Highly sensitive, mechanically robust Al2O3 nanopores are fabricated and characterized. These sensors allow for size control with sub‐nanometer precision, chemical modification, and exhibit superior noise performance and increased lifetime over their solid‐state counterparts. This new class of nanopore sensor is used in dsDNA studies and finds broad application in bio‐nanotechnology.

We have discovered a voltage threshold for permeation through a synthetic nanopore of dsDNA bound to a restriction enzyme that depends on the sequence. Molecular Dynamic simulations reveal that the threshold is associated with a nanoNewton force required to rupture the DNA-protein complex. A single mutation in the recognition site for the restriction enzyme, i.e. a single nucleotide polymorphism (SNP), can easily be detected as a change in the threshold voltage. Consequently, by measuring the threshold voltage in a synthetic nanopore, it may be possible to discriminate between two variants of the same gene (alleles) that differ in one base.Restriction enzymes are used prevalently in recombinant DNA technology for cleaving doublehelical DNA segments containing a specific target sequence. Another use is genotyping. Because the binding to the target is extraordinarily sequence specific, restriction enzymes can be used to identify single nucleotide polymorphisms (SNPs) that occur when variants of the same gene (alleles) differ in one base.We have discovered a method for discriminating between alleles that uses a synthetic nanopore to measure the binding of a restriction enzyme to DNA. When a voltage is applied across a membrane containing a nanopore, polyanionic DNA immersed in electrolyte at the cathode diffuses toward the anode and is driven across the membrane by the electric field in the pore. The force due to the field acting on the strand during the translocation impels DNA to bend and stretch within the pore. 1-4 At low fields ℰ < 500mV/10nm, double-stranded DNA (dsDNA) easily permeates pores with diameters ≥2.4nm because the double helix (~2nm diameter) is smaller than the pore. 5 But the permeability of DNA through the pore changes dramatically if it is bound to a restriction enzyme.To study the binding of a restriction enzyme like EcoRI to DNA, we introduced an excess of the enzyme in solution with DNA without the Mg +2 cofactor that is required for cleaving the nucleic acid. Under these conditions, EcoRI is thought to bind and diffuse along DNA. 6,7 The diffusive motion along the strand is arrested at the cognate site, i.e. -GAATTC-for EcoRI. Bulk measurements of the binding at the cognate site indicate a free energy of formation ΔG =−15.2kcal/mol. 6-9 However, the introduction of any mutation among the cognate sites produces a position-dependent reduction in the binding energy that ranges from 6-13kcal/mol. 8,9 Site-specific DNA-binding proteins also have an affinity for nonspecific DNA. In contrast with site-specific binding or binding to a non-cognate site with a single nucleotide mutation, a nonspecifically bound complex is not localized to a particular site. For EcoRI, sites that differ from the cognate sequence by two or more base-pairs(bps) are considered nonspecific since they are not cleaved and show low binding constants. For a nonspecifically bound EcoRI-DNA complex, the free energy of formation is reduced to −4.8kcal/mol. 8,9We measured the permeability of dsDNA in solution with EcoRI ...

Nanobiosensors based on silicon nanowire field effect transistors offer advantages of low cost, label-free detection, and potential for massive parallelization. As a result, these sensors have often been suggested as an attractive option for applications in point-of-care (POC) medical diagnostics. Unfortunately, a number of performance issues, such as gate leakage and current instability due to fluid contact, have prevented widespread adoption of the technology for routine use. High-k dielectrics, such as hafnium oxide (HfO2), have the known ability to address these challenges by passivating the exposed surfaces against destabilizing concerns of ion transport. With these fundamental stability issues addressed, a promising target for POC diagnostics and SiNWFETs has been small oligonucleotides, more specifically, microRNA (miRNA). MicroRNAs are small RNA oligonucleotides which bind to mRNAs, causing translational repression of proteins, gene silencing, and expressions are typically altered in several forms of cancer. In this paper, we describe a process for fabricating stable HfO2 dielectric-based silicon nanowires for biosensing applications. Here we demonstrate sensing of single-stranded DNA analogues to their microRNA cousins using miR-10b and miR-21 as templates, both known to be upregulated in breast cancer. We characterize the effect of surface functionalization on device performance using the miR-10b DNA analogue as the target sequence and different molecular weight poly-l-lysine as the functionalization layer. By optimizing the surface functionalization and fabrication protocol, we were able to achieve <100 fM detection levels of the miR-10b DNA analogue, with a theoretical limit of detection of 1 fM. Moreover, the noncomplementary DNA target strand, based on miR-21, showed very little response, indicating a highly sensitive and highly selective biosensing platform.

We report on the design and demonstration of an optical imaging system capable of exciting surfacebound fluorophores within the resonant evanescent electric field of a photonic crystal surface and gathering fluorescence emission that is directed toward the imaging objective by the photonic crystal. The system also has the ability to quantify shifts in the local resonance angle induced by the adsorption of biomolecules on the photonic crystal surface for label-free biomolecular imaging. With these two capabilities combined within a single detection system, we demonstrate label-free images selfregistered to enhanced fluorescence images with 328× more sensitive fluorescence detection relative to a glass surface. This technique is applied to a DNA microarray where label-free quantification of immobilized capture DNA enables improved quality control and subsequent enhanced fluorescence detection of dye-tagged hybridized DNA yields 3× more genes to be detected versus commercially available microarray substrates.

A series of three-arm star block copolymers were examined using atomic force microscopy (AFM). These stars consisted of a polystyrene core composed of ca. 111 styrene units/branch with poly(ethylene oxide) (PEO) chains at the star periphery. Each star contained different amounts of PEO, varying from 107 to 415 ethylene oxide units/branch. The stars were spread as thin films at the air/water interface on a Langmuir trough and transferred onto mica at various surface pressures. Circular domains representing 2D micelle-like aggregated molecules were observed at low pressures. Upon further compression, these domains underwent additional aggregation in a systematic manner, including micellar chaining. At this point, domain area and the number of molecules/domain increased with increasing pressure. In addition, it was found that longer PEO chains led to greater intermolecular separation and less aggregation. These AFM results correspond to attributes seen in the surface pressure-area isotherms of the stars. In addition, they demonstrate the viability of AFM as a quantitative characterization technique.