Double-stranded RNA-stimulated enzyme activities isolated from human placental extracts

A (2′–5′)A_n synthetase activity was isolated from human placental extracts by affinity chromatography on poly(rI)·poly(rC)-agarose. The oligonucleotide (2′–5′)A_n was identified by (1) chromatography on PEI-cellulose and DEAE-cellulose, (2) inhibition of polypeptide synthesis in lysed rabbit reticulocytes (3) competition of the binding of pppA(pA)3,3′-[³²P]pCp to rabbit reticulocyte lysates, and (4) alkaline phosphatase digestion. The synthetase activity in most placental preparations is activated by natural or synthetic dsRNA. However, in a few placental synthetase preparations, dsRNA is only marginally stimulatory and only becomes effective by prior treatment of the enzyme preparations with the calcium-dependent micrococal nuclease. This suggeststhat there is an endogenous placental dsRNA contaminant in the enzyme preparations. In some synthetase preparations, a second dsRNA-stimulated product, tentatively identified as the nucleotide 5′-IMP, is also observed. Because the specific AMP deaminase inhibitor coformycin (10 μM) blocks the formation of IMP from ATP and causes a quantitative accumulation of AMP, and because the formation of IMp becomes independent of dsRNA when ADP or AMP is used in plase of ATP, the presence of a dsRNA-stimulated ATP phosphohydrolase (ATPase) activity in human placenta is suggested.     

Nano carriers that enable co-delivery of chemotherapy and RNAi agents for treatment of drug-resistant cancers

Tumor cells exhibit drug resistant phenotypes that decrease the efficacy of chemotherapeutic treatments. The drug resistance has a genetic basis that is caused by an abnormal gene expression. There are several types of drug resistance: efflux pumps reducing the cellular concentration of the drug, alterations in membrane lipids that reduce cellular uptake, increased or altered drug targets, metabolic alteration of the drug, inhibition of apoptosis, repair of the damaged DNA, and alteration of the cell cycle checkpoints ( and ). siRNA is used to silence the drug resistant phenotype and prevent this drug resistance response. Of the listed types of drug resistance, pump-type resistance (e.g., high expression of ATP-binding cassette transporter proteins such as P-glycoproteins (Pgp; also known as multi-drug resistance protein 1 or MDR1, encoded by the ATP-Binding Cassette Sub-Family B Member 1 (ABCB1) gene)) and apoptosis inhibition (e.g., expression of anti-apoptotic proteins such as Bcl-2) are the most frequently targeted for gene silencing. The co-delivery of siRNA and chemotherapeutic drugs has a synergistic effect, but many of the current projects do not control the drug release from the nanocarrier. This means that the drug payload is released before the drug resistance proteins have degraded and the drug resistance phenotype has been silenced. Current research focuses on cross-linking the carrier's polymers to prevent premature drug release, but these carriers still rely on environmental cues to release the drug payload, and the drug may be released too early. In this review, we studied the release kinetics of siRNA and chemotherapeutic drugs from a broad range of carriers. We also give examples of carriers used to co-deliver siRNA and drugs to drug-resistant tumor cells, and we examine how modifications to the carrier affect the delivery. Lastly, we give our recommendations for the future directions of the co-delivery of siRNA and chemotherapeutic drug treatments.     

The interaction of chromium with nucleic acids

Native and denatured calf thymus DNA, and homopolyribonucleotides were compared with respect to chromium and protein binding after an in vitro incubation with rat liver microsomes, NADPH, and chromium(VI) or chromium(III). A significant amount of chromium bound to DNA when chromium(VI) was incubated with the native or the denatured form of DNA in the presence of microsomes and NADPH. For both native and denatured DNA the amount of protein bound to DNA increased with the amount of chromium bound to DNA. Denatured DNA had much higher amounts of chromium and protein bound than native DNA. There was no interaction between chromium(VI) and either form of DNA in the absence of the complete microsomal reducing system. The binding of chrornium(III) to native or denatured DNA was small and relatively unaffected by the presence of microsomes and NADPH. The binding of chromium and protein to polyriboadenylic acid (poly(A)), polyribocytidylic acid (poly(C), polyri-boguanylic acid (poly(G)) and polyribouridylic acid (poly(U)) was determined after incubation with chromium(VI) in the presence of microsomes and NADPH. The magnitude of chromium and protein binding to the ribo-polymers was found to be poly(G) ? poly(A) ? poly(C) ? poly(U). These results suggest that the metabolism of chromium(VI) is necessary in order for chromium to interact significantly with nucleic acids. The metabolically-produced chromium preferentially binds to the base guanine and results in DNA-protein cross-links. These findings are discussed with respect to the proposed scheme for the carcinogenicity of chromium(VI). Keywords: DNA-protein cross-links — Chromium-guanine interaction-Microsomal reduction of chromate     

Molecular flexibility and discontinuous translocation of a non-templated polymerase

Little is known regarding the translocation of non-templated nucleic acid polymerases with respect to single-stranded primers. VP55, the vaccinia virus poly(A) polymerase, translocates as it processively adds a approximately 3-7 adenylate tail to primers possessing only three ribouridylate residues (as an (rU)(2)-N(15)-rU motif), and a approximately 25-30 adenylate tail to primers that are more U-rich. Here, three models were addressed for the translocation of VP55 with respect to its primer, namely: (a) rigid protein/rigid nucleic acid; (b) flexible protein/rigid nucleic acid; (c) rigid protein/flexible nucleic acid. Analysis of free and covalently VP55-attached primers favored either (b) or a version of (c) incorporating a passive steric block, and suggested two regions of relative motion between polymerase and primer. Inclusion of a 6nt uridylate-rich patch at the primer 3' end switched the polymerase from approximately 3-7 nt to approximately 25-30 nt tail addition without affecting initial binding affinity. By synthesizing this patch as a (rU/dC) pool, discontinuous polymerase movements could be detected.     

三乙酸甘油酯对PLA/PBAT共混体系性能影响

利用转矩流变仪将聚乳酸(PLA)、聚己二酸对苯二甲酸丁二酯(PBAT)和三乙酸甘油酯(GTA)熔融共混,利用差示扫描量热仪(DSC)、动态热机械分析仪(DMA)、万能材料试验机、冲击试验机、扫描电子显微镜(SEM)对共混物的热力学性能、力学性能以及微观形态结构进行测试和表征。实验发现,加入GTA后共混物的两相玻璃化转变温度呈相互靠近趋势,冷结晶温度和熔融温度都降低。当GTA加入量为3份时,共混物中分散相粒径减小,PLA/PBAT/GTA(80/20/3)组分的断裂伸长率得到明显提升,增加了2.6倍,由未加入GTA时的17.7%增长到64.1%。     

Theoretical analysis on the structure and properties of thiourea dioxide crystal

The equilibrium geometry, electronic structure and optical properties of thiourea S, S-dioxide crystal have been studied using DFT within generalized gradient approximation (GGA) and the local density approximation (LDA), implemented using ultrasoft pseudo-potentials. The optimum bulk geometry is in good agreement with crystallographic data. An analysis of electronic structure, charge and bond order is presented. The energy gap of thiourea dioxide with GGA and LDA calculation is 3.217 or 3.210 eV, respectively, indicating that the compound is an insulator. The calculated absorption spectrum shows a number of absorption peaks, which are believed to be associated with different exciton states, in the fundamental absorption region.     

Dynamic compressive loading influences degradation behavior of PEG-PLA hydrogels

Biodegradable hydrogels are attractive 3D environments for cell and tissue growth. In cartilage tissue engineering, mechanical stimulation has been shown to be an important regulator in promoting cartilage development. However, the impact of mechanical loading on the gel degradation kinetics has not been studied. In this study, we examined hydrolytically labile gels synthesized from poly(lactic acid)-b-poly(ethylene glycol)-b-poly-(lactic acid) dimethacrylate macromers, which have been used for cartilage tissue engineering. The gels were subject to physiological loading conditions in order to examine the effects of loading on hydrogel degradation. Initially, hydrogels were formed with two different cross-linking densities and subject to a dynamic compressive strain of 15% at 0.3, 1, or 3 Hz. Degradation behavior was assessed by mass loss, equilibrium swelling and compressive modulus as a function of degradation time. From equilibrium swelling, the pseudo-first-order reaction rate constants were determined as an indication of degradation kinetics. The application of dynamic loading significantly enhanced the degradation time for the low cross-linked gels (P < 0.01) while frequency showed no statistical differences in degradation rates or bulk erosion profiles. In the higher cross-linked gels, a 3 Hz dynamic strain significantly increased the degradation kinetics resulting in an overall faster degradation time by 6 days compared to gels subject to the 0.3 and 1 Hz loads (P < 0.0001). The bioreactor set-up also influenced overall degradation behavior where the use of impermeable versus permeable platens resulted in significantly lower degradation rate constants for both cross-linked gels (P < 0.001). The compressive modulus exponentially decreased with degradation time under dynamic loading. Together, our findings indicate that both loading regime and the bioreactor setup influence degradation and should be considered when designing and tuning a biodegradable hydrogel where mechanical stimulation is employed.     

The DNA translocating ATPase of bacteriophage T4 packaging motor

In double-stranded DNA bacteriophages the viral DNA is translocated into an empty prohead shell by a powerful ATP-driven motor assembled at the unique portal vertex. Terminases consisting of two to three packaging-related ATPase sites are central to the packaging mechanism. But the nature of the key translocating ATPase, stoichiometry of packaging motor, and basic mechanism of DNA encapsidation are poorly understood. A defined phage T4 packaging system consisting of only two components, proheads and large terminase protein (gp17; 70 kDa), is constructed. Using the large expanded prohead, this system packages any linear double-stranded DNA, including the 171 kb T4 DNA. The small terminase protein, gp16 (18 kDa), is not only not required but also strongly inhibitory. An ATPase activity is stimulated when proheads, gp17, and DNA are actively engaged in the DNA packaging mode. No packaging ATPase was stimulated by the N-terminal gp17-ATPase mutants, K166G (Walker A), D255E (Walker B), E256Q (catalytic carboxylate), D255E-E256D and D255E-E256Q (Walker B and catalytic carboxylate), nor could these sponsor DNA encapsidation. Experiments with the two gp17 domains, N-terminal ATPase domain and C-terminal nuclease domain, suggest that terminase association with the prohead portal and communication between the domains are essential for ATPase stimulation. These data for the first time established an energetic linkage between packaging stimulation of N-terminal ATPase and DNA translocation. A core pathway for the assembly of functional DNA translocating motor is proposed. Since the catalytic motifs of the N-terminal ATPase are highly conserved among >200 large terminase sequences analyzed, these may represent common themes in phage and herpes viral DNA translocation.     

Secondary association of exogenous polynucleotides with cells and nuclei in uptake experiments

Manipulation of [³H]polynucleotide-treated cells to remove them from the substrate or to isolate nuclei has been shown to result in secondary association of the exogenous polynucleotide with the cells or nuclei. Experiments have shown untreated (control) cultures, when processed with supernatants from [³H]polynucleotide-treated cell monolayers, exhibited a significant amount of radioactive label associated with the nuclei from control cells. In spite of thorough washing of polynucleotide-treated cell monolayers prior to the manipulation, the association was extensive. It is likely to overshadow the association resulting solely from the exposure of monolayer cells to the polynucleotide.     

An S-like ribonuclease gene is used to generate a trap-leaf enzyme in the carnivorous plant Drosera adelae

Carnivorous plants usually grow in nutrient-deficient habitats, and thus they partly depend on insects for nitrogen and phosphate needed for amino acid and nucleotide synthesis. We report that a sticky digestive liquid from a sundew, Drosera adelae, contains an abundant amount of an S-like ribonuclease (RNase) that shows high amino acid-sequence similarity to S-like RNases induced by phosphate starvation or wounding in normal plants. By giving leaves an RNase "coat", D. adelae seems to achieve two requirements simultaneously to adapt itself to its specific surroundings: it obtains phosphates from insects, and defends itself against pathogen attack.     

Evolutionary conservation of a unique amino acid sequence in human DICER protein essential for binding to Argonaute family proteins

The Argonaute family and DICER proteins are major key proteins involved in the RNA-mediated gene silencing mechanism of various species. In this mechanism, cleavage of messenger RNAs (mRNA) or suppression of mRNA translation takes place via small RNAs that are uniquely processed by DICER. Previously, we demonstrated that human Argonaute family proteins bind to DICER. In this study, we identified a unique amino acid sequence of 127 amino acids in the RIBOc-A domain of human DICER protein as a "binding site" to Argonaute proteins. Comparative genomics analysis revealed that this unique amino acid sequence is highly conserved in the vertebrates, but not found in the non-vertebrate species. Significant difference in the RIBOc-A domain of DICER protein between vertebrate and non-vertebrate species may help exploring the functional complexity in the RNA-mediated gene silencing mechanism.     

Synthesis of two non-phosphorylated proteins induced in mouse L-cells by homologous interferon

We have shown that two proteins P1 and P2 of M_r 43000 and 40800 are always detected by two-dimensional gel electrophoresis of interferon-treated mouse L-929 cell extract. These two proteins have an isoelectric point of pH 4.6 and pH 4.7 respectively. If Pl is detectable in small amount in the control gels, P2 is completely absent. Actinomycin D added at the same time as interferon, prevents both P1 and P2 synthesis, but enhances their production when added between 4 to 6 h after interferon. Using molecular weight and isoelectric point as criteria, we have tried to compare P1 and P2 to enzymes induced by interferon. With double-labelled two-dimensional gels by |³⁵S| methionine and |γ³²P| ATP, we have shown that neither P1 nor P2 is phosphorylated. This experimental procedure has allowed us to obtain new data on substrates phosphorylared by interferon induced protein kinase.     

Maturation of mammalian H/ACA box snoRNAs: PAPD5-dependent adenylation and PARN-dependent trimming

Small nucleolar and small Cajal body RNAs (snoRNAs and scaRNAs) of the H/ACA box and C/D box type are generated by exonucleolytic shortening of longer precursors. Removal of the last few nucleotides at the 3' end is known to be a distinct step. We report that, in human cells, knock-down of the poly(A) specific ribonuclease (PARN), previously implicated only in mRNA metabolism, causes the accumulation of oligoadenylated processing intermediates of H/ACA box but not C/D box RNAs. In agreement with a role of PARN in snoRNA and scaRNA processing, the enzyme is concentrated in nucleoli and Cajal bodies. Oligo(A) tails are attached to a short stub of intron sequence remaining beyond the mature 3' end of the snoRNAs. The noncanonical poly(A) polymerase PAPD5 is responsible for addition of the oligo(A) tails. We suggest that deadenylation is coupled to clean 3' end trimming, which might serve to enhance snoRNA stability.     

Cordycepin and early effects of estradiol on the immature rat uterus.

Estradiol induces the synthesis of a specific protein fraction (IP) in the uterus of the immature rat. The injection of cordycepin (3' deoxyadenosine), an inhibitor of poly A synthesis, inhibits the synthesis of IP. This fact suggests that one of the earliest effects of estrogen is the production of Hn-RNA poly-A relative to IP. Moreover, using electron microscopy, the stimulation by estradiol of the nucleolus of the immature rat uterine epithelium has been shown. Cordycepin does not affect this stimulation to any appreciable extent. Biochemical studies (incorporation of radioactive stracers into NRA, affinity chromatography on poly U-Sepharose) carried out in parallel with and under conditions comparable to those used in electron microscopy show that cordycepin does not greatly affect the increase in ribosomal RNA observed under the effect of estradiol. The blocking of IP by cordycepin and the lack of inhibition at the nucleolus level under the same conditions, show that the two early effects of the action of estrogen on the immature rat uterus are not directly correlated.     

Effect of aging on induction of rat liver messenger RNA activity for malic enzyme

Rats were fasted and then refed a high carbohydrate-fat free diet, and the activities of the mRNA coding for liver malic enzyme [EC 1.1.1.40] in 6-week-old and 10-month-old male rats were determined by in vitro translation of the liver cytoplasmic poly(A)-containing RNA in a rabbit reticulocyte lysate. After refeeding the mRNA activities of the young rats were about 7-fold of those of the aged rats, and roughly parallel to the enzyme activities. This suggests that the age-dependent impairment of the enzyme induction [Iritani, N. et al. (1981) Biochim. Biophys. Acta 665, 636] can be ascribed to the decrease of mRNA activity.