Deoxyribozymes inhibit the expression ofperiod1 genein vitro

Throughout biology, a broad range of biochemical and physiological processes oscillate with approxi-mately 24-h rhythms or circadian rhythms as synchro-nizing with the rhythmic environment (day/night cy-cles, seasons, etc.). The circadian rhythms are under the control of an endogenous oscillator, the circadian clock[1]. Period (per), the first genetically identified circadian mutant[2], is assumed to be a key molecule in the regulation and functioning of the mammalian cir-cadian clock which is…     

Activity identification of chimeric anti-caspase-3 mRNA hammerhead ribozyme in vitro and in vivo

To study the expression activity of various vectors containing anti-caspase-3 ribozyme cassettesin vivo, and to further study the role of caspas-3 in the apoptotic pathway, we constructed anti-caspase-3 hammerhead ribozyme embedded into the human snRNA U6, and detected the activity of the ribozymein vitro andin vivo. Meanwhile we compared it with the self-cleaving hammerhead ribozymes that we previously studied, and with the general ribozyme, cloned into RNA polymerase II expression systems. The results showed that the three ribozymes, p1.5RZ107, pRZ107 and pU6RZ107 had the correct structure, and that they could cleave caspase-3 mRNA exactly to produce two fragments: 143nt/553nt. p1.5RZ107 has the highest cleavage efficiencyin vitro, almost 80%. However, the U6 chimeric ribozyme, pU6RZ107, has the highest cleavage activityin vivo, almost to 65%, though it has lower cleavage activityin vitro. The cleavage results demonstrated that the pU6RZ107, the U6 chimeric ribozyme, could more efficiently express and downregulate the level of caspase-3in vivo, and the ribozyme could provide an alternative approach to the research into the mechanism of apoptosis and human gene therapy also.     

Molecular cloning and expression of glycoprotein IIb and IIIa

Objective To amplify the cDNA genes of GPIIb, GPIIIa, then construct the eukaryotic expression carriers of GPIIb and GPIIIa respectively, finally establish CHO cell lines stably expressing GPIIb and GPIIIa. Methods Human erythroleukemia (HEL) cells were cultured for total RNA extraction. RT-PCR was accomplished using the specific GPIIb, GPIIIa primers designed according to Genbank by Primer 5, then each of cDNAs were obtained. The expressive vector pcDNA3.1(+) and PCR products were cut by NheI and HindIII, and then the fragements were directly cloned to pcDNA3.1(+) because of having the same adhesive ends. Then pcDNA3.1(+)IIb and pcDNA3.1(+)IIIa were transfected into CHO cells respectively by Lipofectamine 2000. The cell lines expressing GPIIb, GPIIIa were screened by G418. Then the Chinese hamster ovary (CHO) cell lines were examed through flow cytometry (FCM) and RT-PCR to detect the expression of GPIIb, GPIIIa in CHO cells. Results The cDNAs of GPIIb and GPIIIa were amplidied by RT-PCR, and the pcDNA3.1(+)IIb and pcDNA3.1(+)IIIa were constructed respectively. By sequencing and double digestion, pcDNA3.1(+)IIb and pcDNA3.1(+)IIIa were all correct. Expression of GPIIb and GPIIIa were detected on transfected CHO cells by FCM and RT-PCR. Conclusions (1) Succeeded in constructing pcDNA3.1(+)IIb, pcDNA3.1(+)IIIa. (2) Succeeded in getting the cell lines expressing GPIIb, GPIIIa.     

In vitro catalytic activities of DNA/RNA chimeric hammerhead ribozymes against AML1-MTG8 mRNA, a fused gene transcript in acute myeloid leukemia with t(8;21)

In order to design the best construct for therapeutic hammerhead ribozymes against AML1-MTG8, the t(8;21)-associated fusion mRNA of acute myeloid leukemia, we synthesized DNA/RNA chimeric ribozymes directed to the area adjacent to the fusion point between AML1 and MTG8. Catalytic efficiency and fusion gene specificity of ribozymes were examined by kinetic studies of the cleavage reactions of AML1-MTG8, AML1, and MTG8 RNAs transcribed in vitro. Ribozyme 2 (Rz2) specifically cleaved AML1-MTG8 RNA at three nucleotides downstream of the fusion junction with high efficiency. The highest cleavage efficiency was achieved by Rz4.3, which targeted non-contiguous sequences and cleaved at 19 nucleotides downstream of the fusion junction. Rz4.3 also cleaved MTG8 RNA but the cleavage efficiency was three orders of magnitude lower than that for AML1-MTG8 RNA. Therefore, Rz4.3 and Rz2 are the proper ribozymes for in vivo application to modulate gene expression of the AML1-MTG8.     

In vitro and in vivo transfection and expression of plasmid-based non-viral vector for erythropoietin gene therapy

A non-viral gene therapy vector, pcDNA3-EPO, was constructed by subcloning erythropoietin (EPO) cDNA into plasmid pcDNA3. After liposome-mediated transfection of the NIH 3T3 cells in vitro, EPO expression in the culture medium was detected by ELISA and amounted to 1.25 ± 0.3 IU ml^–1. The biological activity of this EPO in the medium was detected after intramuscular injection of BALB/c mice. PCR of genomic DNA and RT-PCR of total RNA also confirmed that the plasmid pcDNA3-EPO had been transfected into the cells. A pool of pcDNA3-EPO transfectants, which stably expressed EPO, was obtained by G418 selection. When pcDNA3-EPO was combined into liposomes and intramuscularly injected into BALB/c mice, the reticulocyte ratio in the positive mice was three times higher than that in the control mice. In vivo expression was maintained in mice for at least one month.     

In vitro selection, characterization, and application of deoxyribozymes that cleave RNA

Over the last decade, many catalytically active DNA molecules (deoxyribozymes; DNA enzymes) have been identified by in vitro selection from random-sequence DNA pools. This article focuses on deoxyribozymes that cleave RNA substrates. The first DNA enzyme was reported in 1994 and cleaves an RNA linkage. Since that time, many other RNA-cleaving deoxyribozymes have been identified. Most but not all of these deoxyribozymes require a divalent metal ion cofactor such as Mg²⁺ to catalyze attack by a specific RNA 2′-hydroxyl group on the adjacent phosphodiester linkage, forming a 2′,3′-cyclic phosphate and a 5′-hydroxyl group. Several deoxyribozymes that cleave RNA have utility for in vitro RNA biochemistry. Some DNA enzymes have been applied in vivo to degrade mRNAs, and others have been engineered into sensors. The practical impact of RNA-cleaving deoxyribozymes should continue to increase as additional applications are developed.     

Improved deoxyribozymes for synthesis of covalently branched DNA and RNA

A covalently branched nucleic acid can be synthesized by joining the 2′-hydroxyl of the branch-site ribonucleotide of a DNA or RNA strand to the activated 5′-phosphorus of a separate DNA or RNA strand. We have previously used deoxyribozymes to synthesize several types of branched nucleic acids for experiments in biotechnology and biochemistry. Here, we report in vitro selection experiments to identify improved deoxyribozymes for synthesis of branched DNA and RNA. Each of the new deoxyribozymes requires Mn²⁺ as a cofactor, rather than Mg²⁺ as used by our previous branch-forming deoxyribozymes, and each has an initially random region of 40 rather than 22 or fewer combined nucleotides. The deoxyribozymes all function by forming a three-helix-junction (3HJ) complex with their two oligonucleotide substrates. For synthesis of branched DNA, the best new deoxyribozyme, 8LV13, has k_obs on the order of 0.1 min⁻¹, which is about two orders of magnitude faster than our previously identified 15HA9 deoxyribozyme. 8LV13 also functions at closer-to-neutral pH than does 15HA9 (pH 7.5 versus 9.0) and has useful tolerance for many DNA substrate sequences. For synthesis of branched RNA, two new deoxyribozymes, 8LX1 and 8LX6, were identified with broad sequence tolerances and substantial activity at pH 7.5, versus pH 9.0 for many of our previous deoxyribozymes that form branched RNA. These experiments provide new, and in key aspects improved, practical catalysts for preparation of synthetic branched DNA and RNA.     

Parallel Selections In Vitro Reveal a Preference for 2′–5′ RNA Ligation upon Deoxyribozyme-Mediated Opening of a 2′,3′-Cyclic Phosphate

We previously used in vitro selection to identify Mg²⁺-dependent deoxyribozymes that mediate the ligation reaction of an RNA 5′-hydroxyl group with a 2′,3′-cyclic phosphate. In these efforts, all of the deoxyribozymes were identified via a common in vitro selection strategy, and all of the newly formed RNA linkages were non-native 2′–5′ phosphodiester bonds rather than native 3′–5′ linkages. Here we performed several new selections in which the relative arrangements of RNA and DNA were different as compared with the earlier studies. In all cases, we again find deoxyribozymes that create only 2′–5′ linkages. This includes deoxyribozymes with an arrangement that favors 3′–5′ linkages for a different chemical reaction, that of a 2′,3′-diol plus 5′-triphosphate. These data indicate a strong and context-independent chemical preference for creating 2′–5′ RNA linkages upon opening of a 2′,3′-cyclic phosphate with a 5′-hydroxyl group. Preliminary assays show that some of the newly identified deoxyribozymes have promise for ligating RNA in a sequence-general fashion. Because 2′,3′-cyclic phosphates are the products of uncatalyzed RNA backbone cleavage, their ligation reactions may be of direct relevance to the RNA World hypothesis.[Reviewing Editor: Niles Lehman]     

A new steroidal saponin from Allium ampeloprasum var. porrum with antiinflammatory and gastroprotective effects

A new steroidal saponin was isolated from the bulbs of Allium ampeloprasum var. porrum. On the basis of chemical conversions and detailed analyses of ¹H and ¹³C NMR spectra including 2D NMR spectroscopic techniques, its structure was established as 3-[(O-β-d-glucopyranosyl-(1 → 3)-β-d-glucopyranosyl-(1 → 2)-O-[O-β-d-glucopyranosyl-(1 → 3)]-O-β-d-glucopyranosyl-(1 → 4)-β-d-galactopyranosyl)oxy]-2,6-dihydroxy-(2α,3β,5α,6β,25R)-spirostane. Results of the present study indicated that the steroidal saponin showed haemolytic effects in the in vitro assays and demonstrated antiinflammatory activity and gastroprotective property using in vivo models.     

赤桉ACT1和ACT2基因的克隆与生物信息学分析

为了解赤桉(Eucalyptus camaldulensis)肌动蛋白(Actin)在生长发育过程中的功能,根据赤桉幼苗转录组数据库中的肌动蛋白基因序列,从赤桉嫩叶中克隆了2条Actin基因片段,并利用RACE技术获得Actin基因的全长cDNA,分别命名为ECACT1和EC-ACT2基因。生物信息学分析表明,这两条基因的全长cDNA分别为1533 bp和1387 bp,均含有1个编码377个氨基酸的开放阅读框。经比对分析,赤桉Actin蛋白的氨基酸序列与其他植物Actin蛋白的具有较高的相似性,并且具有Actin蛋白特有的保守序列和相关特征。因此推测这两条基因对桉树的生长发育具有一定的调控作用。     

In vitro polyoma DNA synthesis: Involvement of RNA in discontinuous chain growth

Short fragments of DNA (5 S) isolated by denaturation from polyoma replicative intermediates pulse-labeled in vitro were shown to have RNA covalently attached by three criteria: (1) such fragments were slightly denser than bulk viral DNA. (2) They could be labeled directly with α-³²P-labeled ribotriphosphates. (3) Alkaline hydrolysis of fragments labeled with α-³²P-labeled deoxynucleoside triphosphates showed ³²P transfer to 3′ ribonucleoside monophosphates. Except for a preference of transfer from dC, the link showed little sequence specificity. The data are compatible with the notion that all short fragments in replicating viral DNA are initiated by an RNA primer. This RNA is maximally 30 bases long and is rather short-lived.     

Structure and function of sawB , a gene involved in differentiation of Streptomyces ansochromogenes

A partial DNA library ofStreptomyces ansochromogenes 7100 was constructed by using plasmid pl J702 as vector and white mutant W19 as recipient. About 3 000 clones were obtained, two of which gave rise to the grey phenotype as wild type 7100. The plasmids were isolated from two transformants. The result indicated that the 5.2 kb and 5.8 kb DNA fragments were inserted into plJ702. The resulting recombinant plasmids were designated as pNL-1 and pNL-2 respectively. The 1.25 kbPstl I -Apa I DNA fragment from pNL-1 was recognized as its complementarity to W19 strain. The nucleotide sequence of the 3.0 kbPst I DNA fragment including 1.25 kb was determined and analyzed. The result indicated that this DNA fragment contains one complete open reading frame (ORF1) which encodes a protein with 295 amino acid residues, and this gene was designated assawB. The deduced protein has 81% amino acid identities in comparison with that encoded bywhiH inStreptomyces coelicolor. The function ofsawB gene was studied by using strategy of gene disruption, and the resultingsawB mutant failed to form spores and produced loosely coiled aerial hyphal. The result showed thatsawB is closely related to hyphal coiling and sporulation in S.ansochromogenes, and also indicated that thesawB can complementwhiH mutant (C119) to restore the grey phenotype ofStreptomyces coelicolor J 1501 (wild type).     

Molecular cloning and expression of glycoprotein IIIa<Superscript>T1565C</Superscript>

Objective To construct the eukaryotic expression vectors of mutant GPIIIa, establish CHO cell lines stably expressing mutant GPIIIa. Methods Total RNA were extracted from HEL cells. Mutant GPIIIa cDNA was synthesized by RT-PCR using the specific primers designed according to Genbank by Primer 5, then leaded to T1565C. The expression vector pcDNA3.1(+) and PCR products were respectively digested by NheI and HindIII, the specific cDNA fragments were directly inserted to the pcDNA3.1(+) because of having the same adhesive ends. Then wild type pcDNA3.1(+)IIIa and mutant pcDNA3.1(+)IIIa were respectively transfected into CHO cells using Lipofectamine 2000 reagent. The cell lines expressing GPIIIa and GPIIIa^T1565C were screened by G418. Expression of GPIIIa and GPIIIa^T1565C on transfected CHO cell surface were evaluated by flow cytometry and by RT-PCR to substantiate mRNA. Results The cDNAs of GPIIIa and GPIIIa^T1565C were amplified by RT-PCR, and the recombinant of mutant pcDNA3.1(+)IIIa were constructed. By sequencing and enzyme digestion, it was be confirmed that there is a mutant of GPIIIa on 1565(T → C). The result of flow cytometric analysis showed fluorescence intensity in the CHO cells transfected by recombinant is much higher than that by pcDNA3.1(+)IIIa. Conclusions (1) Succeeded in constructing recombinants pcDNA3.1(+)IIIa^T1565C. (2) Succeeded in getting the cell lines expressing GPIIIa^T1565C Supported by Heilongjiang Science & Technology bereau found GB06C40303.