。序列测定表明,克隆得到的核酶序列与设计的核酶序列完全一致。经ＳＰ６ＲＮＡ多聚酶体外转录得到核酶ＲＮＡ。当核酶ＲＮＡ与以同样方法转录得到的靶基因ＲＮＡ混合反应,可得到预期结果相同的切割片段,表明两种核酶在体外均具有特异性切割活性。     

In vitro selection of hammerhead ribozymes containing a bulged nucleotide in stem II.

Hammerhead ribozymes were transcribed from a dsDNA template containing four random nucleotides between stems II and III, which replace the naturally occurring GAA nucleotides. In vitro selection was used to select hammerhead ribozymes capable of in cis cleavage using denaturing polyacrylamide gels for the isolation of cleaving sequences. Self-cleaving ribozymes were cloned after the first and second rounds of selection, sequenced and characterised. Only sequences containing 5'-HGAA-3', where H is A, C or U, between stems II and III were active; G was clearly not tolerated at this position. Thus, only three sequences out of the starting pool of 256 (4(4)) were active. The Michaelis-Menten parameters were determined for the in trans cleaving versions of these ribozymes and indicate that selected ribozymes are less efficient than the native sequence. We propose that the selected ribozymes accommodate the extra nucleotide as a bulge in stem II.