Norbert O. Reich

Fabrication of Ag@SiO2@Y2O3:Er Nanostructures for Bioimaging: Tuning of the Upconversion Fluorescence with Silver Nanoparticles

We demonstrated that the nanostructures comprising silver cores and dense layers of Y(2)O(3):Er separated by a silica shell are an excellent model system to study the interaction between upconversion materials and metals in nanoscale. This architecture allows for versatile control of the Y(2)O(3):Er-metal interaction through control of the silica dielectric spacer thickness and the metal-core size. Finally, the nanoparticles are potentially interesting as fluorescent labels in, for instance (single particle), imaging experiments or bioassays which require low background or tissue penetrating wavelengths.

Laser-Activated Gene Silencing via Gold Nanoshell−siRNA Conjugates

The temporal and spatial control over the delivery of materials such as siRNA into cells remains a significant technical challenge. We demonstrate the pulsed near-infrared (NIR) laser-dependent release of siRNA from coated 40 nm gold nanoshells. Tat-lipid coating mediates the cellular uptake of the nanomaterial at picomolar concentration, while spatiotemporal silencing of a reporter gene (green fluorescence protein) was studied using photomasking. The NIR laser-induced release of siRNA from the nanoshells is found to be power- and time-dependent, through surface-linker bond cleavage, while the escape of the siRNA from endosomes occurs above a critical pulse energy attributed to local heating and cavitation. NIR laser-controlled drug release from functional nanomaterials should facilitate more sophisticated developmental biology and therapeutic studies.

Mapping local pH in live cells using encapsulated fluorescent SERS nanotags.

Understanding uptake and processing of nanomaterials by cells has implications for therapeutics and diagnostics. Although nanoparticle agents have been developed as proven imaging agents and promising drug-delivery vehicles, much remains to be learned regarding their internalization as local environmental sensors, even for the relatively simple case of pH determination at the nanoscale. Strategies for in vitro cell culture have been reported that use cargo-containing or dyelabeled nanoparticles with a cationic agent, which promotes binding to the cell membrane through an electrostatic interaction, inducing the cell membrane to wrap around the particle, which is then internalized through endocytosis. Nutrients and molecules that are not able to cross the membrane through active transport or diffusion and inorganic particles bigger than a few nanometers use this route. This complex process is also exploited in the uptake of nucleic acids, drugs and peptides, and of polymers for drug delivery, sensing and biocompatibility applications. Although promising efforts to monitor the interior pH in a cell after endocytosis of pHsensitive dual-color fluorescent polymers have been reported, issues of photostability and wavelength optimization remain. An ideal nanoprobe would be photostable, sensitive, and excitable with near-infrared (NIR) wavelengths at which cells and tissues are somewhat transparent and autofluorescence is minimized. A wide range of fluorescence-based materials have been developed as imaging agents and as local probes of the presence of specific biomarkers or of local environmental conditions. For example pH-sensitive fluorescence probes have been used to determine the time-dependent acidity of endosomes through a comparison of the intensity ratio between two

Etchable plasmonic nanoparticle probes to image and quantify cellular internalization

There is considerable interest in using nanoparticles as labels or to deliver drugs and other bioactive compounds to cells in vitro and in vivo. Fluorescent imaging, commonly used to study internalization and subcellular localization of nanoparticles, does not allow unequivocal distinction between cell surface-bound and internalized particles, since there is no methodology to turn particles ‘off.’ We have developed a simple technique to rapidly remove silver nanoparticles outside living cells leaving only the internalized pool for imaging or quantification. The silver nanoparticle (AgNP) etching is based on the sensitivity of Ag to a hexacyanoferrate/thiosulfate redox-based destain solution. In demonstration of the technique we present a new class of multicolored plasmonic nanoprobes comprising dye-labeled AgNPs that are exceptionally bright and photostable, carry peptides as model targeting ligands, can be etched rapidly and with minimal toxicity in mice and that show tumour uptake in vivo.

The Inherent Processivity of the Human de Novo Methyltransferase 3A (DNMT3A) Is Enhanced by DNMT3L

Human DNMT3A is responsible for de novo DNA cytosine methylation patterning during development. Here we show that DNMT3A methylates 5–8 CpG sites on human promoters before 50% of the initially bound enzyme dissociates from the DNA. Processive methylation is enhanced 3-fold in the presence of DNMT3L, an inactive homolog of DNMT3A, therefore providing a mechanism for the previously described DNMT3L activation of DNMT3A. DNMT3A processivity on human promoters is also regulated by DNA topology, where a 2-fold decrease in processivity was observed on supercoiled DNA in comparison with linear DNA. These results are the first observation that DNMT3A utilizes this mechanism of increasing catalytic efficiency. Processive de novo DNA methylation provides a mechanism that ensures that multiple CpG sites undergo methylation for transcriptional regulation and silencing of newly integrated viral DNA.

DIRECT REAL TIME OBSERVATION OF BASE FLIPPING BY THE ECORI DNA METHYLTRANSFERASE

DNA methyltransferases are excellent prototypes for investigating DNA distortion and enzyme specificity because catalysis requires the extrahelical stabilization of the target base within the enzyme active site. The energetics and kinetics of base flipping by the EcoRI DNA methyltransferase were investigated by two methods. First, equilibrium dissociation constants (K D DNA) were determined for the binding of the methyltransferase to DNA containing abasic sites or base analogs incorporated at the target base. Consistent with a base flipping mechanism, tighter binding to oligonucleotides containing destabilized target base pairs was observed. Second, total intensity stopped flow fluorescence measurements of DNA containing 2-aminopurine allowed presteady-state real time observation of the base flipping transition. Following the rapid formation of an enzyme-DNA collision complex, a biphasic increase in total intensity was observed. The fast phase dominated the total intensity increase with a rate nearly identical to k methylation determined by rapid chemical quench-flow techniques (Reich, N. O., and Mashoon, N. (1993) J. Biol. Chem. 268, 9191–9193). The restacking of the extrahelical base also revealed biphasic kinetics with the recovered amplitudes from these off-rate experiments matching very closely to those observed during the base unstacking process. These results provide the first direct and continuous observation of base flipping and show that at least two distinct conformational transitions occurred at the flipped base subsequent to complex formation. Furthermore, our results suggest that the commitment to catalysis during the methylation of the target site is not determined at the level of the chemistry step but rather is mediated by prior intramolecular isomerization within the enzyme-DNA complex.

Mutations in DNA methyltransferase (DNMT3A) observed in acute myeloid leukemia patients disrupt processive methylation

Background: De novo DNA methyltransferase 3A is mutated in acute myeloid leukemia (AML) patients. Results: AML mutations disrupt DNMT3A tetramerization and the processive methylation of human promoters in vitro. Conclusion: DNMT3A oligomeric interfaces control processivity, which may alter methylation patterns in AML patients. Significance: DNMT3A provides a plausible explanation for changes in epigenetic regulation in AML patients. DNA methylation is a key regulator of gene expression and changes in DNA methylation occur early in tumorigenesis. Mutations in the de novo DNA methyltransferase gene, DNMT3A, frequently occur in adult acute myeloid leukemia patients with poor prognoses. Most of the mutations occur within the dimer or tetramer interface, including Arg-882. We have identified that the most prevalent mutation, R882H, and three additional mutants along the tetramer interface disrupt tetramerization. The processive methylation of multiple CpG sites is disrupted when tetramerization is eliminated. Our results provide a possible mechanism that accounts for how DNMT3A mutations may contribute to oncogenesis and its progression.

Reagentless, electrochemical approach for the specific detection of double- and single-stranded DNA binding proteins.

Here we demonstrate a reagentless, electrochemical platform for the specific detection of proteins that bind to single- or double-stranded DNA. The sensor is composed of a double- or single-stranded, redox-tagged DNA probe which is covalently attached to an interrogating electrode. Upon protein binding the current arising from the redox tag is suppressed, indicating the presence of the target. Using this approach we have fabricated sensors against the double-stranded DNA binding proteins TATA-box binding protein and M.HhaI methyltransferase, and against the single-strand binding proteins Escherichia coli SSBP and replication protein A. All four targets are detected at nanomolar concentrations, in minutes, and in a convenient, general, readily reusable, electrochemical format. The approach is specific; we observed no significant cross-reactivity between the sensors. Likewise the approach is selective; it supports, for example, the detection of single strand binding protein directly in crude nuclear extracts. The generality of our approach (including its ability to detect both double- and single-strand binding proteins) and a strong, non-monotonic dependence of signal gain on probe density support a collisional signaling mechanism in which binding alters the collision efficiency, and thus electron transfer efficiency, of the attached redox tag. Given the ubiquity with which protein binding will alter the collisional dynamics of an oligonucleotide, we believe this approach may prove of general utility in the detection of DNA and RNA binding proteins.

Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease

Specific recognition by EcoRV endonuclease of its cognate, sharply bent GATATC site at the center TA step occurs solely via hydrophobic interaction with thymine methyl groups. Mechanistic kinetic analyses of base analog-substituted DNAs at this position reveal that direct readout provides 5 kcal mol–1 toward specificity, with an additional 6–10 kcal mol–1 arising from indirect readout. Crystal structures of several base analog complexes show that the major-groove hydrophobic contacts are crucial to forming required divalent metal-binding sites, and that indirect readout operates in part through the sequence-dependent free-energy cost of unstacking the center base-pair step of the DNA.

Peptide Mapping of the Murine DNA Methyltransferase Reveals a Major Phosphorylation Site and the Start of Translation

The murine DNA methyltransferase catalyzes the transfer of methyl groups from S-adenosylmethionine to cytosines within d(CpG) dinucleotides. The enzyme is necessary for normal embryonic development and is implicated in a number of important processes, including the control of gene expression and cancer. Metabolic labeling and high pressure liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) were performed on DNA methyltransferase purified from murine erythroleukemia cells. Serine 514 was identified as a major phosphorylation site that lies in a domain required for targeting of the enzyme to the replication foci. These results present a potential mechanism for the regulation of DNA methylation. HPLC-ESI-MS peptide mapping data demonstrated that the purified murine DNA methyltransferase protein contains the N-terminal regions predicted by the recently revised 5′ gene sequences (Yoder, J. A., Yen, R.-W. C., Vertino, P. M., Bestor, T. H., and Baylin, S. B. (1996) J. Biol. Chem. 271, 31092–31097). The evidence suggests a start of translation at the first predicted methionine, with no alternate translational start sites. Our peptide mapping results provide a more detailed structural characterization of the DNA methyltransferase that will facilitate future structure/function studies.