Selective inhibition of miR-21 by phage display screened peptide

miRNAs are nodal regulators of gene expression and deregulation of miRNAs is causally associated with different diseases, including cancer. Modulation of miRNA expression is thus of therapeutic importance. Small molecules are currently being explored for their potential to downregulate miRNAs. Peptides have shown to have better potency and selectivity toward their targets but their potential in targeting and modulating miRNAs remain unexplored. Herein, using phage display we found a very selective peptide against pre-miR-21. Interestingly, the peptide has the potential to downregulate miR-21, by binding to pre-miR-21 and hindering Dicer processing. It is selective towards miR-21 inside the cell. By antagonising miR-21 function, the peptide is able to increase the expression of its target proteins and thereby increase apoptosis and suppress cell proliferation, invasion and migration. This peptide can further be explored for its anti-cancer activity in vivo and may be even extended to clinical studies

High Resolution Methylome Map of Rat Indicates Role of Intragenic DNA Methylation in Identification of Coding Region

DNA methylation is crucial for gene regulation and maintenance of genomic stability. Rat has been a key model system in understanding mammalian systemic physiology, however detailed rat methylome remains uncharacterized till date. Here, we present the first high resolution methylome of rat liver generated using Methylated DNA immunoprecipitation and high throughput sequencing (MeDIP-Seq) approach. We observed that within the DNA/RNA repeat elements, simple repeats harbor the highest degree of methylation. Promoter hypomethylation and exon hypermethylation were common features in both RefSeq genes and expressed genes (as evaluated by proteomic approach). We also found that although CpG islands were generally hypomethylated, about 6% of them were methylated and a large proportion (37%) of methylated islands fell within the exons. Notably, we obeserved significant differences in methylation of terminal exons (UTRs); methylation being more pronounced in coding/partially coding exons compared to the non-coding exons. Further, events like alternate exon splicing (cassette exon) and intron retentions were marked by DNA methylation and these regions are retained in the final transcript. Thus, we suggest that DNA methylation could play a crucial role in marking coding regions thereby regulating alternative splicing. Apart from generating the first high resolution methylome map of rat liver tissue, the present study provides several critical insights into methylome organization and extends our understanding of interplay between epigenome, gene expression and genome stability

Lamination of cationic perylene in montmorillonite nano-gallery: induced J-aggregated nanostructure with enhanced photophysical and thermogravimetric aspect

Intercalation of perylenediimide dye into host layer of native Na-montmorillonite (Na-MMT) by anion exchange method is studied. Three cationic perylene diimides (PMC, PEC, and PBC) with different side chains have been synthesized and intercalated into Na-MMT to produce three composites PM-MMT, PE-MMT, and PB-MMT, respectively. Perylene-MMT composites with well-defined intercalated morphology have been prepared. XRPD and FT-IR and HR-TEM investigations show successful intercalation of cationic perylene and the interlayer distances are 0.74 nm for PM-MMT, 0.84 nm for PE-MMT, and 1.24 nm for PB-MMT. These values support the presence of monolayer arrangement of intercalated perylene dye molecules inclined within MMT nanogalleries. Photophysical properties of these intercalated composites have been measured with UV-vis spectroscopy, photoluminescence spectroscopy, and fluorescence microscopy. The results indicate that the perylene dyes are stacked as J-type aggregation in the interlayer region. Intercalated perylene molecules show enhanced thermal and photophysical stability

Immobilization of poly(fluorene) within clay nanocomposite: An easy way to control keto defect

Blue light emitting cationic polyfluorene polymer(PF)/montmorillonite (MMT) nanocomposites were prepared by solution intercalation and exfoliation method to evaluate the effect of MMT on the nanocomposite structures, properties and morphologies. The properties of PF-MMT composites, containing 1-50 mass% MMT, were characterized unambiguously with the help of multiple analytical techniques, with focus on the keto defect and photostability of PF in the nanocomposites. XRD and HRTEM studies reveal both exfoliation of MMT galleries at lower content of MMT in composites and intercalation of PF chains into the MMT galleries at higher MMT content. The nanocomposites show higher thermal stability than pristine PF as anchorage of nanoclay in PF matrix occur through the electrostatic interaction between nanoclay and polymer. The decrease in Si-O-Si stretching frequency during exfoliation is much higher than in intercalation, as Si-O-Si experience lesser hindrance to vibrate in exfoliated MMT galleries. The gradual redshift of pi-pi* transition peak of PF with increasing MMT content in composites confirms the uncoiling of PF in clay galleries. The photoluminescence characteristics reveal interruption of interchain interaction in this intercalated and exfoliated organic/inorganic hybrid system, which reduces the low-energy emission that results from keto defect. Due to very high aspect ratio of MMT, it can act as an efficient exciton blocking layer and a barrier to oxygen diffusion, which may lead to a device with high color purity and enhanced photostability. Again current-voltage characteristics of nanocomposite films confirm the retention of LED properties after nanocomposite formation. (C) 2011 Elsevier Inc. All rights reserved

Intercalation of Perylenediimide Dye into LDH Clays: Enhancement of Photostability

Intercalation of perylenediimide dye into a host layer of layered double hydroxide (LDH) by the anion-exchange method is studied N,N'-Bis(4-benzosulfonic acid)-perylene-3,4,9,10-tetracarboxylbisimide disodium salt (PRSA) has been synthesized and intercalated into the perchlorate form of ZnAl-, CoAl-, and NiAl-LDH. LDH composite with well-defined morphology has been prepared. XRPD and FT-IR investigation show successful intercalation of PRSA, and the interlayer distances are 32.5 angstrom for ZnAl-LDH-PRSA, 30.0 angstrom for CoAl-LDH-PRSA, and 31.2 angstrom for NiAl-LDH-PRSA. These values support the presence of monolayer arrangement of intercalated PRSA molecules in the composite and also indicate vertical orientation of PRSA molecules with the basal plane of LDH. Photophysical properties of these intercalated composites have been measured with UV-vis spectroscopy, photoluminescence spectroscopy, and confocal laser scanning microscopy. The results indicate that the PRSA molecules are stacked in J-type aggregation in the interlayer region. Intercalated PRSA molecules show enhanced thermal and photophysical stabilities

NMR structural analysis of a peptide mimic of the bridging sheet of HIV-1 gp120 in methanol and water

gp120 is a subunit of the Env (viral envelope protein) of HIV-1. The protein consists of inner and outer domains linked by a bridging sheet. Several gp120 residues that bind the neutralizing antibody 17b as well as the cellular co-receptor CCR5 (CC chemokine receptor 5), are located in the bridging sheet. Peptides that mimic the 17b-binding regions of gp120 would be useful potential immunogens for the generation of neutralizing antibodies against HIV-1. Towards this end, a 26-residue, four-stranded β-sheet peptide was designed on the basis of the structure of the bridging sheet, and its structure was characterized in methanol by NMR. In methanol, amide and α-proton resonances were well resolved and dispersed. A number of interstrand NOEs (nuclear Overhauser effects) were observed, providing good evidence for multiple turn β-hairpin structure. NOEs also provided good evidence for all Xxx–D-Pro bonds in the trans configuration and all three turns formed by a two residue D-Pro–Gly segment to be of type II′ turn. The structure conforms well to the designed four-stranded β-sheet structure. Approx. 20% of the peptide was estimated to adopt a folded conformation in water, as evidenced by CD spectroscopy. This was consistent with smaller, but still significant, downfield shifts of C(α)H protons relative to random-coil values. A second peptide was designed with two disulphide bonds to further constrain the peptide backbone. While structured in methanol, this peptide, like the previous one, also exhibits only partial structure formation in water, as evidenced by CD spectroscopy

Suppression of keto defects and thermal stabilities of polyfluorene-kaolinite clay nanocomposites

A solution blending process for preparation of polymer nanocomposites composed of cationic polyfluorene (PF) and dimethyl sulfoxide (DMSO) -intercalated kaolinite (Ka) clay has been taken to evaluate the effect of Ka nanostructure on the nanocomposite structures, morphology, and properties. Composites containing 2, 5, 7.5, and 10 wt % clay have been characterized with the help of X-ray diffraction (XRD), field emission scanning electron microscopy (FE-SEM), high-resolution transmission electron microscopy (HRTEM), thermogravimetric analysis (TGA), Fourier transform infrared spectroscopy (FTIR), UV-visible spectroscopy, photoluminescence studies, etc. Additionally, the keto defect, inhibition of interchain interaction; and photostability of PF in the nanocomposites have been explored. The XRD and HRTEM studies show the exfoliation of Ka layers at lower content in composites. Intercalation of PF chains into the Ka interlayer space occurs at relatively higher clay content. Nanocomposites exhibit higher thermal stability than pristine PF due to lamination of PF into clay nanogallery through the interchange of DMSO by cationic polyfluorene. The presence of an Si-O-Si stretching band in the composites supports the formation of nanocomposites of PF with Ka. The movement of absorption maxima to higher wavelength indicates the increase of overall conjugation length of PF chains in the nanocomposites. Upon formation of nanocomposite with Ka, the keto defect sites of PF are significantly reduced. This can be attributed to the lamination of single PP chains by Ka interlayer gallery that act as a barrier to oxygen and inhibit the exciton diffusion. Current-voltage characteristics of nanocomposite films have also shown good switching behavior with low forward junction potential