Recognition imaging of chromatin and chromatin-remodeling complexes in the atomic force microscope.

Atomic force microscopy (AFM) can directly visualize single molecules in solution, which makes it an extremely powerful technique for carrying out studies of biological complexes and the processes in which they are involved. A recent development, called Recognition Imaging, allows the identification of a specific type of protein in solution AFM images, a capability that greatly enhances the power of the AFM approach for studies of complex biological materials. In this technique, an antibody against the protein of interest is attached to an AFM tip.

Prussian Blue Dispersed Sphere Catalytic Labels for Amplified Electronic Detection of DNA.

A highly sensitive electrochemical DNA hybridization assay using Prussian blue (PB)-modified polymeric spheres as the oligonculeotide labeling tag is described. The sandwich assay relies on a secondary nucleic-acid probe functionalized with polystyrene beads loaded with numerous Prussian blue nanoparticles. The very strong catalytic activity of the captured PB 'artificial peroxidase' tag towards the reduction of hydrogen peroxide, along with the encapsulation of numerous catalytic particles onto polymeric beads, allows amperometric detection of the DNA target down to the 50 fM level (2.

Aptamer-based potentiometric measurements of proteins using ion-selective microelectrodes.

We here report on the first example of an aptamer-based potentiometric sandwich assay of proteins. The measurements are based on CdS quantum dot labels of the secondary aptamer, which were determined with a novel solid-contact Cd2+-selective polymer membrane electrode after dissolution with hydrogen peroxide. The electrode exhibited cadmium ion detection limits of 100 pM in 100 mL samples and of 1 nM in 200 microL microwells, using a calcium-selective electrode as a pseudoreference electrode.

Alloy nanowires bar codes based on nondestructive X-ray fluorescence readout.

We demonstrate here the ability to generate ternary Co-Ni-Cu alloy nanowires with distinct X-ray fluorescence (XRF) barcode patterns using a one-step template-guided electrodeposition. Such coupling of one-step templated synthesis with a nondestructive XRF readout of the composition patterns greatly simplifies practical applications of barcoded nanomaterials. The new protocol leads to alloy nanowires with broad composition range and hence to an extremely large number of distinguishable XRF signatures.

Mechanisms underlying production of double-strand breaks in plasmid DNA after decay of 125I-Hoechst.

Previously, the kinetics of strand break production by (125)I-labeled m-iodo-p-ethoxyHoechst 33342 ((125)IEH) in supercoiled (SC) plasmid DNA had demonstrated that approximately 1 DSB is produced per (125)I decay both in the presence and absence of the hydroxyl radical scavenger DMSO. In these experiments, an (125)IEH:DNA molar ratio of 42:1 was used. We now hypothesize that this DSB yield (but not the SSB yield) may be an overestimate due to subsequent decays occurring in any of the 41 (125)IEH molecules still bound to nicked (N) DNA.

Glutaraldehyde modified mica: a new surface for atomic force microscopy of chromatin.

We have found that mica surfaces functionalized with aminopropyltriethoxysilane and aldehydes bind chromatin strongly enough to permit stable and reliable solution imaging by atomic force microscopy. The method is highly reproducible, uses very small amounts of material, and is successful even with very light degrees of surface modification. This surface is far superior to the widely used aminopropyltriethoxysilane-derivatized mica surface and permits resolution of structure on the nanometer-scale in an aqueous environment, conditions that are particularly important for chromatin studies.