Synthesis and characterization of oligonucleotides containing conformationally constrained bicyclo[3.1.0]hexane pseudosugar analogs

Oligodeoxyribonucleotides containing pseudorotationally locked sites derived from bicyclo[3.1.0]hexane pseudosugars have been synthesized using adenosine, thymidine and abasic versions of North- and South-methanocarba nucleosides. The reaction conditions for coupling and oxidation steps of oligonucleotide synthesis have been investigated and optimized to allow efficient and facile solid-phase synthesis using phosphoramidite chemistry. Our studies demonstrate that the use of iodine for P(III) to P(V) oxidation leads to strand cleavage at the sites where the pseudosugar is North. In contrast, the same cleavage reaction was not observed in the case of South pseudosugars. Iodine oxidation generates a 5′-phosphate oligonucleotide fragment on the resin and releases the North pseudosugar into the solution. This side reaction, which is responsible for the extremely low yields observed for the incorporation of the North pseudosugar analogs, has been studied in detail and can be easily overcome by replacing iodine with t-butylhydroperoxide as oxidant.     

2'-O-[2-[(N,N-dimethylamino)oxy]ethyl]-modified oligonucleotides inhibit expression of mRNA in vitro and in vivo

Synthesis and antisense activity of oligonucleotides modified with 2′-O-[2-[(N,N-dimethylamino)oxy] ethyl] (2′-O-DMAOE) are described. The 2′-O-DMAOE-modified oligonucleotides showed superior metabolic stability in mice. The phosphorothioate oligonucleotide ‘gapmers’, with 2′-O-DMAOE- modified nucleoside residues at the ends and 2′-deoxy nucleosides residues in the central region, showed dose-dependent inhibition of mRNA expression in cell culture for two targets. ‘Gapmer’ oligonucleotides have one or two 2′-O-modified regions and a 2′-deoxyoligonucleotide phosphorothioate region that allows RNase H digestion of target mRNA. To determine the in vivo potency and efficacy, BalbC mice were treated with 2′-O-DMAOE gapmers and a dose-dependent reduction in the targeted C-raf mRNA expression was observed. Oligonucleotides with 2′-O-DMAOE modifications throughout the sequences reduced the intercellular adhesion molecule-1 (ICAM-1) protein expression very efficiently in HUVEC cells with an IC₅₀ of 1.8 nM. The inhibition of ICAM-1 protein expression by these uniformly modified 2′-O-DMAOE oligonucleotides may be due to selective interference with the formation of the translational initiation complex. These results demonstrate that 2′-O-DMAOE- modified oligonucleotides are useful for antisense-based therapeutics when either RNase H-dependent or RNase H-independent target reduction mechanisms are employed.     

BLMT

Statistical analysis of amino acid and nucleotide sequences, especially sequence alignment, is one of the most commonly performed tasks in modern molecular biology. However, for many tasks in bioinformatics, the requirement for the features in an alignment to be consecutive is restrictive and "n-grams" (aka k-tuples) have been used as features instead. N-grams are usually short nucleotide or amino acid sequences of length n, but the unit for a gram may be chosen arbitrarily. The n-gram concept is borrowed from language technologies where n-grams of words form the fundamental units in statistical language models. Despite the demonstrated utility of n-gram statistics for the biology domain, there is currently no publicly accessible generic tool for the efficient calculation of such statistics. Most sequence analysis tools will disregard matches because of the lack of statistical significance in finding short sequences. This article presents the integrated Biological Language Modeling Toolkit (BLMT) that allows efficient calculation of n-gram statistics for arbitrary sequence datasets. AVAILABILITY: BLMT can be downloaded from http://www.cs.cmu.edu/~blmt/source and installed for standalone use on any Unix platform or Unix shell emulation such as Cygwin on the Windows platform. Specific tools and usage details are described in a "readme" file. The n-gram computations carried out by the BLMT are part of a broader set of tools borrowed from language technologies and modified for statistical analysis of biological sequences; these are available at http://flan.blm.cs.cmu.edu/.     

Modulation of plasma protein binding and in vivo liver cell uptake of phosphorothioate oligodeoxynucleotides by cholesterol conjugation

Several studies have shown improved efficacy of cholesteryl-conjugated phosphorothioate antisense oligodeoxynucleotides. To gain insight into the mechanisms of the improved efficacy in vivo, we investigated the disposition of ISIS-9388, the 3′-cholesterol analog of the ICAM-1-specific phosphoro­thioate oligodeoxynucleotide ISIS-3082, in rats. Intravenously injected [³H]ISIS-9388 was cleared from the circulation with a half-life of 49.9 ± 2.2 min (ISIS-3082, 23.3 ± 3.8 min). At 3 h after injection, the liver contained 63.7 ± 3.3% of the dose. Compared to ISIS-3082, the hepatic uptake of ISIS-9388 is ~2-fold higher. Endothelial, Kupffer and parenchymal cells accounted for 45.7 ± 5.7, 33.0 ± 5.9 and 21.3 ± 2.6% of the liver uptake of [³H]ISIS-9388, respectively, and intracellular concentrations of ~2, 75 and 50 µM, respectively, could be reached in these cells (1 mg/kg dose). Preinjection with polyinosinic acid or poly­adenylic acid reduced the hepatic uptake of [³H]ISIS-9388, which suggests the involvement of (multiple) scavenger receptors. Size exclusion chromatography of mixtures of the oligonucleotides and rat plasma indicated that ISIS-9388 binds to a larger extent to high molecular weight proteins than ISIS-3082. Analysis by agarose gel electrophoresis indicated that ISIS-9388 binds more tightly to plasma proteins than ISIS-3082. The different interaction of the oligonucleotides with plasma proteins possibly explains their different dispositions. We conclude that cholesterol conjugation results in high accumulation of phosphorothioate oligodeoxynucleotides in various liver cell types, which is likely to be beneficial for antisense therapy of liver-associated diseases.     

CpG PatternFinder: a Windows-based utility program for easy and rapid identification of the CpG methylation status of DNA

The bisulfite genomic sequencing technique is one of the most widely used techniques to study sequence-specific DNA methylation because of its unambiguous ability to reveal DNA methylation status to the order of a single nucleotide. One characteristic feature of the bisulfite genomic sequencing technique is that a number of sample sequence files will be produced from a single DNA sample. The PCR products of bisulfite-treated DNA samples cannot be sequenced directly because they are heterogeneous in nature; therefore they should be cloned into suitable plasmids and then sequenced. This procedure generates an enormous number of sample DNA sequence files as well as adding extra bases belonging to the plasmids to the sequence, which will cause problems in the final sequence comparison. Finding the methylation status for each CpG in each sample sequence is not an easy job. As a result CpG PatternFinder was developed for this purpose. The main functions of the CpG PatternFinder are: (i) to analyze the reference sequence to obtain CpG and non-CpG-C residue position information. (ii) To tailor sample sequence files (delete insertions and mark deletions from the sample sequence files) based on a configuration of ClustalW multiple alignment. (iii) To align sample sequence files with a reference file to obtain bisulfite conversion efficiency and CpG methylation status. And, (iv) to produce graphics, highlighted aligned sequence text and a summary report which can be easily exported to Microsoft Office suite. CpG PatternFinder is designed to operate cooperatively with BioEdit, a freeware on the internet. It can handle up to 100 files of sample DNA sequences simultaneously, and the total CpG pattern analysis process can be finished in minutes. CpG PatternFinder is an ideal software tool for DNA methylation studies to determine the differential methylation pattern in a large number of individuals in a population. Previously we developed the CpG Analyzer program; CpG PatternFinder is our further effort to create software tools for DNA methylation studies.     

A crucial role for the phosphorylation of STRAP at Ser188 by MPK38 in STRAP-dependent cell death through ASK1, TGF-β, p53, and PI3K/PDK1 signaling pathways

Serine-threonine kinase receptor-associated protein (STRAP) is a TGF-β receptor-interacting protein that participates in the regulation of cell proliferation and cell death in response to various stresses. Here, we demonstrate that STRAP phosphorylation plays an important role in determining the pro- or anti-apoptotic function of STRAP. Murine protein serine/threonine kinase 38 (MPK38) phosphorylates STRAP at Ser¹⁸⁸ via direct interaction. Complex formation between STRAP and MPK38 is mediated by Cys¹⁵² and Cys²⁷⁰ of STRAP and Cys³³⁹ and Cys³⁷⁷ of MPK38, suggesting the redox dependency of this interaction. MPK38-mediated STRAP Ser¹⁸⁸ phosphorylation contributes to the pro-apoptotic function of STRAP by modulating key steps in STRAP-dependent ASK1, TGF-β, p53, and PI3K/PDK1 signaling pathways. Moreover, knockdown of endogenous MPK38 using an inducible MPK38 shRNA system and in vivo activation of MPK38 by treatment of HEK293 and STRAP-null MEF cells with 1-chloro-2,4-dinitrobenzene (DNCB), a specific inhibitor of Trx reductase, provide evidence that STRAP Ser¹⁸⁸ phosphorylation plays a key role in STRAP-dependent cell death. Adenoviral delivery of MPK38 in mice also demonstrates that STRAP Ser¹⁸⁸ phosphorylation in the liver is tightly associated with cell death and proliferation through ASK1, TGF-β, p53, and PI3K/PDK1 pathways, resulting in apoptotic cell death.     

Green synthesis of silver and gold nanoparticles using Zingiber officinale root extract and antibacterial activity of silver nanoparticles against food pathogens

In the present study, we synthesized silver and gold nanoparticles with a particle size of 10–20 nm, using Zingiber officinale root extract as a reducing and capping agent. Chloroauric acid (HAuCl₄) and silver nitrate (AgNO₃) were mixed with Z. officinale root extract for the production of silver (AgNPs) and gold nanoparticles (AuNPs). The surface plasmon absorbance spectra of AgNPs and AuNPs were observed at 436–531 nm, respectively. Optimum nanoparticle production was achieved at pH 8 and 9, 1 mM metal ion, a reaction temperature 50 °C and reaction time of 150–180 min for AgNPs and AuNPs, respectively. An energy-dispersive X-ray spectroscopy (SEM–EDS) study provides proof for the purity of AgNPs and AuNPs. Transmission electron microscopy images show the diameter of well-dispersed AgNPs (10–20 nm) and AuNPs (5–20 nm). The nanocrystalline phase of Ag and Au with FCC crystal structures have been confirmed by X-ray diffraction analysis. Fourier transform infrared spectroscopy analysis shows the respective peaks for the potential biomolecules in the ginger rhizome extract, which are responsible for the reduction in metal ions and synthesized AgNPs and AuNPs. In addition, the synthesized AgNPs showed a moderate antibacterial activity against bacterial food pathogens.     

Effect of α, β momorcharin on viability,caspase activity,cytochrome c release and on cytosolic calcium levels in different cancer cell lines

A multitude of plants have been used extensively for the treatment of cancers throughout the world. The protein, α, β momorcharin has been extracted from the plant Momordica charantia (MC), and it possesses anti-cancer and anti-HIV properties similar to the crude water and methanol soluble extract of the plant. This study investigated the anti-cancer effects and the cellular mechanisms of action of α, β momocharin (200–800 μM) on 1321N1, Gos-3, U87-MG, Sk Mel, Corl-23 and Weri Rb-1 cancer cell lines compared to normal healthy L6 muscle cell line measuring cell viability using MTT assay kit, Caspase-3 and 9 activities, cytochrome c release and intracellular free calcium concentrations [Ca²⁺]_i. The results show that α, β momorcharin can evoke significant dose-dependent (P < 0.05; Student’s t test) decreases in the viability (increases in cell death) of 1321N1, Gos-3, U87-MG, Sk Mel, Corl-23 and Weri Rb-1 cancer cell lines compared to healthy L6 muscle cell line and untreated glioma cells. α, β momorcharin (800 μM) also evoked significant (P < 0.05) increases in caspase-3 and 9 activities and cytochrome c release. Similarly, α, β momorcharin elicited significant (P < 0.05) time-dependent elevation in [Ca²⁺]_i in all five glioma cell lines compared to untreated cells. Together, the results have demonstrated that α, β momorcharin can exert its anti-cancer effect on different cancer cell lines by intracellular processes involving an insult to the mitochondria resulting in cellular calcium over loading, apoptosis, cytochrome release and subsequently, cell death.     

Viral interleukin-6 encoded by rhesus macaque rhadinovirus is associated with lymphoproliferative disorder (LPD)

Background  Rhesus macaques (RM) co-infected with simian immunodeficiency virus (SIV) and rhesus macaque rhadinovirus (RRV) develop abnormal cellular proliferations characterized as extra-nodal lymphoma and retroperitoneal fibromatosis (RF). RRV encodes a viral interleukin-6 (vIL-6), much like Kaposi's sarcoma-associated herpesvirus, and involvement of the viral cytokine was examined in proliferative lesions.
Methods  Formalin fixed tissue from RM co-infected with SIV and RRV were analyzed for RRV genomes by in situ hybridization and RRV vIL-6 expression by immunofluorescence analysis.
Results  In situ hybridization analysis indicated that RRV is present in both types of lesions. Immunofluorescence analysis of different lymphomas and RF revealed positive staining for vIL-6. Similarly to KS, RF lesion is positive for vimentin, CD117 (c-kit), and smooth muscle actin (SMA) and contains T cell, B cell and monocytes/macrophage infiltrates.
Conclusions  Our data support the idea that vIL-6 may be critical to the development and progression of lymphoproliferative disorder in RRV/SIV-infected RM.