靶向Akt2基因RNA干扰重组表达载体的构建和测序

目的 利用RNA干扰技术,以Akt2为靶基因,设计并构建重组表达载体,并进行测序鉴定.方法 利用GenBank中已知Akt2的mRNA基因序列设计具有短发夹结构的两条寡核甘酸序列,经退火形成互补双链,与pGEM-T Easy载体进行连接,经蓝白筛选后以T7和SP6为引物进行PCR鉴定,对表达载体pRNAT-U6.2及亚克隆产物进行双酶切,将得到的基因及线性化的表达载体再次连接,利用PCR方法进行重组体的筛选鉴定并进行测序分析.结果 将合成的DNA序列克隆到表达载体上,经PCR扩增筛选鉴定和测序鉴定证实为所需序列.结论 Akt2靶向RNA干扰重组表达载体构建成功.     

CTGF靶向RNA干扰重组体的构建及序列分析

目的:利用pEGFP质粒载体构建介导结缔组织生长因子(CTGF)短发夹RNA(shorthairpinRNA,shRNA)表达的质粒.方法:分别设计3对有小发夹结构的两条DNA序列,经退火成互补双链,再克隆至带有U6启动子的质粒载体pEGFP中,构建重组体,转化DH5α菌株,提取质粒行酶切鉴定后,进行测序分析.结果:CTGF的sRNA片段被成功克隆到pEGFP质粒载体中,3个重组质粒shRNA编码序列与设计的片段完全一致,经酶切与测序证实构建成功.结论:成功构建了能表达CTGFshRNA的重组体,为下一步探索肝纤维化基因治疗的新途径打好基础.     

基于微小RNA的乙肝病毒RNA干扰表达载体的构建

目的为优化RNA干扰研究方法，构建了基于微小RNA的乙肝病毒RNA干扰表达载体。方法利用网络工具设计针对乙型肝炎病毒S区的靶干扰序列，将单链寡核苷酸退火形成双链，克隆人pcDNA6．2-GW／EmGFP—miR表达载体。结果经酶切及测序鉴定，插入序列与靶序列一致，载体构建正确。结论成功构建了新型乙肝病毒RNA干扰表达载体，为进一步体外及体内实验奠定了基础。     

大鼠结缔组织生长因子短发夹RNA干扰质粒重组体的构建和鉴定

目的构建靶向大鼠结缔组织生长因子(CTGF)的shRNA真核表达载体质粒,为利用基因沉默技术从转录后水平进行抗心肌纤维化的研究做准备。方法根据大鼠CTGFmRNA序列设计并合成shRNA寡核苷酸片段,退火形成双链并克隆进入载体pGenesil-1,并进行酶切鉴定和测序。结果酶切证明构建的shRNA已插入载体,经测序证明与设计的相同。结论成功构建靶向大鼠CTGF的shRNA真核表达质粒重组体,为质粒的筛选和进一步进行体内外心肌纤维化的RNA干扰研究奠定了基础。     

乙型肝炎病毒P和X区siRNA表达载体的构建与鉴定

目的构建乙型肝炎病毒（HBV）P区和X区的小干扰RNA（siRNA）表达载体,并进行酶切鉴定,为进一步评价siRNA对HBV的抑制作用提供研究基础.方法根据siRNA的设计原则并经Blast比对,设计合成6条siRNA双链复合体,体外退火后在T4连接酶作用下连接入重组载体P-Silencer-cmv 4.1-hygro,连接产物转化JM109感受态细胞,筛选阳性克隆并提取重组体,经琼脂糖凝胶电泳初步鉴定,酶切产物经聚丙稀酰胺凝胶电泳确定插入片段,送公司测序鉴定.结果琼脂糖凝胶电泳得到与质粒大小相近的条带,聚丙稀酰胺凝胶电泳确定已插入大小约55bp的双链DNA片段,测序结果证实重组载体构建成功.结论构建的HBV的siRNA表达载体可用于进一步检测其对病毒的抑制作用.     

STAT3靶向RNAi腺病毒表达载体的构建与鉴定

目的 观察针对STAT3基因的RNAi腺病毒表达载体对大鼠神经胶质瘤细胞的干扰效果,为探索肿瘤基因治疗的新途径奠定基础.方法设计针对STAT3编码区的短发夹结构的两条DNA序列,经退火成互补双链,克隆到PGEM-T中,构建重组体,再对重组质粒进行酶切鉴定,DNA测序分析后再克隆到穿梭质粒PDC316中,通过Lipofectamine2000的介导和腺病毒包装质粒PBHG共转染至人胚肾HEK293细胞株中,经同源重组后获得重组腺病毒rAD-STAT3,应用PCR鉴定重组腺病毒,空斑传代纯化病毒并反复冻融扩增病毒,以50%组织培养感染剂量法(TCID50)测定病毒滴度.以阴性为对照,转染到大鼠神经胶质瘤(C6)细胞,Western印迹法检测STAT3蛋白质表达量的改变,RT-PCR法观察STAT3基因表达改变.结果酶切鉴定和测序分析均提示STAT3靶向RNAi病毒表达载体构建成功,阳性病毒载体转染后C6细胞STAT3基因表达及蛋白质表达均较阴性转染的对照组显著下降.结论 STAT3靶向RNAi腺病毒表达载体成功构建,并能有效抑制C6细胞中STAT3基因表达.     

靶向表皮生长因子受体shRNA质粒表达载体的构建和鉴定

目的构建靶向表皮生长因子受体（EGFR）的短发卡状RNA（shRNA）质粒表达载体并进行鉴定。方法设计两个小分子干扰RNA（siRNA）序列，体外合成DNA模板引物，与Pgenesil-1质粒构建成编码shRNA的表达载体，进行酶切鉴定和测序，再转染人大肠癌LoVo细胞，进行荧光摄像和G418抗性筛选。结果构建的质粒表达载体完全符合设计要求，转染成功的细胞在荧光显微镜下显示为绿色，G418可以筛选出阳性克隆。结论成功构建了编码EGFR—shRNA的质粒表达载体，并可以进行稳定筛选。     

靶向Midkine基因的siRNA真核表达载体的构建及鉴定

目的 构建靶向midkine基因的siRNA 的表达载体,为研究midkine在肿瘤中作用提供一个新的方向.方法 根据基因库中midkine cDNA 序列设计和合成针对人midkine 基因的siRNA 寡核苷酸,定向克隆入质粒载体PGCsiU6,对该重组表达载体进行酶切鉴定及DNA 测序.结果 酶切鉴定、DNA 测序证实表达质粒构建成功,无碱基突变.结论 成功构建了靶向midkine 基因表达的siRNA 干扰质粒载体PGCsiU6/midkine,为进一步运用RNA干扰技术进行midkine 基因功能研究奠定了基础.     

抑制MDR1基因表达shRNA RNAi系统的构建

目的构建抑制多药耐药基因(MDR1)表达的短发夹RNA(sh RNA)真核表达载体系统.方法根据MDR1基因已知序列,设计两段21个碱基的MDR1特异性靶序列,合成两对62nt 并含有编码shRNA序列的寡核苷酸,双链退火后,克隆到经过BamH I和Xba I双酶切后线性 PG E-1载体的U6启动子下游,重组构建RNA干扰(RNAi)质粒.结果对重新构建的pshRNA-MDR1载体经P CR扩增后行电泳分析,并对含有插入基因片段行测序分析.结果表明,62个碱基均成功插入到预计位点,并且序列完全一致.结论载体的成功构建为研究其对MDR1 基因表达的抑制作用打下基础,同时使我们发展了在体内合成siRNA的方法.     

靶向大鼠Caveolin-1基因的短发夹RNA表达载体的构建

目的构建靶向大鼠caveolin-1基因的shRNA表达载体。方法化学合成靶向caveolin-1的单核苷酸链,经退火成双链。将退火得到的双链DNA克隆至表达载体pLL3.7中得到重组质粒,经限制性内切酶酶切、DNA测序进行鉴定。结果通过限制性内切酶酶切、DNA测序证实,成功构建大鼠pLL3.7-cav-1表达载体。结论成功构建了靶向大鼠caveolin-1的shRNA表达载体,为以后进行caveolin-1与ALI/ARDS的相关研究奠定了基础。     

Thoughts on how to think (and talk) about RNA structure

Recent events have pushed RNA research into the spotlight. Continued discoveries of RNA with unexpected diverse functions in healthy and diseased cells, such as the role of RNA as both the source and countermeasure to a severe acute respiratory syndrome coronavirus 2 infection, are igniting a new passion for understanding this functionally and structurally versatile molecule. Although RNA structure is key to function, many foundational characteristics of RNA structure are misunderstood, and the default state of RNA is often thought of and depicted as a single floppy strand. The purpose of this perspective is to help adjust mental models, equipping the community to better use the fundamental aspects of RNA structural information in new mechanistic models, enhance experimental design to test these models, and refine data interpretation. We discuss six core observations focused on the inherent nature of RNA structure and how to incorporate these characteristics to better understand RNA structure. We also offer some ideas for future efforts to make validated RNA structural information available and readily used by all researchers.     

衰老人胚肺成纤维细胞核转录活性的研究

目的研究人胚肺成纤维细胞（简称２ＢＳ）核体外转录活性与代龄的关系。方法用３ＨＵＴＰ掺入法研究不同代龄２ＢＳ细胞核体外转录活性。结果衰老２ＢＳ细胞核转录活性较年轻组下降３３％（Ｐ＜００１），其催化ｒＲＮＡ和ｔＲＮＡ合成的ＲＮＡ聚合酶（ＲＮＰ）Ⅰ和Ⅲ的转录活性下降２４％（Ｐ＜００５），催化合成ｍＲＮＡ的ＲＮＰⅡ转录活性下降３８％（Ｐ＜００１）；衰老２ＢＳ细胞核内ＲＮＡ被转运至核外的量为总合成量的２９％，明显低于年轻细胞组的４５％（Ｐ＜００１）。结论衰老２ＢＳ细胞核转录活性的下降可能与其ＲＮＰ的活性与ＲＮＡ的转运水平下降有关。     

Interaction of JMJD6 with single-stranded RNA

JMJD6 is a Jumonji C domain-containing hydroxylase. JMJD6 binds α-ketoglutarate and iron and has been characterized as either a histone arginine demethylase or U2AF65 lysyl hydroxylase. Here, we describe the structures of JMJD6 with and without α-ketoglutarate, which revealed a novel substrate binding groove and two positively charged surfaces. The structures also contain a stack of aromatic residues located near the active center. The side chain of one residue within this stack assumed different conformations in the two structures. Interestingly, JMJD6 bound efficiently to single-stranded RNA, but not to single-stranded DNA, double-stranded RNA, or double-stranded DNA. These structural features and truncation analysis of JMJD6 suggest that JMJD6 may bind and modify single-stand RNA rather than the previously reported peptide substrates.     

DEAD-box protein CYT-19 is activated by exposed helices in a group I intron RNA

DEAD-box proteins are nonprocessive RNA helicases and can function as RNA chaperones, but the mechanisms of their chaperone activity remain incompletely understood. The Neurospora crassa DEAD-box protein CYT-19 is a mitochondrial RNA chaperone that promotes group I intron splicing and has been shown to resolve misfolded group I intron structures, allowing them to refold. Building on previous results, here we use a series of tertiary contact mutants of the Tetrahymena group I intron ribozyme to demonstrate that the efficiency of CYT-19–mediated unfolding of the ribozyme is tightly linked to global RNA tertiary stability. Efficient unfolding of destabilized ribozyme variants is accompanied by increased ATPase activity of CYT-19, suggesting that destabilized ribozymes provide more productive interaction opportunities. The strongest ATPase stimulation occurs with a ribozyme that lacks all five tertiary contacts and does not form a compact structure, and small-angle X-ray scattering indicates that ATPase activity tracks with ribozyme compactness. Further, deletion of three helices that are prominently exposed in the folded structure decreases the ATPase stimulation by the folded ribozyme. Together, these results lead to a model in which CYT-19, and likely related DEAD-box proteins, rearranges complex RNA structures by preferentially interacting with and unwinding exposed RNA secondary structure. Importantly, this mechanism could bias DEAD-box proteins to act on misfolded RNAs and ribonucleoproteins, which are likely to be less compact and more dynamic than their native counterparts.DEAD-box proteins constitute the largest family of RNA helicases and function in all stages of RNA metabolism (1, 2). In vivo, many DEAD-box proteins have been implicated in assembly and conformational rearrangements of large structured RNAs and ribonucleoproteins (RNPs), including the ribosome, spliceosome, and self-splicing introns (3). Thus, it is important to establish how these proteins use their basic mechanisms of RNA binding and helix unwinding to interact with and remodel higher-order RNA structures.Structural and mechanistic studies have elucidated the basic steps of the ATPase cycle of DEAD-box proteins and have provided an understanding of the coupling between ATPase and duplex unwinding activities (4–11). The conserved helicase core consists of two flexibly linked RecA-like domains that contain at least 12 conserved motifs, including the D-E-A-D sequence in the ATP-binding motif II (3, 12). Binding of ATP and double-stranded RNA to domains 1 and 2, respectively, induces domain closure, which completes the formation of an ATPase active site at the domain interface and introduces steric clashes in the RNA binding site, leading to the displacement of one of the RNA strands (6, 7). ATP hydrolysis and inorganic phosphate release are then thought to regenerate the open enzyme conformation (4, 8, 13). Unlike conventional helicases, DEAD-box proteins have not been found to translocate, limiting the unwinding activity to short helices that can be disrupted in a single cycle of ATP binding and hydrolysis (4, 8, 9, 14–16). This mechanism is compatible with the physiological roles of DEAD-box proteins, because cellular RNAs rarely contain continuous base-paired regions that are longer than one or two helical turns.The interactions of DEAD-box proteins with structured RNAs have been extensively studied using two homologous proteins that function as general RNA chaperones: CYT-19 from Neurospora crassa and Mss116 from Saccharomyces cerevisiae. In vivo, CYT-19 is required for efficient splicing of several mitochondrial group I introns and can promote splicing of group I and group II introns in yeast mutants that lack functional Mss116 (17, 18). Both proteins have been shown to act as general RNA chaperones during group I and group II intron folding in vitro and are thought to act primarily by reversing misfolding of the intron RNAs, although additional mechanisms may be used for some substrates (17–23). Importantly, the chaperone activities of these and other DEAD-box proteins correlate with their ATP-dependent helix unwinding activities, suggesting that DEAD-box proteins function by lowering the energy barriers for transitions between alternative structures that involve disruption of base pairs (24, 25).In vitro studies using the group I intron ribozyme from Tetrahymena thermophila have been instrumental in probing the chaperone mechanism of CYT-19 (17, 26–28). This ∼400-nt RNA folds into a compact, globular structure composed of a conserved core and a series of peripheral elements that encircle the core by forming long-range tertiary contacts (Fig. 1) (29–31). Upon addition of Mg²⁺ ions, the majority of the ribozyme population becomes trapped in a long-lived misfolded conformation, which then slowly refolds to the native state (32). The misfolded intermediate is remarkably similar to the native ribozyme, forming a complete native network of secondary and tertiary interactions and a globally compact fold (33, 34). Despite these similarities, refolding to the native state requires extensive unfolding, including disruption of all five peripheral tertiary contacts and the core helix P3 (33, 35). To explain these results, a topological error has been proposed, wherein two single-stranded joining elements are crossed incorrectly in the core of the misfolded ribozyme, and transient disruption of the surrounding native structure is required for refolding (33, 35).Open in a separate windowFig. 1.The Tetrahymena group I intron ribozyme. (A) Secondary structure and mutations. Peripheral elements are colored and thick arrows mark the long-range peripheral tertiary contacts. Paired regions (P) and loops that were mutated in this study (L) are labeled based on group I intron nomenclature in ref. 31. The mutated regions are enclosed in dashed boxes and labeled in bold, with sequence substitutions indicated nearby. Sequences that were deleted to construct the helix truncation mutants (Fig. 6) are enclosed in gray dashed boxes and the replacement nucleotides are shown in gray italic font. (B) Tertiary structure model of the ribozyme (31). Peripheral elements (colored surface) and the locations of the long-range peripheral tertiary contacts (circles) are highlighted using the same color scheme as in A. The ribozyme core is shown in silver. The block arrows indicate the approximate positions of tertiary contacts not visible in each respective view of the ribozyme. The figures were prepared using PyMOL.Given the structural similarity between the native and misfolded ribozyme, it is interesting that CYT-19 can accelerate refolding of the misfolded intermediate by at least an order of magnitude without detectably unfolding the native ribozyme (26). Insights into this apparent preference for the misfolded ribozyme came from studies of two ribozyme mutants in which the tertiary structure was destabilized, making the stability of the native ribozyme comparable to that of the misfolded intermediate (28). CYT-19 unfolded the native and misfolded conformers of these mutants with comparable efficiencies, suggesting that the efficiency of chaperone-mediated unfolding depended on the stability of ribozyme tertiary structure. However, the mutations studied were concentrated in one region of the ribozyme, leaving open the possibility that CYT-19 recognizes local disruptions rather than global stability.Here we investigate the roles of RNA stability in CYT-19-mediated unfolding of the Tetrahymena ribozyme by using a series of ribozyme mutants with disruptions of each of the five peripheral tertiary contacts. We observe a strong correlation between CYT-19 activity and global stability of ribozyme tertiary structure. Further, we find that the RNA-dependent ATPase activity of CYT-19 depends on the accessibility of secondary structure in the ribozyme. Our results lead to a general model for recognition and remodeling of unstable or incorrectly folded RNAs by a DEAD-box protein.     

Structural and biochemical insights into 2′-O-methylation at the 3′-terminal nucleotide of RNA by Hen1

Small RNAs of ≈20–30 nt have diverse and important biological roles in eukaryotic organisms. After being generated by Dicer or Piwi proteins, all small RNAs in plants and a subset of small RNAs in animals are further modified at their 3′-terminal nucleotides via 2′-O-methylation, carried out by the S-adenosylmethionine-dependent methyltransferase (MTase) Hen1. Methylation at the 3′ terminus is vital for biological functions of these small RNAs. Here, we report four crystal structures of the MTase domain of a bacterial homolog of Hen1 from Clostridium thermocellum and Anabaena variabilis, which are enzymatically indistinguishable from the eukaryotic Hen1 in their ability to methylate small single-stranded RNAs. The structures reveal that, in addition to the core fold of the MTase domain shared by other RNA and DNA MTases, the MTase domain of Hen1 possesses a motif and a domain that are highly conserved and are unique to Hen1. The unique motif and domain are likely to be involved in RNA substrate recognition and catalysis. The structures allowed us to construct a docking model of an RNA substrate bound to the MTase domain of bacterial Hen1, which is likely similar to that of the eukaryotic counterpart. The model, supported by mutational studies, provides insight into RNA substrate specificity and catalytic mechanism of Hen1.     

A host dicer is required for defective viral RNA production and recombinant virus vector RNA instability for a positive sense RNA virus

Defective interfering (DI) RNAs, helper virus-dependent deletion mutant RNAs derived from the parental viral genomic RNA during replication, have been described for most RNA virus taxonomic groups. We now report that DI RNA production in the chestnut blight fungus, Cryphonectria parasitica, persistently infected by virulence-attenuating positive sense RNA hypoviruses, depends on one of two host dicer genes, dcl-2. We further report that nonviral sequences that are rapidly deleted from recombinant hypovirus RNA virus vectors in wild-type and dicer gene dcl-1 deletion mutant strains are stably maintained and expressed in the Deltadcl-2 mutant strain. These results establish a requirement for dcl-2, the C. parasitica dicer gene responsible for antiviral defense and generation of virus-derived small interfering RNAs, in DI RNA production and recombinant virus vector RNA instability.     

The cellular HIV-1 Rev cofactor hRIP is required for viral replication

An important goal of contemporary HIV type 1 (HIV-1) research is to identify cellular cofactors required for viral replication. The HIV-1 Rev protein facilitates the cytoplasmic accumulation of the intron-containing viral gag-pol and env mRNAs and is required for viral replication. We have previously shown that a cellular protein, human Rev-interacting protein (hRIP), is an essential Rev cofactor that promotes the release of incompletely spliced HIV-1 RNAs from the perinuclear region. Here, we use complementary genetic approaches to ablate hRIP activity and analyze HIV-1 replication and viral RNA localization. We find that ablation of hRIP activity by a dominant-negative mutant or RNA interference inhibits virus production by mislocalizing Rev-directed RNAs to the nuclear periphery. We further show that depletion of endogenous hRIP by RNA interference results in the loss of viral replication in human cell lines and primary macrophages; virus production was restored to wild-type levels after reintroduction of hRIP protein. Taken together, our results indicate that hRIP is an essential cellular cofactor for Rev function and HIV-1 replication. Because hRIP is not required for cell viability, it may be an attractive target for the development of new antiviral strategies.