A graphene oxide-based fluorescence assay for the sensitive detection of DNA exonuclease enzymatic activity.

The 3'-5' exonuclease enzyme plays a dominant role in multiple pivotal physiological activities, such as DNA replication and repair processes. In this study, we designed a sensitive graphene oxide (GO)-based probe for the detection of exonuclease enzymatic activity. In the absence of Exo III, the strong π-π interaction between the fluorophore-tagged DNA and GO causes the efficient fluorescence quenching via a fluorescence resonance energy transfer (FRET). In contrast, in the presence of Exo III, the fluorophore-tagged 3'-hydroxyl termini of the DNA probe was digested by Exo III to set the fluorophore free from adsorption when GO was introduced, causing an inefficient fluorescence quenching. As a result, the fluorescence intensity of the sensor was found to be proportional to the concentration of Exo III; towards the detection of Exo III, this simple GO-based probe demonstrated a highly sensitive and selective linear response in the low detection range from 0.01 U mL-1 to 0.5 U mL-1 and with the limit of detection (LOD) of 0.001 U mL-1. Compared with other fluorescent probes, this assay exhibited superior sensitivity and selectivity in both buffer and fetal bovine serum samples, in addition to being cost effective and having a simple setup.

Multiplex analysis of serum hormone and cytokine in patients with cervical cOPLL: towards understanding the potential pathogenic mechanisms.

Cervical ossification of the posterior longitudinal ligament (cOPLL) is one of the major causes of myelopathy. However, the mechanism underlying remains elusive. In the present study, using MILLIPLEX magnetic bead panel, we investigated four serum hormones and six serum cytokines in cOPLL patients and healthy subjects. The results showed that tumor necrosis factore-α (TNF-α) were significantly increased, and DDK-1 was significantly decreased in the serum from male and female cOPLL patients compared with those from healthy controls, respectively. Osteopontin (OPN) and fibroblast growth factor-23 (FGF-23) were significantly increased in male cOPLL patients compared with that in healthy male controls. Further analysis showed that FGF-23 and OPN significantly increased, dickkopf-1 (DKK-1) decreased in the extensive cOPLL group. In addition, a significant positive correlation between the OPN and FGF-23 was observed in male cOPLL patients. The results are useful for understanding the mechanism underlying cOPLL.

Circulating Endothelial Markers in Retinal Vasculopathy With Cerebral Leukoencephalopathy and Systemic Manifestations.

BACKGROUND AND PURPOSE: Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (RVCL-S) is a monogenic small vessel disease, caused by C-terminal truncating TREX1 mutations, that can be considered a model for stroke and vascular dementia. The pathophysiology of RVCL-S is largely unknown, but systemic endothelial involvement has been suggested, leading to pathology in the brain and other highly vascularized organs. Here, we investigated circulating endothelial markers to confirm endothelial involvement and identify biomarkers for disease activity. METHODS: We measured circulating levels of von Willebrand factor (VWF) antigen, VWF propeptide, and angiopoietin-2 in members of 3 Dutch RVCL-S families and matched unrelated healthy controls. Stratified analyses based on symptomatology and age were performed. RESULTS: We found elevated levels of VWF antigen, VWF propeptide, and angiopoietin-2 in TREX1 mutation carriers (n=31) compared with family members without a TREX1 mutation (n=33) and unrelated healthy controls (n=31; Kruskal-Wallis test P<0.001 for all comparisons). Effects were most pronounced in mutation carriers with clinical manifestations aged ≥40 years (Mann-Whitney U test P<0.001 for all comparisons). Compared with healthy controls, levels of VWF antigen (P=0.02) and angiopoietin-2 (P=0.04) were also elevated in mutation carriers aged <40 years. All 3 markers showed moderate correlations with markers of kidney and liver disease and inflammation (ie, systemic symptoms of RVCL-S). CONCLUSIONS: Our results confirm an important role of the endothelium in RVCL-S pathophysiology. VWF antigen, VWF propeptide, and angiopoietin-2 might serve as early biomarkers of disease activity. Our findings might also help to understand the pathophysiology of common neurovascular disorders, such as stroke.

A "turn-on" and label-free fluorescent assay for the rapid detection of exonuclease III activity based on Tb(3+)-induced G-quadruplex conjugates.

A "turn-on" and label-free fluorescent assay for the specific, rapid, and sensitive detection of 3' → 5' exonuclease III activity is reported in this study. The assay is based on the Tb(3+)-promoted G-quadruplex, which lead to the enhancement of Tb(3+) fluorescence due to the energy transfer from guanines. The proposed assay is highly simple, rapid, and cost-effective, and does not require sophisticated experimental techniques such as gel-based equipment or radioactive labels. It can be used for the rapid detection of exonuclease III activity with a detection limit of 0.8 U and a RSD (n = 6) <5 %. Notably, no dye was covalently conjugated to the DNA strands, which offers the advantages of low-cost and being interference-free.

Resistance of decoy PNA-DNA chimeras to enzymatic degradation in cellular extracts and serum.

Double-stranded molecules based on peptide nucleic acids (PNAs)-DNA chimeras carrying binding sites for known transcription factors could be of great interest in decoy pharmacotherapy of neoplastic diseases. For instance, decoy molecules recognizing Sp1 and NF-kappaB transcription factors were found to inhibit tumor cell growth and invasion activity. In this respect, we have recently found that double-stranded PNA-DNA chimeras carrying NF-kappaB binding sites inhibit the binding of NF-kappaB p52 and p50 transcription factors to target DNA molecules. In this article we determined the resistance of double-stranded decoy molecules based on PNA-DNA chimeras to exonucleases (both 3'-->5' and 5'-->3' exonucleases), endonucleases, and 5'-phosphatases. In addition, we performed experiments aimed at determining the resistance of these molecules in cellular extracts and serum. Finally, we used liposomes as protective agents in experimental conditions in which the decoy molecules employed were found to be unstable (high concentrations of enzymes, cellular extracts, or serum). The results obtained demonstrated that decoy molecules based on PNA-DNA chimeras are more resistant than DNA-based decoys to exo- and endonucleases, serum, and cellular extracts. In addition, the resistance of DNA/PNA hybrids in the presence of high concentrations of serum and cellular extracts was increased after complexation to cationic liposomes, due to the fact that double-stranded PNA-DNA-PNA chimeras bind to these delivery systems. The results obtained in the present study support the proposal of molecules based on PNA-DNA chimeras for an efficient decoy treatment of tumor cells both in vitro and in vivo.

Bioactive and nuclease-resistant L-DNA ligand of vasopressin.

In vitro selection experiments have produced nucleic acid ligands (aptamers) that bind tightly and specifically to a great variety of target biomolecules. The utility of aptamers is often limited by their vulnerability to nucleases present in biological materials. One way to circumvent this problem is to select an aptamer that binds the enantiomer of the target, then synthesize the enantiomer of the aptamer as a nuclease-insensitive ligand of the normal target. We have so identified a mirror-image single-stranded DNA that binds the peptide hormone vasopressin and have demonstrated its stability to nucleases and its bioactivity as a vasopressin antagonist in cell culture.

Stability of stereoregular oligo(nucleoside phosphorothioate)s in human plasma: diastereoselectivity of plasma 3'-exonuclease.

The stability of stereoregular oligo(nucleoside phosphorothioate)s (PS-oligos) in human plasma has been studied. 3'-Exonuclease present in human plasma appeared to be RP specific, that is, it cleaves internucleotide phosphorothioate linkages of [RP]-configuration and not those of [SP]-configuration. Therefore, PS-oligos containing all phosphorothioate internucleotide linkages of [RP]-configuration [RP-PS-oligos]) are more effectively degraded by the enzyme than PS-oligos prepared via nonstereo-controlled methods (so-called random mixture of diastereomers [Mix-PS-oligos]), whereas oligo(nucleoside phosphorothioate)s of [S(P)]-configuration remain intact. The enzyme activity depends on the sequence of nucleobases. The presence of deoxycytidine units (three or more residues) at the 3'-end of PS-oligo substrate significantly inhibits the enzyme activity.

A monoclonal antibody extends the half-life of an anti-HIV oligodeoxynucleotide and targets it to CD4+ cells.

An approach was sought to increase the half-life and target cell specificity of antisense oligodeoxynucleotides (oligos). A monoclonal antibody (MAb) was derived from mice immunised with an oligo complementary to a region (1-20) of the HIV genome. This MAb exerts a protective effect on the oligo from the degradation induced by plasma exonucleases in vitro and in vivo. Moreover the anti-oligo MAb dissociates from the oligo in the presence of its complementary sequence to allow hybridization of the two complementary strands. To direct the oligo to CD4+ cells the anti-oligo MAb was cross-linked to an anti-CD4 MAb. The heteroaggregate determines a 5-fold increase in the cellular membrane binding of the oligo to CD4+ lymphocytes. These findings suggest a new approach to enhancing the therapeutic action and the target specificity of antisense oligodeoxynucleotides useful for the selective inhibition of HIV replication in vivo.

Substrate specificity and kinetics of degradation of antisense oligonucleotides by a 3' exonuclease in plasma.

The pathways of degradation of oligodeoxynucleotides in plasma from several mammalian species, including human, were investigated. In all cases, hydrolysis occurred exclusively by a 3' to 5' exonucleolytic activity. Human, mouse, and rat plasma degraded oligonucleotides in this fashion at comparable rates, whereas rabbit plasma was severalfold more active. Single-stranded oligonucleotides were more susceptible to hydrolysis than double-stranded oligonucleotides. The rate of hydrolysis was sequence dependent: 3' pyrimidine nucleotides were cleaved more rapidly than 3' purines. The Km and Vmax values for an oligonucleotide 15-mer with the sequence TAGCACCATGGTTTC in human plasma were 50 microM and 4.5 microM/min, respectively. Substitution of the 3'-terminal phosphodiester internucleoside linkage with a phosphotriester rendered this substrate completely resistant to hydrolysis, showing that the enzyme is a pure 3' to 5' exonuclease and that there are no other nucleolytic activities in plasma. Modification at this position is required to inhibit rapid nuclease degradation of antisense compounds in vivo and in tissue culture systems requiring serum.