Hydroxyproline-based DNA mimics provide an efficient gene silencing in vitro and in vivo

To be effective, antisense molecules should be stable in biological fluids, non-toxic, form stable and specific duplexes with target RNAs and readily penetrate through cell membranes without non-specific effects on cell function. We report herein that negatively charged DNA mimics representing chiral analogues of peptide nucleic acids with a constrained trans-4-hydroxy-N-acetylpyrrolidine-2-phosphonate backbone (pHypNAs) meet these criteria. To demonstrate this, we compared silencing potency of these compounds with that of previously evaluated as efficient gene knockdown molecules hetero-oligomers consisting of alternating phosphono-PNA monomers and PNA-like monomers based on trans-4-hydroxy-L-proline (HypNA-pPNAs). Antisense potential of pHypNA mimics was confirmed in a cell-free translation assay with firefly luciferase as well as in a living cell assay with green fluorescent protein. In both cases, the pHypNA antisense oligomers provided a specific knockdown of a target protein production. Confocal microscopy showed that pHypNAs, when transfected into living cells, demonstrated efficient cellular uptake with distribution in the cytosol and nucleus. Also, the high potency of pHypNAs for down-regulation of Ras-like GTPase Ras-dva in Xenopus embryos was demonstrated in comparison with phosphorodiamidate morpholino oligomers. Therefore, our data suggest that pHypNAs are novel antisense agents with potential widespread in vitro and in vivo applications in basic research involving live cells and intact organisms

Artificial genetic selection for an efficient translation initiation site for expression of human RACK1 gene in Escherichia coli

In bacterial expression systems, translation initiation is usually the rate limiting and the least predictable stage of protein synthesis. Efficiency of a translation initiation site can vary dramatically depending on the sequence context. This is why many standard expression vectors provide very poor expression levels of some genes. This notion persuaded us to develop an artificial genetic selection protocol, which allows one to find for a given target gene an individual efficient ribosome binding site from a random pool. In order to create Darwinian pressure necessary for the genetic selection, we designed a system based on translational coupling, in which microorganism survival in the presence of antibiotic depends on expression of the target gene, while putting no special requirements on this gene. Using this system we obtained superproducing constructs for the human protein RACK1 (receptor for activated C kinase)

Enzymatic Processes to Unlock the Lignin Value

Main hurdles of lignin valorization are its diverse chemical composition, recalcitrance, and poor solubility due to high-molecular weight and branched structure. Controlled fragmentation of lignin could lead to its use in higher value products such as binders, coatings, fillers, etc. Oxidative enzymes (i.e., laccases and peroxidases) have long been proposed as a potentially promising tool in lignin depolymerization. However, their application was limited to ambient pH, where lignin is poorly soluble in water. A Finnish biotechnology company, MetGen Oy, that designs and supplies industrial enzymes, has developed and brought to market several lignin oxidizing enzymes, including an extremely alkaline lignin oxidase MetZyme® LIGNO™, a genetically engineered laccase of bacterial origin. This enzyme can function at pH values as high as 10–11 and at elevated temperatures, addressing lignin at its soluble state. In this article, main characteristics of this enzyme as well as its action on bulk lignin coming from an industrial process are demonstrated. Lignin modification by MetZyme® LIGNO™ was characterized by size exclusion chromatography, UV spectroscopy, and dynamic light scattering for monitoring particle size of solubilized lignin. Under highly alkaline conditions, laccase treatment not only decreased molecular weight of lignin but also increased its solubility in water and altered its dispersion properties. Importantly, organic solvent-free soluble lignin fragmentation allowed for robust industrially relevant membrane separation technologies to be applicable for product fractionation. These enzyme-based solutions open new opportunities for biorefinery lignin valorization thus paving the way for economically viable biorefinery business

Analysis of the reduction of TurboGFP levels by antisense mimic oligomers in Phoenix Eco cells transfected with p2FP-RNAi vector

<p><b>Copyright information:</b></p><p>Taken from "Hydroxyproline-based DNA mimics provide an efficient gene silencing and "</p><p>Nucleic Acids Research 2006;34(8):2247-2257.</p><p>Published online 2 May 2006</p><p>PMCID:PMC1456331.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> Co-transfection of oligomers was performed in the presence of LFA. The cells transformed with the vector alone were analyzed as controls. () Sequences of oligomers designed to target the translational start site of the TurboGFP mRNA. () Analysis of green and red fluorescence intensity of the cells treated with 0.5 µM oligomers, or with 0.2 µM dsRNA, after 24 h. The average data of three separate experiments are shown. () Fluorescent microscopy images of the cells transfected with p2FP-RNAi and treated with 0.5 µM mimic oligomer samples for 16 and 24 h. Panels show examples of cells treated with 0.2 µM dsRNA (a); mismatched pHypNA oligomer (b); duplex of antisense pHypNA oligomer with CT-ODN (c); duplex of antisense HypNA-pPNA oligomer with CT-ODN (d); antisense pHypNA oligomer (e) and antisense HypNA-pPNA oligomer (f). Panel (g) shows cells untreated with oligomers. () Effect of the antisense oligomer concentration on the TurboGFP production in cells. Fluorescence was measured 24 h after the transfection. Average data points from three independent experiments are shown

Images of tadpole heads as seen from the dorsal side and the sequences of MO, pHypNA and HypNA-pPNA oligomers used in mRNA translation inhibitory assays

<p><b>Copyright information:</b></p><p>Taken from "Hydroxyproline-based DNA mimics provide an efficient gene silencing and "</p><p>Nucleic Acids Research 2006;34(8):2247-2257.</p><p>Published online 2 May 2006</p><p>PMCID:PMC1456331.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> The injection of antisense oligomers results in severe abnormalities of the head structure. The side of injection is shown by red arrow. () A control tadpole head; ( and ) heads of tadpoles developed from the embryos microinjected with the antisense MO, pHypNA and HypNA-pPNA oligomers, respectively; ( and ) heads of tadpoles developed from the embryos microinjected with the mismatched pHypNA and HypNA-pPNA oligomers

Cellular uptake and intracellular distribution of the fluorescein-labeled mimic oligomers (TCACTCAACACTCAC-Flu)

<p><b>Copyright information:</b></p><p>Taken from "Hydroxyproline-based DNA mimics provide an efficient gene silencing and "</p><p>Nucleic Acids Research 2006;34(8):2247-2257.</p><p>Published online 2 May 2006</p><p>PMCID:PMC1456331.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> () Fluorescent analysis of the delivery of oligomers (1 µM) into Phoenix Eco cells performed 20 h after the treatment under various delivery conditions: in the presence, or in the absence, of LFA, 6 mM CaCl, and 100 µM chloroquine (ClQ). () Confocal microscopy images of the pHypNA oligomer uptake after 20 h incubated with unfixed Phoenix Eco cells in the presence of: LFA (1); LFA/6mM Ca (2); CT-ODN/LFA (3) and LFA/100 µM ClQ (4)

Dose-dependent inhibition of firefly luciferase translation by the mimic antisense oligomers targeted against the translational start site of FLuc mRNA

<p><b>Copyright information:</b></p><p>Taken from "Hydroxyproline-based DNA mimics provide an efficient gene silencing and "</p><p>Nucleic Acids Research 2006;34(8):2247-2257.</p><p>Published online 2 May 2006</p><p>PMCID:PMC1456331.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> () Sequences of HypNA-pPNA and pHypNA oligomers designed to target the FLuc mRNA; () Analysis of firefly luciferase translation inhibition by the oligomers. Firefly luciferase activity was calculated relative to the activity in the absence of any oligomer and normalized respect to luciferase production

Analysis of the stability of the fluorescein-labeled pHypNA oligomer (Flu-1) by the electrophoresis in a 15% polyacrylamide gel in denaturing conditions

<p><b>Copyright information:</b></p><p>Taken from "Hydroxyproline-based DNA mimics provide an efficient gene silencing and "</p><p>Nucleic Acids Research 2006;34(8):2247-2257.</p><p>Published online 2 May 2006</p><p>PMCID:PMC1456331.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> The oligomer (5 µM) was incubated at 37°C in 500 µl of DMEM/10% FBS. Aliquots (20 µl) were taken at each 24 h and frozen at −20°C until analysis by electrophoresis. () The image shows probes of the mimic oligomer taken after 48 h (1), 72 h (2), 120 h (3) and 0 h (4) incubation; the visualization was in UV-light at 365 nm. () The comparison of the stability of the fluorescein-labeled pHypNA oligomer and the control 3′-fluorescein-labeled oligodeoxyribonucleotide of the same sequence. Densitometric calculations of the amount of full-length oligomer were done using UVP Bio-Imaging system and LabWorks imaging software