This invention provides methods of monitoring the expression levels of a multiplicity of genes. The methods involve hybridizing a nucleic acid sample to a high density array of oligonucleotide probes where the high density array contains oligonucleotide probes complementary to subsequences of target nucleic acids in the nucleic acid sample. In one embodiment, the method involves providing a pool of target nucleic acids comprising RNA transcripts of one or more target genes, or nucleic acids derived from the RNA transcripts, hybridizing said pool of nucleic acids to an array of oligonucleotide probes immobilized on surface, where the array comprising more than 100 different oligonucleotides and each different oligonucleotide is localized in a predetermined region of the surface, the density of the different oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2, and the oligonucleotide probes are complementary to the RNA transcripts or nucleic acids derived from the RNA transcripts; and quantifying the hybridized nucleic acids in the array.

Expression monitoring by hybridization to high density oligonucleotide arrays

A direct-write “dip-pen” nanolithography (DPN) has been developed to deliver collections of molecules in a positive printing mode. An atomic force microscope (AFM) tip is used to write alkanethiols with 30-nanometer linewidth resolution on a gold thin film in a manner analogous to that of a dip pen. Molecules are delivered from the AFM tip to a solid substrate of interest via capillary transport, making DPN a potentially useful tool for creating and functionalizing nanoscale devices.

https://science.sciencemag.org/content/sci/283/5402/661.full.pdf

"Dip-Pen" Nanolithography

A synthetic strategy for the creation of large scale chemical diversity. Solid-phase chemistry, photolabile protecting groups, and photolithography are used to achieve light-directed spatially-addressable parallel chemical synthesis. Binary masking techniques are utilized in one embodiment. A reactor system, photoremovable protective groups, and improved data collection and handling techniques are also disclosed. A technique for screening linker molecules is also provided.

Arrays of materials attached to a substrate

A method and apparatus for preparation of a substrate containing a plurality of sequences. Photoremovable groups are attached to a surface of a substrate. Selected regions of the substrate are exposed to light so as to activate the selected areas. A monomer, also containing a photoremovable group, is provided to the substrate to bind at the selected areas. The process is repeated using a variety of monomers such as amino acids until sequences of a desired length are obtained. Detection methods and apparatus are also disclosed.

Very large scale immobilized polymer synthesis

Array of oligonucleotides on a solid substrate

A process for producing metal plated paths on a solid substrate of the kind which has polar functional groups at its surface, utilizing a self-assembling film that is chemically absorbed on the substrate's surface. The solid substrate may, for example, be an insulator of the kind used for substrates in printed circuitry or may, as another example, be a semiconductor of the kind used in semiconductor microcircuitry. The chemical reactivity in regions of the ultra-thin film is altered to produce a desired pattern in the film. A catalytic precursor which adheres only to those regions of the film having enough reactivity to bind the catalyst is applied to the film's surface. The catalyst coated structure is then immersed in an electroless plating bath where metal plates onto the regions activated by the catalyst.

High resolution patterning on solid substrates

With a scanning tunneling microscope (STM) operating in vacuum, we have studied the lithographic patterning of self‐assembling organosilane monolayer resist films. Where the organic group is benzyl chloride, the resist layer can be patterned with electrons down to 4 eV in energy. The patterned films have been used as templates for the electroless plating of thin Ni films. Linewidths down to ∼20 nm have been observed in scanning electron micrographs of the plated films. Still smaller features are observed in STM images of the exposed organosilane films.

Low voltage electron beam lithography in self‐assembled ultrathin films with the scanning tunneling microscope

The surface morphology of a surface-bound colloidal Pd(II) catalyst and its effect on the particle sizes with the largest particles reaching approximately 50 nm in diameter. Catalyst surface coverages as low as 20% are found to be sufficient to initiate complete and homogeneous metallization. The distribution of particle sizes for the electroless metal deposit, found to be a function of plating time, is broad with the maximum Ni particle size exceeding 120 nm. Results indicate controlling the size of the bound catalyst is the principal determining factor in controlling the particle size of the electroless deposit. Modification of the surface by depleting the concentration of surface functional groups capable of binding catalyst is used to shift the size distribution of bound catalyst to smaller values. A resulting three-to fourfold reduction in the particle size of the electroless deposit is demonstrated.

The Morphology of Electroless Ni Deposition on a Colloidal Pd(II) Catalyst

A process for producing metal plated paths on a solid substrate of the kind which has polar functional groups at its surface utilizes a self-assembling monomolecular film that is chemically adsorbed on the substrate's surface. The solid substrate may, for example, be an insulator of the kind used for substrates in printed circuitry or may, as another example, be a semiconductor of the kind used in semiconductor microcircuitry. The chemical reactivity in regions of the ultra-thin film is altered to produce a desired pattern in the film. A catalytic precursor which adheres only to those regions of the film having enough reactivity to bind the catalyst is applied to the film's surface. The catalyst coated structure is then immersed in an electrolers plating bath where metal plates onto the regions activated by the catalyst.

High resolution metal patterning of ultra-thin films on solid substrates

Organosilane precursor molecules, here (aminoethylaminomethyl)phenethyltrimethoxysilane, or PEDA, are chemisorbed onto a Si surface forming a monolayer thick film. These films are patterned using the scanning tunneling microscope to locally modify the chemical reactivity and are then used as a template for selective electroless plating of a thin Ni film. Reactive ion etching in a C2F6/O2 mixture transfers this pattern into the substrate. Improvement over previous lithographic performance is achieved by growing the films on a passivated and lightly oxidized Si surface, optimizing the patterning conditions, and improving the metallization and etch chemistry. In this way, we have generated deep trenches on the order of 15±4 nm width, with edge roughness of 3 nm. We believe this demonstrates the resolution limiting factors of this lithographic process.

Fabrication of 15 nm wide trenches in Si by vacuum scanning tunneling microscope lithography of an organosilane self-assembled film and reactive ion etching

Christie R. K. Marrian

Papers

High resolution patterning on solid substrates

Low voltage electron beam lithography in self‐assembled ultrathin films with the scanning tunneling microscope

The Morphology of Electroless Ni Deposition on a Colloidal Pd(II) Catalyst

High resolution metal patterning of ultra-thin films on solid substrates

Fabrication of 15 nm wide trenches in Si by vacuum scanning tunneling microscope lithography of an organosilane self-assembled film and reactive ion etching