Patterned flow-cells useful for nucleic acid analysis
First Claim
1. A method of making an analyte array, comprising(a) providing a surface comprising mask regions and transparent regions, the mask regions having a composition that blocks transmittance of radiation in a first part of the electromagnetic spectrum and transparent regions having a composition that transmits radiation in the first part of the electromagnetic spectrum, wherein a continuous gel layer coats the surface across the mask regions and the transparent regions;
- (b) contacting the continuous gel layer with a fluid comprising a population of different analytes under conditions wherein analytes from the population become attached to the gel layer and wherein a first subpopulation of the analytes attach to portions of the gel layer that coat the mask regions and a second subpopulation of the analytes attach to portions of the gel layer that coat the transparent regions; and
(c) irradiating the surface with radiation in the first part of the electromagnetic spectrum, thereby selectively modifying the analytes of one of the subpopulations compared to the analytes of the other subpopulation,wherein the selectively modifying comprises selectively removing the analytes of the second subpopulation compared to the analytes of the first subpopulation.
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Abstract
Provided is a surface having metal regions and an interstitial region having a composition that differs from the metal regions, wherein a continuous gel layer coats the surface across the metal regions and the interstitial regions. Nucleic acids or other analytes can be attached to the continuous gel layer such that a greater amount is attached over the metal regions than over the interstitial region. Also provided are methods for making such surfaces. Methods are also provided for making an array of nucleic acids or other analytes using such surfaces.
155 Citations
34 Claims
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1. A method of making an analyte array, comprising
(a) providing a surface comprising mask regions and transparent regions, the mask regions having a composition that blocks transmittance of radiation in a first part of the electromagnetic spectrum and transparent regions having a composition that transmits radiation in the first part of the electromagnetic spectrum, wherein a continuous gel layer coats the surface across the mask regions and the transparent regions; -
(b) contacting the continuous gel layer with a fluid comprising a population of different analytes under conditions wherein analytes from the population become attached to the gel layer and wherein a first subpopulation of the analytes attach to portions of the gel layer that coat the mask regions and a second subpopulation of the analytes attach to portions of the gel layer that coat the transparent regions; and (c) irradiating the surface with radiation in the first part of the electromagnetic spectrum, thereby selectively modifying the analytes of one of the subpopulations compared to the analytes of the other subpopulation, wherein the selectively modifying comprises selectively removing the analytes of the second subpopulation compared to the analytes of the first subpopulation. - View Dependent Claims (2, 3, 4, 11)
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5. A method of making an analyte array, comprising
(a) providing a surface comprising mask regions and transparent regions, the mask regions having a composition that blocks transmittance of radiation in a first part of the electromagnetic spectrum and transparent regions having a composition that transmits radiation in the first part of the electromagnetic spectrum, wherein a continuous gel layer coats the surface across the mask regions and the transparent regions; -
(b) contacting the continuous gel layer with a fluid comprising a population of different analytes under conditions wherein analytes from the population become attached to the gel layer and wherein a first subpopulation of the analytes attach to portions of the gel layer that coat the mask regions and a second subpopulation of the analytes attach to portions of the gel layer that coat the transparent regions; and (c) irradiating the surface with radiation in the first part of the electromagnetic spectrum, thereby selectively modifying the analytes of one of the subpopulations compared to the analytes of the other subpopulation, wherein the analytes comprise nucleic acids, further comprising amplifying the nucleic acids on the portions of the gel layer that coat the mask regions. - View Dependent Claims (6, 7, 8, 9, 10)
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12. A method of making an analyte array, comprising
(a) providing a surface comprising mask regions and transparent regions, the mask regions having a composition that blocks transmittance of radiation in a first part of the electromagnetic spectrum and transparent regions having a composition that transmits radiation in the first part of the electromagnetic spectrum, wherein a continuous gel layer coats the surface across the mask regions and the transparent regions; -
(b) contacting the continuous gel layer with a fluid comprising a population of different analytes under conditions wherein analytes from the population become attached to the gel layer and wherein a first subpopulation of the analytes attach to portions of the gel layer that coat the mask regions and a second subpopulation of the analytes attach to portions of the gel layer that coat the transparent regions; and (c) irradiating the surface with radiation in the first part of the electromagnetic spectrum, thereby selectively modifying the analytes of one of the subpopulations compared to the analytes of the other subpopulation, wherein the surface of the mask regions comprise metal, thereby forming metal regions on the surface. - View Dependent Claims (14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34)
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13. A method of making an analyte array, comprising
(a) providing a surface comprising mask regions and transparent regions, the mask regions having a composition that blocks transmittance of radiation in a first part of the electromagnetic spectrum and transparent regions having a composition that transmits radiation in the first part of the electromagnetic spectrum, wherein a continuous gel layer coats the surface across the mask regions and the transparent regions; -
(b) contacting the continuous gel layer with a fluid comprising a population of different analytes under conditions wherein analytes from the population become attached to the gel layer and wherein a first subpopulation of the analytes attach to portions of the gel layer that coat the mask regions and a second subpopulation of the analytes attach to portions of the gel layer that coat the transparent regions; and (c) irradiating the surface with radiation in the first part of the electromagnetic spectrum, thereby selectively modifying the analytes of one of the subpopulations compared to the analytes of the other subpopulation, wherein the surface is located in a flow-cell.
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18. A method of making a nucleic acid array, comprising
(a) providing a surface comprising metal regions and interstitial regions, the interstitial regions having a composition that differs from the metal regions, wherein a continuous gel layer coats the surface across the metal regions and the interstitial regions; -
(b) contacting the continuous gel layer with a fluid comprising analytes; and (c) selectively modifying the portions of the gel layer that coat the interstitial regions compared to the portions of the gel layer that coat the metal regions, thereby attaching the analytes to the gel layer, wherein a greater amount of the analytes from the fluid attach to portions of the gel layer that coat the metal regions than the amount of analytes that attach to portions of the gel layer that coat the interstitial regions. - View Dependent Claims (21, 22, 23, 24, 25, 26, 27)
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19. A method of making a nucleic acid array, comprising
(a) providing a surface comprising metal regions and interstitial regions, the interstitial regions having a composition that differs from the metal regions, wherein a continuous gel layer coats the surface across the metal regions and the interstitial regions; - and
(b) contacting the continuous gel layer with a fluid comprising analytes under conditions wherein the analytes become attached to the gel layer and wherein a greater amount of the analytes from the fluid attach to portions of the gel layer that coat the metal regions than the amount of analytes that attach to portions of the gel layer that coat the interstitial regions, wherein the analytes comprise nucleic acids, further comprising removing the metal regions from the surface under conditions wherein the nucleic acids remain attached to the gel layer on the surface. - View Dependent Claims (20)
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Specification