The Influence of Length and Sequence of Complementary Oligonucleotides on the Spectral and Time-Resolved Fluorescence Properties of an H-Type Excitonic Dimer-Bearing Antisense Oligonucleotide.

We have previously found that the presence of an H-type excitonic dimer formed by two fluorophores covalently bound to an oligonucleotide allows the delivery of such a polymer into live cells without inducing toxicity. We are now using time-resolved fluorescence measurements in solution to understand the molecular dynamics of an antisense probe and how pairing with complementary sense strands of various lengths and degrees of complementarity affects the antisense strand's properties. We report that a DNA strand composed of 30 residues and labeled with an H-type excitonic Cyanine-5/Cyanine-5 dimer shows a predominant 1.

An Oligonucleotide Delivery Platform to Enable Assessment of Intracellular Transcripts in Live Cells by Flow Cytometry.

The measurement of mRNA transcripts in live cells has been limited by inefficient delivery vehicles for oligonucleotides. Using a delivery platform which utilizes fluorophores capable of forming intramolecular H-type excitonic dimers, we show that antisense oligonucleotides (ASOs) can be delivered across the plasma membrane directly into the cytosol without receptor mediation. With HIV infection of CD4 lymphocytes as a model system, we quantitate the level of viral infection present in live single cells with flow cytometry by measuring the hybridization of ASOs to viral sequences; we then compare this measurement with a standard HIV analysis, that is, binding of an antibody against the HIV cell surface protein gp120.

IFITM-2 and IFITM-3 but not IFITM-1 restrict Rift Valley fever virus.

We show that interferon-induced transmembrane protein 1 (IFITM-1), IFITM-2, and IFITM-3 exhibit a broad spectrum of antiviral activity against several members of the Bunyaviridae family, including Rift Valley fever virus (RVFV), La Crosse virus, Andes virus, and Hantaan virus, all of which can cause severe disease in humans and animals. We found that RVFV was restricted by IFITM-2 and -3 but not by IFITM-1, whereas the remaining viruses were equally restricted by all IFITMs. Indeed, at low doses of alpha interferon (IFN-α), IFITM-2 and -3 mediated more than half of the antiviral activity of IFN-α against RVFV.

High-throughput quantitative analysis of HIV-1 and SIV-specific ADCC-mediating antibody responses.

We have developed a high-throughput platform to detect the presence of HIV-1 and SIV-specific ADCC-mediating antibody responses. The assay is based on the hydrolysis of a cell-permeable fluorogenic peptide substrate containing a sequence recognized by the serine protease, Granzyme B (GzB). GzB is delivered into target cells by cytotoxic effector cells as a result of antigen (Ag)-specific Ab-Fcγ receptor interactions.

Multiparametric analysis of apoptosis by flow cytometry.

Flow cytometry is the most widely used technology for analyzing apoptosis. The multiparametric nature of flow cytometry allows several apoptotic characteristics to be combined in a single sample, making it a powerful tool for analyzing the complex progression of apoptotic death. This chapter provides guidelines for combining caspase detection, annexin V binding, DNA dye exclusion, and other single apoptotic assays into multiparametric assays.

A method in enzymology for measuring hydrolytic activities in live cell environments.

The capability of determining the physiologic role(s) of cellular enzymes requires probes with access to all intracellular and extracellular environments. Importantly, reporter molecules must be able to cross not only the plasma membrane but also enter organelles inside live cells without disturbing the physiologic integrity of the system under study. Additionally, each enzyme must recognize a probe by the same linear and conformational characteristics as it would a physiologic substrate or inhibitor.

Lytic granule loading of CD8+ T cells is required for HIV-infected cell elimination associated with immune control.

Virus-specific CD8+ T cells probably mediate control over HIV replication in rare individuals, termed long-term nonprogressors (LTNPs) or elite controllers. Despite extensive investigation, the mechanisms responsible for this control remain incompletely understood. We observed that HIV-specific CD8+ T cells of LTNPs persisted at higher frequencies than those of treated progressors with equally low amounts of HIV.

Direct visualization of protease activity on cells migrating in three-dimensions.

Determining the specific role(s) of proteases in cell migration and invasion will require high-resolution imaging of sites of protease activity during live-cell migration through extracellular matrices. We have designed a novel fluorescent biosensor to detect localized extracellular sites of protease activity and to test requirements for matrix metalloprotease (MMP) function as cells migrate and invade three-dimensional collagen matrices. This probe fluoresces after cleavage of a peptide site present in interstitial collagen by a variety of proteases including MMP-2, -9, and -14 (MT1-MMP) without requiring transfection or modification of the cells being characterized.

Intracellular protease activation in apoptosis and cell-mediated cytotoxicity characterized by cell-permeable fluorogenic protease substrates.

Over the past decade the importance of signaling from reporter molecules inside live cells and tissues has been clearly established. Biochemical events related to inflammation, tumor metastasis and proliferation, and viral infectivity and replication are examples of processes being further defined as more molecular tools for live cell measurements become available. Moreover, in addition to quantitating parameters related to physiologic processes, real-time imaging of molecular interactions that compose basic cellular activities are providing insights into understanding disease mechanisms as well as extending clinical efficacy of therapeutic regimens.

Granzyme B activity in target cells detects attack by cytotoxic lymphocytes.

Lymphocyte-mediated cytotoxicity via granule exocytosis operates by the perforin-mediated transfer of granzymes from CTLs and NK cells into target cells where caspase activation and other death pathways are triggered. Granzyme B (GzB) is a major cytotoxic effector in this pathway, and its fate in target cells has been studied by several groups using immunodetection. In this study, we have used a newly developed cell-permeable fluorogenic GzB substrate to measure this protease activity in three different living targets following contact with cytotoxic effectors.

Multiparametric analysis of apoptosis by flow and image cytometry.

Flow cytometric assays for apoptosis are now in widespread use. The multiparametric nature of flow cytometry allows multiple assays for several apoptotic characteristics to be combined in a single sample, providing a powerful tool for elucidating the complex progression of apoptotic death in a variety of cell types. This chapter describes one such assay, allowing simultaneous analysis of caspase activation, annexin V binding to "flipped" phosphatidylserine residues and membrane permeability to DNA binding dyes.

Assessment of lymphocyte-mediated cytotoxicity using flow cytometry.

Cytotoxic lymphocytes, including cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells, kill target cells by releasing granules containing perforin and granzymes, and/or via Fas-Fas ligand interactions. Both pathways lead to prompt activation within target cells of caspase cascades responsible for apoptosis induction and cell death. We have utilized cell-permeable fluorogenic caspase substrates and multiparameter flow cytometry to detect caspase activation in target cells, and applied these tools to quantify and visualize cytotoxic lymphocyte activities.

Caspase activity is not sufficient to execute cell death.

Molecular studies of the physiological cell death process have focused attention on the role of effector caspases as critical common elements of the lethal mechanism. Diverse death signals act afferently via distinct signaling pathways to activate these resident proenzyme molecules post-translationally. Whether this molecular convergence represents the mechanistic point of irreversible commitment to cell death has not been established.

The effector phase of physiological cell death relies exclusively on the posttranslational activation of resident components.

Inhibitors of transcription and translation can protect cells from physiological cell deaths induced by a variety of stimuli. These observations have been taken to suggest that de novo macromolecular synthesis may be an essential component of the cell death process. Paradoxically, the same inhibitors, at higher concentrations, themselves trigger the death of cells.

Visualization and quantification of T cell-mediated cytotoxicity using cell-permeable fluorogenic caspase substrates.

We have developed a non-radioactive flow-cytometry assay to monitor and quantify the target-cell killing activities mediated by cytotoxic T lymphocytes (CTLs). This flow-cytometry CTL (FCC) assay is predicated on measurement of CTL-induced caspase activation in target cells through detection of the specific cleavage of fluorogenic caspase substrates. Here we show that this assay reliably detects antigen-specific CTL killing of target cells, and demonstrate that it provides a more sensitive, more informative and safer alternative to the standard 51Cr-release assay most often used to quantify CTL responses.

Detection of localized caspase activity in early apoptotic cells by laser scanning cytometry.

Background: Caspase activation is a critical early step in the onset of apoptosis. Cell-permeable fluorogenic caspase substrates have proven valuable in detecting caspase activation by flow cytometry. Nevertheless, detection of early low-level caspase activation has been difficult using conventional area or peak fluorescence analysis by flow cytometry, despite the apparent presence of these cells as observed by microscopy.