Methods and compositions are disclosed relating to the localization of nucleic acids to arrays such as silane-free arrays, and of sequencing the nucleic acids localized thereby.

Systems and methods for the formation of single-analyte arrays are described. Array sites are formed via the patterning of surface-linked organic layers by electromagnetic radiation. Each array site may be modified after patterning to produce a chemistry at the array site that facilitates the controlled deposition of a single analyte at the array site.

The invention provides a novel array method for nucleic acid sequence detection with improved specificity which allows for detection of genetic variation, from simple SNPs (where the variation occurs at a fixed position and is of limited allelic number) to more complex sequence variation patterns (such as with multigene families or multiple genetic strains of an organism where the sequence variation between the individual members is neither fixed nor consistent). The array is comprised of short, synthetic oligonucleotide probes attached to a solid surface which are hybridized to single-stranded targets. Single stranded targets can be produced using a method that employs primers modified on the 5′ end to prohibit degradation by a 5′-exonuclease that is introduced to degrade the unprotected strand. The invention further provides for printing buffers/solutions for the immobilization of oligonucleotide probes to an array surface. The invention also provides hybridization and wash buffers and conditions to maximize hybridization specificity and signal intensity, and reduce hybridization times.

This invention relates generally to the field of nucleic acid detection. In particular, the invention provides a lab-on-chip system for analyzing a nucleic acid, which system comprises, inter alia, controllably closed space, and a target nucleic acid can be prepared and/or amplified, and hybridized to a nucleic acid probe, and the hybridization signal can be acquired if desirable, in the controllably closed space without any material exchange between the controllably closed space and the outside environment. Methods for analyzing a nucleic acid using the lab-on-chip system is also provided.

An apparatus and method for performing analysis and identification of molecules have been presented. In one embodiment, a portable molecule analyzer includes a sample input/output connection to receive a sample, a nanopore-based sequencing chip to perform analysis on the sample substantially in real-time, and an output interface to output result of the analysis.

An example of a flow cell includes a substrate; a first primer set attached to a first region on the substrate, the first primer set including an un-cleavable first primer and a cleavable second primer; and a second primer set attached to a second region on the substrate, the second primer set including a cleavable first primer and an un-cleavable second primer.

Method for immobilization of a labeled oligonucleotide on a non-modified polymer substrate, the method comprising the following steps: a) providing a mixture comprising liquid, and a labeled oligonucleotide b) applying the mixture of step a) on a non-modified polymer substrate, wherein the oligonucleotide is immobilized on the non-modified polymer substrate via physisorption conveyed by the label of the oligonucleotide and wherein the label for immobilization is covalently bound to the oligonucleotide; and microarrays achieved by this method. The invention further relates to the use of a label attached to an oligonucleotide for immobilization of the labeled oligonucleotide on a non-modified polymer substrate by physisorption. Furthermore the invention relates to the use of the microarrays achieved by the method describe herein for assays and diagnostic kits comprising such microarrays.

The invention provides a method for immobilization of biological molecules such as nucleic acids, peptides and proteins onto the surface of a glass or plastic solid support.

Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducial markers may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducial markers may include features and materials that are provided on or in the support of a patterned array and that return at least a portion of incident light by reflection. The fiducial markers may form gratings or other encoding configurations that assist in image processing, alignment, or other aspects of processing of the patterned array.

A device for synthesis of macromolecules is disclosed. In one aspect, the device comprises an ion-releaser having a synthesis surface comprising an array of synthesis locations arranged for synthesis of the macromolecules. The ion-releaser also includes an ion-source electrode, which is arranged to contain releasable ions and is arranged to be in contact with each of the synthesis locations of the synthesis surface, thereby release ions to the synthesis locations. The ion-releaser further comprises activating electrodes, which are arranged to be in contact with the ion-source electrode, wherein each one of the activating electrodes is arranged in association with one of the synthesis locations via the ion-source electrode. The ion-releaser is arranged to release at least a portion of the releasable ions from the ion-source electrode to one of the synthesis locations, by activation of the activating electrode associated with the synthesis location.