Solid-state nanopores are sensors capable of analyzing individual unlabelled DNA molecules in solution. While the critical information obtained from nanopores (e.g., DNA sequence) is the signal collected during DNA translocation, the throughput of the method is determined by the rate at which molecules arrive and thread into the pores. Here we study the process of DNA capture into nanofabricated silicon nitride pores of molecular dimensions. For fixed analyte concentrations we find an increase in capture rate as the DNA length increases from 800 to 8,000 basepairs, a length-independent capture rate for longer molecules, and increasing capture rates when ionic gradients are established across the pore. In addition, we show that application of a 20-fold salt gradient enables detection of picomolar DNA concentrations at high throughput. The salt gradients enhance the electric field, focusing more molecules into the pore, thereby advancing the possibility of analyzing unamplified DNA samples using nanopores.

We demonstrate a purely electrical method for single-molecule detection of specific DNA sequences, achieved by hybridizing double-stranded DNA (dsDNA) with peptide nucleic acid (PNA) probes and electrophoretically threading the DNA through sub-5 nm silicon nitride pores. Bis-PNAs were used as the tagging probes, in order to achieve high affinity and sequence-specificity. Sequence detection is performed by reading the ion current traces of individual translocating DNA molecules, which display a characteristic secondary blockade level, absent in untagged molecules. The potential for barcoding DNA is demonstrated through nanopore analysis of once-tagged and twice-tagged DNA at different locations on the same genomic fragment. Our high-throughput, long-read length method can be used to identify key sequences embedded in individual DNA molecules, without the need for amplification or fluorescent/radio labeling. This opens up a wide range of possibilities in human genomics, as well as in pathogen detection for fighting infectious diseases. KeywordsPNA; invasion; sequence detection; nanopore; DNA Numerous techniques in life sciences, biotechnology, medicine, and forensics are based on nucleic acid hybridization. The invention of nucleic acid analogs with improved hybridization affinity, hybridization rate, and/or mismatch discrimination as compared to natural nucleic acids, has significantly extended the diagnostic utilities of these applications. Peptide nucleic acids (PNAs), a prominent class of artificial nucleic acid analogs, are neutral, oligomers with peptide-like backbone onto which nucleobases are grafted in a designed sequence. Moreover, bis-PNA molecules, consisting of two PNA oligomers connected by a flexible linker, spontaneously invade double-stranded DNA (dsDNA) molecules, binding to one of the two dsDNA strands with high affinity and sequence-specificity, owing to the simultaneous formation of Watson-Crick and Hoogsteen base-pairs 1-3 . This high affinity and sequencespecificity makes bis-PNA, and other synthetic variants (e.g., pseudocomplementary PNA 2, 4 and γ-PNA 5, 6 ) extremely promising sequence-tagging candidates for analysis of individual dsDNA fragments. Single-molecule mapping methods, which detect and localize PNA/DNA hybridization on minute quantities of dsDNA can lead to cheaper and faster pathogen and mutation diagnostics platforms. Low-cost and high speed platforms are essential for effective response to emerging threats of infection and will ultimately result in more accurate treatment, as well as an overall decrease in morbidity and mortality. While a

in a free standing silicon nitride membrane. The translocation of CTPR proteins was measured in KCl solution at pH below and above its isoelectric point (pI), as well as with and without denaturing agent, Guanidine HCl. When a CTPR protein molecule transits through a nanopore driven by an applied voltage, it partially blocks the ions (K þ and Cl -) flow in the nanopore and generates a characteristic electric current blockage signal. The current blockage signal reveals information about the size, conformation, and primary sequence of the CTPR protein molecule. Previous translocation studies carried out with DNA have established that higher bias voltages result in shorter duration current blockages indicating that DNA translocates faster at a stronger electric field. However, CTPR translocation studies presented here show that longer duration current blockades were observed at higher bias voltages. We explain this surprising result by theoretical analysis of CTPR protein translocation in solid state nanopores. We discuss how the inhomogeneous distribution of the primary charge sequence of the CTPR proteins predicts translocation barriers that are proportional to the bias voltage. Larger barriers at higher bias voltages will result in longer translocation times, consistent with our experimental results.

Although the clustering of GFAP immunopositive astrocytes around amyloid-β plaques in Alzheimer's disease has led to the widespread assumption that plaques attract astrocytes, recent studies suggest that astrocytes stay put in injury. Here we reexamine astrocyte migration to plaques, using quantitative spatial analysis and computer modeling to investigate the topology of astrocytes in 3D images obtained by two-photon microscopy of living APP/PS1 mice and WT littermates. In WT mice, cortical astrocyte topology fits a model in which a liquid of hard spheres exclude each other in a confined space. Plaques do not disturb this arrangement except at very large plaque loads, but, locally, cause subtle outward shifts of the astrocytes located in three tiers around plaques. These data suggest that astrocytes respond to plaque-induced neuropil injury primarily by changing phenotype, and hence function, rather than location.T he role of astrocytes in amyloid-β deposition during Alzheimer's disease-whether they prevent, potentiate, or have no effect on plaque formation-remains unknown. The peer-reviewed literature indicates that it is widely believed that amyloid-β plaques attract astrocytes, with statements such as "astrocytes migrate to amyloid-β plaques," "amyloid-β plaques recruit astrocytes," and variations thereof frequently appearing. The idea that astrocytes are attracted to plaques is an extension of the notion that astrocytes migrate to zones of injury (1, 2) and is mostly based on the immunohistochemical observation that amyloid-β deposits are typically surrounded by concentric rings of "reactive astrocytes," defined by increased GFAP immunoreactivity and hypertrophy. However, recent studies question the capacity of astrocytes to move (3, 4). These suggest instead that astrocytes may be restricted to their birthplace (3), which in the neocortex seems to be within neuronal columns derived from radial glia (5). Recent stereological assessments of astrocytes in Alzheimer's disease suggest that their most prominent change is phenotypic (i.e., GFAP immunoreactivity and hypertrophy) rather than proliferative (6). Thus, doubts have risen over the recruitment of astrocytes by plaques.Using the APPSwe/PS1dE9 (APP/PS1) double-transgenic mouse model of Alzheimer's disease, we revisited the idea that astrocytes migrate to plaques. Our approach improved on the traditional GFAP immunohistochemical analysis postmortem in three ways. First, the analyses were performed in 3D reconstructions of images captured in vivo through cranial windows by two-photon microscopy. These materials are superior to sectioned specimens from fixed brains because they preserve true spatial relationships in 3D to great depths (up to 200 μm from the cortical surface), providing accurate positional information for each astrocyte. Second, astrocytes were labeled with sulforhodamine 101 (SR101), a selective fluorescent marker of reactive and nonreactive astrocytes (7), thus avoiding the bias of identifying only a subset of astrocytes as with GFAP. Third, ...

Brain fiber pathways are presumed to follow smooth curves but recent high angular resolution diffusion MRI (dMRI) suggests that instead they follow 3 primary axes often nearly orthogonal. To investigate this, we analyzed axon pathways under monkey primary motor cortex with (1) dMRI tractography, (2) axon tract tracing, and (3) axon immunohistochemistry. dMRI tractography shows the predicted crossings of axons in mediolateral and dorsoventral orientations and does not show axon turns in this region. Axons labeled with tract tracer in the motor cortex dispersed in the centrum semiovale by microscopically sharp axonal turns and/or branches (radii ≤15 µm) into 2 sharply defined orientations, mediolateral and dorsoventral. Nearby sections processed with SMI-32 antibody to label projection axons and SMI-312 antibody to label all axons revealed axon distributions parallel to the tracer axons. All 3 histological methods confirmed preponderant axon distributions parallel with dMRI axes with few axons (<20%) following smooth curves or diagonal orientations. These findings indicate that axons navigate deep white matter via microscopic sharp turns and branches between primary axes. They support dMRI observations of primary fiber axes, as well as the prediction that fiber crossings include navigational events not yet directly resolved by dMRI. New methods will be needed to incorporate coherent microscopic navigation into dMRI of connectivity.