Some embodiments described herein relate to a substrate with a surface comprising a silane or a silane derivative covalently attached to optionally substituted cycloalkene or optionally substituted heterocycloalkene for direct conjugation with a functionalized molecule of interest, such as a polymer, a hydrogel, an amino acid, a nucleoside, a nucleotide, a peptide, a polynucleotide, or a protein. In some embodiments, the silane or silane derivative contains optionally substituted norbornene or norbornene derivatives. Method for preparing a functionalized surface and the use in DNA sequencing and other diagnostic applications are also disclosed.

Provided are the nucleic acid-mediated pattern replication and a method of manufacturing a 2-D material using the same. A method of manufacturing a 2-D material according to an embodiment may include preparing a first material having a first nucleic acid patterned on a surface thereof, bonding a linker-nucleic acid to the first nucleic acid, bonding the first nucleic acid and a second nucleic acid attached to a surface of a second material through the linker-nucleic acid and replicating a pattern of the first material to the surface of the second material, separating the first material, and applying a third material on a pattern replicated to the surface of the second material.

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.

A DNA canvas comprising a plurality of uniquely-coded polymer strands immobilized on a substrate can be used to provide a reference map comprising a set of reference association polymers having a dual-barcode generated by nondestructively associating spatially-adjacent polymers on the DNA canvas, encoding digital information on the DNA canvas to provide a patterned DNA canvas by disabling a pattern of selected plurality of polymers strands to provide a set of data association polymers having a single bar code that corresponds to a single bit in the bitmap. The digital information capable of being retrieved by sequencing the set of reference and data association polymers, computationally recovering spatial locations of each of the selected polymer strands that were disabled and recovering the bitmap encoded in the pattern of disabled polymer strands by comparison of the set of reference association polymer sequences to the set of data association polymer sequences.

There is disclosed an electrode array architecture employing continuous and discontinuous circumferential electrodes. There is further disclosed a process for the neutralization of acid generated at anode(s) by base generated at cathode(s) circumferentially located to each other so as to confine a region of pH change. The cathodes can be displayed as concentric rings (continuous) or as counter electrodes in a cross pattern (discontinuous). In this way reagents, such as acid, generated in a center electrode are countered (neutralized) by reagents, such as base, generated at the corners or at the outer ring.

Disclosed herein are formulations, substrates, and arrays for the synthesis of PNA chains and PNA-DNA chimera on microarrays. In some embodiments, the formulations include a photo-protective compound that shields any PNA monomers, PNA polymers, or PNA-DNA chimera already attached to a microarray from radiation exposure during the synthesis of the PNA or PNA-DNA chains. In some embodiments, substrates and arrays comprise a porous or a planar layer for synthesis and attachment of PNA or DNA monomers, or PNA or PNA-DNA polymers. In some embodiments, disclosed herein are formulations and methods for high efficiency coupling of PNA monomers or PNA polymers to a microarray substrate.

Disclosed is a biogel nanosensor for detection of an analyte that includes an acryloyl or methacryloyl modified hydrogel and nucleic acid amplification reagents in picoliter or nanoliter volume in the form of microarray. Also disclosed are methods of making the disclosed biogel nanosensor, and methods of using the biogel nanosensors.

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.

A gene sequencing chip is provided, which includes: an upper substrate including a plurality of liquid inlets for inletting liquid drops; a lower substrate opposite to the upper substrate and spaced therefrom by a gap, the gap being provided for allowing the liquid drops to move therein, the lower substrate including a liquid drop operation region, the liquid drop operation region including a manipulation electrode array. The manipulation electrode array includes multiple first manipulation electrode array for preparing a gene library, multiple second manipulation electrode array for sequencing the gene library which is prepared, each first sub-array being adjacent to one of the multiple second manipulation electrode array. Based on the gene sequencing chip provided in this disclosure, operations to tiny liquid drops such as movement, fusion and splitting can be accurately manipulated by using digital microfluidic techniques, and all steps of the gene sequencing from library preparation to gene sequencing can be completed on one chip.

A gene sequencing chip is provided, which includes: an upper substrate including a plurality of liquid inlets for inletting liquid drops; a lower substrate opposite to the upper substrate and spaced therefrom by a gap, the gap being provided for allowing the liquid drops to move therein, the lower substrate including a liquid drop operation region, the liquid drop operation region including a manipulation electrode array. The manipulation electrode array includes multiple first sub-arrays for preparing a gene library, multiple second sub-arrays for sequencing the gene library which is prepared, each first sub-array being adjacent to one of the multiple second sub-arrays. Based on the gene sequencing chip provided in this disclosure, operations to tiny liquid drops such as movement, fusion and splitting can be accurately manipulated by using digital microfluidic techniques, and all steps of the gene sequencing from library preparation to gene sequencing can be completed on one chip.