Described herein are methods for the synthesis of DNA polynucleotides and polynucleotides, as well as methods for their deprotection and methods for the use of said compounds and compositions comprising said compounds. In particular, such compounds and compositions comprising them are used in methods for light-directed synthesis of DNA microarrays.

Provided are a chip matrix, a sequencing chip, and a manufacturing method thereof. The chip matrix includes: a wafer layer (111), the wafer layer (111) having cutting lines that are evenly distributed thereon; a first silicon oxide layer (112), the first silicon oxide layer (112) being made of silicon oxide and formed on an upper surface of the wafer layer (111); a transition metal oxide layer (113), the transition metal oxide layer (113) being made of transition metal oxide and formed on an upper surface of the first silicon oxide layer (112). The chip matrix has characteristics such as resistances against high temperature, high humidity and other harsh environments. Meanwhile, by changing pH, surfactant and other components of a solution containing sequences to be sequenced, a surface functional region of the chip matrix can specifically adsorb a sequence to be sequenced.

An example of a flow cell includes a substrate, a plurality of chambers defined on or in the substrate, and a plurality of depressions defined in the substrate and within a perimeter of each of the plurality of chambers. The depressions are separated by interstitial regions. Primers are attached within each of the plurality of depressions, and a capture site is located within each of the plurality of chambers.

According to one embodiment of the present invention, a structure includes: a substrate having a patterned surface of one or more binding sites; and a molecular shape made by a polynucleotide platform having a shape corresponding to a shape of a binding site of the one or more binding sites, the molecular shape being bound to one of the one or more binding sites.

High surface area coatings are applied to solid substrates to increase the surface area available for solid-phase synthesis of polymers. The high surface area coatings use three-dimensional space to provide more area for functional groups to bind polymers than an untreated solid substrate. The polymers may be oligonucleotides, polypeptides, or another type of polymer. The solid substrate is a rigid supportive layer made from a material such as glass, a silicon material, a metal material, and plastic. The coating may be thin films, hydrogels, microparticles. The coating may be made from a metal oxide, a high-κ dielectric, a low-κ dielectric, an etched metal, a carbon material, or an organic polymer. The functional groups may be hydroxyl groups, amine groups, thiolate groups, alkenes, n-alkenes, alkalines, N-Hydroxysuccinimide (NHS)-activated esters, polyaniline, aminosilane groups, silanized oxides, oligothiophenes, and diazonium compounds. Techniques for applying coatings to solid substrates and attaching functional groups are also disclosed.

A sequencing system includes an automated sequencing instrument adapted to determine variant calls for one or more extracted polynucleotide samples with a performance of at least 98.5% raw read accuracy and a total instrument run time in a range of 16 hours to 22 hours to determine variant calls when sequencing 6 cfTNA extracted polynucleotide samples using a targeted assay with one nucleic acid pool per sample.

Nucleic acid memory strands encoding digital data using a sequence of a homopolymer tracts of repeated nucleotides provides a cheaper and faster alternative to conventional digital DNA storage techniques. The use of homopolymer tracts allows for lower fidelity, high throughput sequencing techniques such as nanopore sequencing to read data encoded in the memory strands. Specialized synthesis techniques allow for synthesis of long memory strands capable of encoding large volumes of data despite the reduced data density afforded by homopolymer tracts as compared to conventional single nucleotide sequences.

The present invention relates to the field of biochips, and provides a surface linker for a semiconductor chip, a preparation method therefor and an application thereof. The chip surface linker reacts with a chip surface by means of using silanized molecules as a solute and toluene as a solvent so as to form bonding molecules connected to the chip surface, and is prepared by reacting with functionalized molecules to modify a hydroxyl group and an ester group. The chip surface linker obtained by the present invention may be stably bonded to the chip surface, is stable under acidic and alkaline conditions, has good electrical conductivity, electrical stability and resistance to organic solvents required for nucleic acid synthesis, and is extremely advantageous for subsequent nucleic acid.

A method for making on-flow cell three-dimensional polymer structures includes loading a polymer precursor solution onto a flow cell. The polymer precursor solution includes a monomer, a crosslinker, and a photoinitiator. The flow cell includes at least one channel for receiving the polymer precursor solution. The at least one channel has an upper interior surface and a lower interior surface. The method further includes illuminating the polymer precursor solution through a patterned photomask using a light at a wavelength sufficient to activate the photoinitiator. Activation of the photoinitiator polymerizes at least some of the polymer precursor solution underneath apertures in the patterned photomask and forms three-dimensional polymer structures that extend from the upper interior surface to the lower interior surface of the at least one channel.

In a method, a resin layer of a stack (e.g., resin layer over sacrificial layer over transparent substrate) is imprinted to form a convex region including first region with first height and second region with second height <first height. Stack portions are etched around the convex region to expose a substrate portion. The stack is utilized to develop a curable layer to define a cured layer over the exposed substrate portion. The convex region and cured layer are etched. The resin layer and a sacrificial layer portion underlying the second region are removed. A second substrate portion is exposed and a third substrate portion remains covered by a remaining sacrificial layer portion. The cured layer is substantially co-planar with the remaining sacrificial layer portion. A depression is formed extending to the second substrate portion. The remaining sacrificial layer portion is utilized to define functionalized layers over different depression regions.