Oligonucleotides最新文献

The thermodynamic asymmetry of siRNA duplexes determines their silencing activity. Favorable asymmetry can be achieved by incorporation of mismatches into the 3' part of the sense strand, providing fork-siRNAs, which exhibit higher silencing activity and higher sensitivity to nucleases. Recently, we found that selective 2'-O-methyl modifications of the nuclease-sensitive sites of siRNA significantly improve its nuclease resistance without substantial loss of silencing activity. Here, we examined the impact of nucleotide mismatches and the number and location of 2'-O-methyl modifications on the silencing activity and nuclease resistance of anti-MDR1 siRNAs. We found that both nonmodified and selectively modified fork-siRNAs with 4 mismatches at the 3' end of the sense strand suppress the expression of target gene at lower effective concentrations than the parent siRNAs with classical duplex design. The selective modification of nuclease-sensitive sites significantly improved the stability of fork-siRNAs in the presence of serum. The selectively modified fork-siRNA duplexes provided inhibitory effect over a period of 12 days posttransfection, whereas the gene silencing activity of the nonmodified analogs expired within 6 days. Thus, selective chemical modifications and structural alteration of siRNA duplexes improve their silencing properties and significantly prolong the duration of their silencing effect.

Aptamers are nucleic acid sequences synthesized through in vitro selection and amplification technique, possessing a broader range of applications in therapeutics, biosensing, diagnostics, and research. Aptamers offer a number of advantages over their antibodies counterpart, one of them is their ability to undergo chemical derivatization to increase their life in the body fluids and bioavailability in animals. Although aptamers were discovered in 1990s, they have become one of the most widely investigated molecules, with a huge number of publications in the last decade. This article presents an overview of the advancements that have been made in aptamers. We mainly focused on articles published since 2005.

MicroRNAs (miRNAs) are noncoding RNAs approximately 22 nucleotides in length that play a major role in the regulation of important biological processes, including cellular development, differentiation, and apoptosis. Antisense oligonucleotides against miRNAs are useful tools for studying the biological mechanisms and therapeutic targets of miRNAs. Various antisense oligonucleotides chemistries, including peptide nucleic acids (PNAs), have been developed to enhance nuclease-resistance and affinity and specificity for miRNA targets. PNAs have a greater specificity and affinity for DNA and RNA than do natural nucleic acids, and they are resistant to nucleases-an essential property of an miRNA inhibitor that will be exposed to cellular nucleases. However, the main limiting factor in the use of PNAs is their reduced penetration into cells. Recently, several cell-penetrating peptides (CPPs) have been investigated as a means to overcome the limited penetration of PNAs. Here, we evaluated the ability of 11 CPPs to transport PNAs inside cells in the absence of transfection reagents and then investigated the ability of these CPPs to inhibit miRNAs. Of the 11 CPPs tested, Tat-modified-conjugated PNA showed the most effective penetration into cells in the absence of transfection reagents and most effectively inhibited miRNAs. Our data demonstrate that Tat-modified-conjugated CPP is the most suitable for supporting PNA-mediated miRNA inhibition.

A forced degradation study of a proprietary short interfering RNA (siRNA) molecule most of whose constituent nucleotides have been modified at the 2' position was conducted to assess degradation pathways and stability liabilities. The siRNA was subjected to various conditions as a solid and in solution followed by analysis with reverse-phase ultra-performance liquid chromatography-mass spectrometry. Positional isomers of degradants gave rise to multiple chromatographic peaks with identical masses. In some instances, the exact location of a modification was elucidated, but in most cases although the identity of the nucleotide affected was proposed with a high degree of confidence, its position within the oligonucleotide sequence was not determined. Reaction mechanisms were proposed for all observed major degradants based on reverse-phase ultra-performance liquid chromatography-mass spectrometry data generated in this laboratory and a search of literature sources. This work demonstrates that the chemistry at the 2' position of constituent nucleotides controls degradation pathways of highly modified siRNA molecules under various conditions and that classes of degradants can be predicted with a fair amount of confidence. A table of mass differences is presented that can be used as an aid to making partial structural assignments in oligonucleotide molecules containing similarly modified nucleotides.

Hepatic fibrosis leading to cirrhosis remains a global health problem. The most common etiologies are alcoholism and viral infections. Liver fibrosis is associated with major changes in both quantity and composition of extracellular matix and leads to disorganization of the liver architecture and irreversible damage to the liver function. As of now there is no effective therapy to control fibrosis. The end product of fibrosis is abnormal synthesis and accumulation of type I collagen in the extracellular matrix, which is produced by activated stellate or Ito cells in the damaged liver. Therefore, inhibition of transcription of type I collagen should in principle inhibit its production and accumulation in liver. Normally, DNA exists in a duplex form. However, under some circumstances, DNA can assume triple helical (triplex) structures. Intermolecular triplexes, formed by the addition of a sequence-specific third strand to the major groove of the duplex DNA, have the potential to serve as selective gene regulators. Earlier, we demonstrated efficient triplex formation between the exogenously added triplex-forming oligodeoxyribonucleotides (TFOs) and a specific sequence in the promoter region of the COL1A1 gene. In this study we used a rat model of liver fibrosis, induced by dimethylnitrosamine, to test whether these TFOs prevent liver fibrosis. Our results indicate that both the 25-mer and 18-mer TFOs, specific for the upstream nucleotide sequence from -141 to -165 (relative to the transcription start site) in the 5' end of collagen gene promoter, effectively prevented accumulation of liver collagen and fibrosis. We also observed improvement in liver function tests. However, mutations in the TFO that eliminated formation of triplexes are ineffective in preventing fibrosis. We believe that these TFOs can be used as potential antifibrotic therapeutic molecules.

This study sought to determine if antisense oligodeoxynucleotides would inhibit E-selectin expression, which mediates leukocyte adhesion on endothelial cells, otherwise induced by in vivo endotoxin challenge. Six antisense phosphorothioate oligodeoxynucleotides calculated to bind porcine E-selectin mRNA were tested in porcine aortic endothelial cells. One, ISIS9481, exerted significant inhibition of E-selectin expression induced by tumor necrosis factor-α + endotoxin [lipopolysaccharide (LPS)]. Pigs were challenged with LPS (10 μg/kg) and treated with ISIS9481 (10 mg/kg) (n = 6). Two control groups were used, an antisense inactive in porcine aortic endothelial cells (n = 6) and saline (n = 5), and were combined as control (C = 11). Control pigs challenged with LPS expressed E-selectin in heart, lung, kidneys, and liver, whereas antisense-treated pigs expressed little E-selectin in these tissues. Cardiovascular data indicated that antisense treatment attenuated pathophysiological alterations induced by LPS. Specifically, in control pigs, LPS reduced cardiac output 32% from baseline, increased pulmonary (+116%) and systemic vascular resistances (+16%), and generated neutropenia (from 51,000 at basal to 18,000 polymorphonuclear neutrophils (PMN)/μL after LPS). In antisense-treated pigs, cardiac output decreased only 18%, pulmonary vascular resistance remained unchanged, whereas systemic vascular resistance decreased compared with basal values (-37%). PMN counts remained at 45,000-54,000/μL at 3-4 hours after LPS. These data demonstrate that antisense oligodeoxynucleotides, designed and tested in vitro to interact with 1 gene product, can be developed as either therapeutics or experimental tools in vivo.

Short interfering RNAs (siRNAs) are valuable reagents for sequence-specific inhibition of gene expression via the RNA interference (RNAi) pathway. Recently, it was suggested that 16-bp siRNAs are effective RNAi triggers and superior to "classical" 19-bp siRNAs. This contradiction with generally accepted knowledge prompted us to reinvestigate this issue. Here, in a series of experiments performed with siRNA duplexes of various lengths (from 19 to 15 bp) designed to silence either overexpressed enhanced green fluorescent protein or endogenously expressed CDK9, we demonstrate that 19-bp siRNAs are more active silencers than shorter corresponding duplexes. The discrepancy between our results and those questioned appears to be due to different modes of shortening the duplex (either at the 3'-end or at the 5'-end, with respect to polarity of the guide strand). Importantly, duplexes with intact 5'-ends but shortened at their 3'-ends retain target site specificity, whereas those shortened at the 5'-end are complementary to different target sites located upstream.

Aptamers are single-stranded DNA or RNA oligonucleotides that adopt specific three-dimensional structures binding with high affinity and specificity to their targets. These molecules are being currently used with detection and diagnosis purposes. Parasites of the genus Leishmania cause leishmaniosis in humans and animals. Interestingly, Leishmania do not condense their chromatin during mitosis, and histone genes could be responsible for this fact. Although histones are extremely conserved proteins, reflecting their apparent universality of function, sequence similarity of kinetoplastid core histones with that of higher eukaryotes is found predominantly in the globular region. However, high sequence divergences in the N-terminal and C-terminal domains are found that convert them into potential diagnostic and/or therapeutics targets. We have successfully isolated a pool of DNA aptamers, named SELH3, which binds to Leishmania infantum H3 with high affinity and specificity. Thus, it appears that this novel anti-H3 aptamer population may be of potential application as a diagnostic system for leishmaniosis.

RNA interference has proven to be a powerful tool to inhibit viruses. For the prevention of viral escape, multiple short hairpin RNAs (shRNAs) will have to be employed. This article describes a rapid procedure for the generation of shRNA expression cassettes by parallel cloning as well as a simple strategy for the combination of selected units. After delivery of the shRNA expression cassettes with adeno-associated virus vectors, inhibition of echovirus 30 as well as silencing of an important cellular cofactor of virus replication were achieved. The procedure has the potential to be generally applicable for silencing of multiple endogenous targets or viruses.

Vascular endothelial growth factor (VEGF) plays a critical role in angiogenesis. The aim of this study was to use chitosan/short hairpin VEGF (shVEGF) [short hairpin RNA (shRNA)-expressing pDNA targeting VEGF-A] complexes in the treatment of rat breast cancer model. Therefore, chitosan/shVEGF complexes were prepared in (2/1) ratio and injected to the breast-tumor bearing Sprague-Dawley rats. Intratumoral and intraperitoneal injections were applied and compared. Tumor volumes were measured during the 36 days. To investigate the effect of complexes on the VEGF expression, VEGF were analyzed by immunohistochemistry and western blotting. The mRNA levels of VEGF were determined by real-time polymerase chain reaction. Tumor volume decreased at the end of experiments after shRNA treatment. The highest suppression in the tumor volume was observed after intratumoral complex injection to rats (96%). Compared with intratumoral and intraperitoneal injection, higher tumor inhibition was obtained with intratumoral injection. Free shRNA injection indicated lower tumor suppression. The immunohistochemistry and western blotting results correlated with the real-time polymerase chain reaction and tumor volume measurements. The data suggest that chitosan/shVEGF complexes can be used to inhibit tumor growth in breast carcinoma model of rats.