[show abstract][hide abstract] ABSTRACT: PtCu alloy octahedral nanocrystals (NCs) have been synthesized successfully by using N,N-dimethylformamide as both the solvent and the reducing agent in the presence of cetyltrimethylammonium chloride. Cu underpotential deposition (UPD) is found to play a key role in the formation of the PtCu alloy NCs. The composition in the PtCu alloy can be tuned by adjusting the ratio of metal precursors in solution. However, the Cu content in the PtCu alloy NCs cannot exceed 50 %. Due to the fact that Cu precursor cannot be reduced to metallic copper and the Cu content cannot exceed 50 %, we achieved the formation of the PtCu alloy by using Cu UPD on the Pt surface. In addition, the catalytic activities of PtCu alloy NCs with different composition were investigated in electrocatalytic oxidation of formic acid. The results reveal that the catalytic performance is strongly dependent on PtCu alloy composition. The sample of Pt(50) Cu(50) exhibits excellent activity in electrocatalytic oxidation of formic acid.
[show abstract][hide abstract] ABSTRACT: The surface structure-controlled synthesis of noble metal nanocrystals (NCs) bounded by high-index facets has become a hot research topic due to their potential to significantly improve catalytic performance. This study reports the preparation of monodisperse Au-Pd alloy NCs with systematic shape evolution from rhombic dodecahedral (RD) to trisoctahedral (TOH), and hexoctahedral (HOH) structures by varying the concentration of surfactant in the surfactant-mediated synthesis. The as-prepared three kinds of alloy NCs possess almost the same size and composition as each other. It is suggested that the surfactant containing long-chain octadecyltrimethyl ammonium (OTA(+) ) ions plays a key role in the formation of high index facets, and the crystal growth kinetics may also have an effect on the formation of different nanocrystal morphologies. In addition, the catalytic activities of these NCs are evaluated by structure-sensitive reactions, including ethanol electro-oxidation and the catalytic reduction of 4-nitrophenol (4-NPh). These three types of Au-Pd alloy NCs exhibit different catalytic selectivities towards these two reactions. The catalytic activities toward electro-oxidation of ethanol are in the order of HOH > RD > TOH, which follows the order of their corresponding surface energies. However, the activities toward catalytic reduction of 4-NPh are in the order of RD > TOH > HOH, which should be related to the local structure of the surfaces.
[show abstract][hide abstract] ABSTRACT: A TALE of two assays: Transcription activator-like effectors (TALEs) are programmable proteins that can specifically recognize a DNA sequence. Previous strategies for the synthesis of TALEs were complicated and time-consuming. The solid-phase synthesis strategy demonstrated here allows quick and simple purification of the ligation product.
Angewandte Chemie International Edition 07/2012; 51(34):8505-8. · 13.73 Impact Factor
[show abstract][hide abstract] ABSTRACT: To modulate gene expression in research studies or in potential clinical therapies, transfection of exogenous nucleic acids
including plasmid DNA and small interference RNA (siRNA) are generally performed. However, the cellular processing and the
fate of these nucleic acids remain elusive. By investigating the cellular behavior of transfected nucleic acids using confocal
imaging, here we show that when siRNA was co-transfected into cultured cells with other nucleic acids, including single-stranded
RNA oligonucleotides, single and double-stranded DNA oligonucleotides, as well as long double-stranded plasmid DNA, they all
aggregate in the same cytoplasmic granules. Interestingly, the amount of siRNA aggregating in granules was found not to correlate
with the gene silencing activity, suggesting that assembly of cytoplasmic granules triggered by siRNA transfection may be
separable from the siRNA silencing event. Our results argue against the claim that the siRNA-aggregating granules are the
functional site of RNA interference (RNAi). Taken together, our studies suggest that, independent of their types or forms,
extraneously transfected nucleic acids are processed through a common cytoplasmic pathway and trigger the formation of a new
type of cytoplasmic granules “transfection granules”.
Keywordssmall interference RNA (siRNA)-nucleic acids-P-body-RNA interference (RNAi)-transfection
[show abstract][hide abstract] ABSTRACT: The first enantioselective synthesis of cytotoxic natural products rigidiusculamides A (ent-21) and B (8) has been achieved by two synthetic routes. The first one is convergent based on the common intermediate 11, obtained through a high yielding SmI(2) -mediated Reformatsky-type reaction. A highly diastereoselective one-pot Dess-Martin periodinane-mediated bis-oxidation allowed the direct conversion of the diastereomeric mixture of 11 into rigidiusculamide B (8). Isolation of minor diastereomer 21, in combination with computational work, allowed us to suggest the structure of the natural rigidiusculamide A to be ent-21, as synthesized by the second route. Four diastereomers (7, ent-7, 22a, and 22b) and an enantiomer (21) of rigidiusculamide A (ent-21) have been synthesized. On the basis of literature precedents and computational work, a biosynthetic pathway for rigidiusculamides A and B was proposed to account for the opposite configuration at C-5 of those two congeners.
Chemistry - An Asian Journal 03/2012; 7(3):504-18. · 4.57 Impact Factor
[show abstract][hide abstract] ABSTRACT: The chemically-synthesized siRNA duplex has become a powerful and widely used tool for RNAi loss-of-function studies, but suffers from a high off-target effect problem. Recently, endoribonulease-prepared siRNA (esiRNA) has been shown to be an attractive alternative due to its lower off-target effect and cost effectiveness. However, the current manufacturing method for esiRNA is complicated, mainly in regards to purification and normalization on a large-scale level. In this study, we present a magnetic bead-integrated chip that can immobilize amplification or transcription products on beads and accomplish transcription, digestion, normalization and purification in a robust and convenient manner. This chip is equipped to manufacture ready-to-use esiRNAs on a large-scale level. Silencing specificity and efficiency of these esiRNAs were validated at the transcriptional, translational and functional levels. Manufacture of several normalized esiRNAs in a single well, including those silencing PARP1 and BRCA1, was successfully achieved, and the esiRNAs were subsequently utilized to effectively investigate their synergistic effect on cell viability. A small esiRNA library targeting 68 tyrosine kinase genes was constructed for a loss-of-function study, and four genes were identified in regulating the migration capability of Hela cells. We believe that this approach provides a more robust and cost-effective choice for manufacturing esiRNAs than current approaches, and therefore these heterogeneous RNA strands may have utility in most intensive and extensive applications.
PLoS ONE 01/2012; 7(6):e39419. · 3.73 Impact Factor
[show abstract][hide abstract] ABSTRACT: It has been noted that target sites located in the coding region or the 3'-untranslated region (3'-UTR) can be silenced to significantly different levels by the same siRNA, but little is known about at what specificity the silencing was achieved. In an exploration of positional effects on siRNA specificity by luciferase reporter system, we surprisingly discovered that siRNA had greatly elevated tolerance towards mismatches in target sites in the 3'-UTR of the mRNA compared with the same target sites cloned in the coding region. Assessment of changes in protein and mRNA levels suggested that the differential mismatch tolerance might have resulted from location-specific translational repression in the 3'-UTR. Ablation of argonaute proteins by AGO-specific siRNAs revealed that the AGO2 had major impact on siRNA silencing activity against sites in both coding region and 3'-UTR, while the silencing of nonnucleolytic AGO proteins (AGO1, AGO3 and AGO4) did not significantly affect silencing of sites in either region. This paper revealed the discovery that the specificity of an siRNA can be affected by the location of its target site.
PLoS ONE 01/2012; 7(11):e49309. · 3.73 Impact Factor
[show abstract][hide abstract] ABSTRACT: By introducing a hydrodynamic mechanism into a microfluidics-based electroporation system, we developed a novel laminar flow electroporation system with high performance. The laminar buffer flow implemented in the system separated the cell suspension flow from the electrodes, thereby excluding many unfavorable effects due to electrode reaction during electroporation, such as hydrolysis, bubble formation, pH change, and heating. Compared to conventional microfluidic electroporation systems, these improvements significantly enhanced transfection efficiency and cell viability. Furthermore, successful electrotransfection of plasmid DNA and, more importantly, synthetic siRNA, was demonstrated in several hard-to-transfect cell types using this system.
[show abstract][hide abstract] ABSTRACT: Endoribonuclease-prepared siRNAs (esiRNAs) have the advantages of cost effectiveness and lower off-target effects than chemically synthesized siRNA. However, the current manufacture of esiRNA is a complex process, requiring an expensive instrument and demanding skills to accomplish the transfer, purification, quantification and normalization of liquid samples. These performances significantly hamper the application of esiRNAs on a large-scale level. In this study, we present a polymer microbead-integrated chip capable of the large-scale manufacture of esiRNA in a convenient and robust manner. This chip is able to perform the amplification, transcription and enzymatic digestion of targets on polymer scaffold, thus simplifying the transfer and purification manipulation process. What is also noted, this chip can readily tailor and normalize the amount of esiRNA product by controlling the number of DNA probes and the cycle of the amplification reaction. Thus the esiRNA, also referred to as gel-esiRNA, can be immediately applied to loss-of-function study without any further treatment. The silencing specificity and efficiency of gel-esiRNAs were assessed on transcriptional, translational or cell functional levels. All data of real-time PCR, Western blot assay, or FACS clearly supported that the gel-esiRNA produced specific gene silencing as effectively as the one generated following the conventional approach. We believe that this approach would provide a more robust and cost-effective choice to manufacture esiRNAs, thus promising both more intensive and extensive applications of these heterogeneous RNA strands.
Lab on a Chip 01/2011; 11(6):1036-40. · 5.70 Impact Factor
[show abstract][hide abstract] ABSTRACT: Double-stranded small interfering RNAs (siRNAs) are important modulators of biological processes and hold great promise for therapeutic applications. However, serum processing of synthetic siRNAs is still largely unknown. To address this issue, serum degradation assays of 125 siRNAs were first performed in this study. Four siRNA categories of distinct serum stability were identified, including a group of siRNAs that were stable in their native form for both in vitro and in vivo assays. Fine mapping of the cleavage events occurring in serum treatment demonstrated that most occurred at two vulnerable sites, leading to a speculation that rational modification of these sites might protect most siRNAs from serum degradation. For proof of concept, an exhaustive siRNA modification study was performed. In addition to the consistent stabilization pattern revealed at these sites, our study further showed that a single modification made at the cleavage site stabilized the siRNAs to a large extent, highlighting the importance of these sites in siRNA degradation. In summary, the present study provided a comprehensive picture of serum processing of siRNA as well as a starting point for a rational siRNA modification strategy, both of which are of great importance to in vivo and therapeutic applications of siRNA.
The FASEB Journal 12/2010; 24(12):4844-55. · 5.70 Impact Factor
[show abstract][hide abstract] ABSTRACT: Here we report a novel electroporation microchip with great performance and compatibility with the standard multi-well plate used in biological research. The novel annular interdigitated electrode design makes it possible to achieve efficient cell transfection as high as 90% under low-strength electrical pulses, thereby circumventing the many adverse effects of conventional cuvette-type and previously reported microchip-based electroporation devices. Using this system, we demonstrated substantially improved cell transfection efficacy and viability in cultured and primary cells, for both plasmid and synthetic siRNA. Improvements of this system open new opportunities for high-throughput applications of siRNA technology in basic and biomedical research.
Lab on a Chip 10/2010; 11(1):163-72. · 5.70 Impact Factor
[show abstract][hide abstract] ABSTRACT: Electroporation, in which electric pulses are applied to create transient pores in the cell membrane, is widely used to introduce biologically active molecules into cells. Here we report a novel electroporation chip with great performance and good compatibility with the standard multi-well plate used in biological research. We demonstrated a prototype chip integrating with a 12-well plate and successfully electroporated both adherent and supernatant cells. Using the standard expression cell line HEK-293 and expression vector pEGFP-C3, we realized excellent cell viability (80%) and transfection rate (90%), both much higher than those in previously reported methods.
[show abstract][hide abstract] ABSTRACT: Silencing specificity is a critical issue in the therapeutic applications of siRNA, particularly in the treatment of single nucleotide polymorphism (SNP) diseases where discrimination against single nucleotide variation is demanded. However, no generally applicable guidelines are available for the design of such allele-specific siRNAs. In this paper, the issue was approached by using a reporter-based assay. With a panel of 20 siRNAs and 240 variously mismatched target reporters, we first demonstrated that the mismatches were discriminated in a position-dependent order, which was however independent of their sequence contexts using position 4th, 12th and 17th as examples. A general model was further built for mismatch discrimination at all positions using 230 additional reporter constructs specifically designed to contain mismatches distributed evenly along the target regions of different siRNAs. This model was successfully employed to design allele-specific siRNAs targeting disease-causing mutations of PIK3CA gene at two SNP sites. Furthermore, conformational distortion of siRNA-target duplex was observed to correlate with the compromise of gene silencing. In summary, these findings could dramatically simplify the design of allele-specific siRNAs and might also provide guide to increase the specificity of therapeutic siRNAs.
Nucleic Acids Research 10/2009; 37(22):7560-9. · 8.28 Impact Factor
[show abstract][hide abstract] ABSTRACT: To date, approximately 700 microRNA (miRNA) molecules have been identified in humans. Accurate and sensitive quantification of miRNA levels will help unveil their biological functions. Here, we extend the isothermal ramification amplification (RAM) approach to a sensitive and specific real-time assay for quantitative analysis of miRNA. This RAM miRNA assay is based on the threshold cycle (C(T)) principle similar to that of real-time PCR. It has a dynamic range of at least seven orders of magnitude, allowing for the quantification of miRNA input from 10(3) to 10(10) copies per reaction (10 nM to 1 fM). The capabilities of discriminating single-base mismatch and distinguishing mature miRNAs from their precursors are achieved by coupling the reverse-transcription of miRNA to the generation of a closed C-probe, rather than using expensive detection probes like in real-time PCR. Quantitative measurement of 5 miRNAs (mir-1, miR-122, mir-150, mir-143, and let-7a) across 12 mouse tissues is validated in total RNA samples without further purification. U6 snRNA, snoRNA 135, and miRNA-191 could be simultaneously quantified as endogenous controls. These results suggest that our RAM miRNA assay might provide a universal tool for miRNA detection and functional studies to meet the needs for bench examination, clinical diagnosis, and on-site detection.
[show abstract][hide abstract] ABSTRACT: A high-throughput microfluidic device is developed to handle liquid dispensation in nanoliter range. The dispenser system shows no cross-contamination between the microwells, indicating its great potential in large-scale screening experiments. An array of 115 nl PCR reactions, as well as the single channel addressable chip demonstrate the high flexibility and wide applications of this novel system.
Lab on a Chip 08/2009; 9(13):1831-5. · 5.70 Impact Factor
[show abstract][hide abstract] ABSTRACT: MiRNAs (microRNAs) are a group of endogenous, small noncoding RNA with the length of 18-25 nucleotides, which have recently been demonstrated to play important roles in a wide range of biological processes. In this work, we developed a simple, sensitive, specific, and inexpensive assay through the combination of enzymatic probe ligation and real-time PCR amplification for the measurement of mature miRNAs. A couple of novel DNA probes with a stem-loop structure were implemented to reduce nonspecific ligation by at least 100-fold. The assay has several remarkable features including wide dynamic range, low total RNA input (0.02-0.2 ng), distinct anti-interference from precursor miRNAs (signal-to-noise ratio > 500), and single-base mismatch discrimination among miRNA sequences. In addition, a one-tube assay could be accomplished by designing a couple of universal probes, which makes it feasible to examine the expression of a whole family of miRNA (such as let-7) at one time. Finally, we validated the method for quantifying the expression of four mature miRNAs including miR-122, miR-1, miR-34a, and let-7a across 10 mouse tissues, where U6 snRNA could be simultaneously examined as an endogenous control. Thus, this method revealed a great potential for miRNA quantitation in ordinary laboratory studies and clinical diagnoses.