Illumination systems for nucleic acid sequencing
Patent Information
- Authority / Receiving Office
- HK · HK
- Patent Type
- Applications
- Current Assignee / Owner
- ELEMENT BIOSCIENCES INC
- Filing Date
- 2026-04-16
- Publication Date
- 2026-07-10
Smart Images
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Abstract
Description
Translation 61492 Title: Illumination System for Nucleic Acid Sequencing Abstract This disclosure describes illumination methods and systems that can be used for illumination and sequencing applications such as microscopy and sequencing platforms. The methods and systems disclosed in this invention can provide large-area, flat illumination, thereby reducing errors and increasing system throughput.
Claims
CLAIMSWhat Is Claimed Is:
1. An optical system, comprising: a stage configured to hold a solid support; a light source configured to illuminate said solid support; and an optical assembly disposed at least partly within an optical path from said stage to said light source, wherein said optical assembly is configured to provide an illumination over an area of said solid support that is greater than about 20 square millimeters (mm2) with a peak-to-valley variation of at most about 5%.
2. The optical system of claim 1, wherein said optical assembly does not comprise an objective.
3. The optical system of claim 2, wherein said optical system does not comprise said objective.
4. The optical system of claim 1, wherein said optical assembly does not comprise a tube lens.
5. The optical system of claim 4, wherein said optical system does not comprise said tube lens.
6. The optical system of claim 1, wherein said stage does not adjust in an optical axis of said system.
7. The optical system of claim 1, wherein said illumination has an irradiance of at least about 40 milliwatts per square millimeter.
8. The optical system of claim 1, wherein said optical assembly is configured to receive an emission light from said solid support.
9. The optical system of claim 8, wherein said optical assembly has a numerical aperture (NA) of at least about 0.3.
10. The optical system of claim 8, wherein said emission light has a wavelength of about 500 nanometers to about 750 nanometers.
11. The optical system of claim 1, wherein said optical assembly has a working distance of at least about 1mm to 25mm.
12. The optical system of claim 1, further comprising a motion coil housed within said optical assembly configured to move a focusing element within said optical path of said optical system.
13. The optical system of claim 1, wherein a motor external to said optical system is configured to move a focusing element along the optical axis in one or both directions.
14. The optical system of claim 13, wherein said motor is coupled directly with a piece of a first, second, or third housing of said optical assembly, and the piece of the first, second, or third housing of said optical assembly is coupled directly with said focusing element.
15. The optical system of claim 1, wherein said light source is a pulsed light source.
16. The optical system of claim 1, wherein said optical system has a composite root mean square error of less than about 0.05.
17. The optical system of claim 1, wherein said optical assembly has an illumination efficiency of at least about 90%.
18. The optical system of claim 1, wherein said area is greater than 30 mm2.
19. The optical system of claim 1, wherein said area is greater than 50 mm2or 60 mm2.
20. The optical system of claim 1, further comprising said solid support within said stage.
21. The optical system of claim 20, wherein said solid support comprises two or more surfaces having one or more samples immobilized thereon which are imaged by said optical system.
22. The optical system of claim 21, wherein said solid support comprises three or more surfaces having one or more samples immobilized thereon imaged by said optical system.
23. The optical system of claim 22, wherein said three or more surfaces are axially displaced from each other at least along an optical axis of said optical system.
24. The optical system of claim 20, wherein said solid support comprises a probe configured to bind a nucleic acid molecule.
25. The optical system of claim 24, wherein said probe is bound to a surface of said solid support.
26. The optical system of claim 1, wherein said light source is a laser light source.
27. The optical system of claim 1, wherein said optical assembly comprises a dichroic filter configured to transmit said illumination.
28. The optical system of claim 1, wherein said optical assembly comprises a first segment comprising a first housing comprising a first plurality of lenses, a second segment comprising a second housing, and a third segment comprising a third housing comprising a second plurality of lenses.
29. The optical system of claim 28, wherein said first segment and said third segment are optically aligned.
30. The optical system of claim 28, wherein said first segment is positioned between said third segment and said stage.
31. The optical system of claim 28, wherein said third segment is positioned between said first segment and an image sensor of the optical system.
32. The optical system of claim 28, wherein said first plurality of lenses are movable along said optical path with a range of about 0 to about 2 millimeters.
33. The optical system of claim 28, wherein said first plurality of lenses comprises an asymmetric convex-convex lens.
34. The optical system of claim 28, wherein said second plurality of lenses comprises an asymmetric concave-concave lens.
35. The optical system of claim 34, wherein said asymmetric concave-concave lens is an aspheric asymmetric concave-concave lens.
36. The optical system of claim 1, wherein said optical system is configured to acquire images of said solid support without moving an optical compensator into the optical path between said solid support and a detector of the optical system.
37. The optical system of claim 1, wherein said optical system is configured to acquire images of said solid support without moving an optical compensator out from the optical path between the sample and a detector of the optical system.
38. The optical system of claim 1, wherein said solid support is a flow cell.
39. The optical system of claim 1, wherein said optical assembly is configured to generate one or more spatial constrictions lateral to said optical path of light which travels therethrough.
40. The optical system of claim 1, wherein said optical assembly is configured to generate one or more field curvature corrections lateral to said optical path of light which travels therethrough.
41. The optical system of claim 1, wherein said optical assembly is configured to generate at least one field curvature correction lateral to the optical path of light travels therethrough in a first segment, second segment, or third segment.
42. A method of analyzing a biological molecule, comprising:(a) providing a solid support comprising said biological molecule comprising a label;(b) using an optical system comprising a light source to provide illumination to said biological molecule comprising said label, thereby generating a signal light or a change thereof, wherein said illumination is provided over an area of said solid support that is greater than about 20 square millimeters (mm2) with a peak-to-valley variation of at most about 5%;(c) detecting, using a detector of said optical system, said signal light or said change thereof; and(d) processing at least in part said signal light or said change thereof to analyze said biological molecule.
43. The method of claim 42, wherein said biological molecule is a nucleic acid molecule, a protein, or a polypeptide.
44. The method of claim 43, wherein said biological molecule is a nucleic acid.
45. The method of claim 42, further comprising, prior to (a), binding said biological molecule to a probe bound to said solid support, and coupling said label to said biological molecule.
46. The method of claim 42, wherein said label is coupled to said biological molecule by hybridization.
47. The method of claim 42, wherein said optical system does not comprise an objective.
48. The method of claim 42, wherein said solid support is not moved in an optical axis of said optical system.
49. The method of claim 48, wherein a plurality of images of said solid support are acquired without moving said solid support in said optical axis.
50. The method of claim 42, wherein said illumination has an irradiance of at least about 40 milliwatts per square millimeter.
51. The method of claim 42, wherein said signal light has a wavelength of about 500 nanometers to about 750 nanometers.
52. The method of claim 42, wherein said detecting of (c) is performed using an optical element with a numerical aperture of at least about 0.3.
53. The method of claim 42, further comprising, in (b), using a motion coil within said optical system to move a focusing element within an optical path of said optical system, thereby changing a focus of said optical system on said solid support.
54. The method of claim 42, wherein said light source is a pulsed light source.
55. The method of claim 42, wherein said illumination is provided with an efficiency of at least about 90%.
56. The method of claim 42, further comprising repeating (b) - (d) for an additional biological molecule coupled to an additional surface of said solid support.
57. The method of claim 42, further comprising, subsequent to (c), removing said label from said biological molecule.
58. The method of claim 57, further comprising repeating (a) - (d) for an additional label that binds to another portion of the biological molecule.
59. The method of claim 42, wherein an optical assembly is configured to generate one or more spatial constrictions lateral to said optical path of light which travels therethrough.
60. The method of claim 42, wherein an optical assembly is configured to generate one or more field curvature corrections lateral to said optical path of light which travels therethrough.
61. The method of claim 42, wherein an optical assembly is configured to generate at least one field curvature correction lateral to the optical path of light that travels therethrough in a first segment, second segment, or third segment.
62. The method of claim 42, wherein (d) comprises processing, at least in part, said signal light or said change thereof to generate one or more solid support images and analyze said one more solid support images to generate base calls of the sample.
63. The method of claim 62, wherein each of said solid support images comprises a field-of- view (FOV) that is greater than 20 square millimeters (mm2).
64. The method of claim 42, wherein said solid support is a flow cell.
65. An optical system, comprising: a stage configured to hold a solid support; a light source configured to illuminate said solid support; and a despeckler optically coupled to said light source and disposed within an optical path from said light source to said stage.
66. The optical system of claim 65, further comprising an additional light source optically coupled into said despeckler.
67. The optical system of claim 66, wherein light from said additional light source is configured to illuminate said solid support with a different wavelength of light from said light source.
68. The optical system of claim 66, wherein at least about 4 light sources are coupled into said despeckler.
69. The optical system of claim 65, wherein said despeckler is a vibrational despeckler.
70. The optical system of claim 65, wherein said despeckler is a passive despeckler.
71. The optical system of claim 70, wherein said passive despeckler comprises a diffuse scattering plate.
72. The optical system of claim 65, wherein said despeckler is a tension despeckler.
73. The optical system of claim 65, wherein said despeckler is configured to reduce speckle noise to at most about 5%.
74. The optical system of claim 65, wherein said solid support is a flow cell.
75. A method for analyzing a biological molecule, comprising:(a) providing a solid support comprising a biological sample comprising a label;(b) using an optical system comprising a light source to provide illumination to said biological sample comprising said label, thereby generating a signal light or a change thereof, wherein said illumination is provided through a despeckler in an optical path of said optical system;(c) detecting, using a detector of said optical system, said signal light or said change thereof; and(d) processing at least in part said signal light or said change thereof to analyze said biological molecule.
76. The method of claim 75, further comprising repeating (b) - (d) for an additional biological sample coupled to an additional surface of said solid support.
77. The method of claim 75, further comprising, subsequent to (c), removing said label from said biological sample.
78. The method of claim 77, further comprising repeating (a) - (d) for an additional label that binds to said biological sample.
79. The method of claim 75, wherein said despeckler uses vibration to despeckle said illumination.
80. The method of claim 75, further comprising using an additional light source to illuminate said solid support.
81. The method of claim 80, wherein said additional light source provides a different wavelength of light to said solid support.
82. The method of claim 80, wherein said additional light source is optically coupled to said despeckler.
83. The method of claim 75, wherein said biological sample comprises a nucleic acid molecule, a protein, or a polypeptide.
84. The method of claim 83, wherein said biological sample comprises a nucleic acid.
85. The optical system of claim 1, wherein the optical assembly is disposed at least partly within an optical path from said stage to a detector of the optical system.
86. The optical system of claim 1, wherein an illumination system of the optical assembly is disposed within an optical path from said stage to a detector of the optical system.
87. A sample stage for holding DNA samples for DNA sequencing reactions and imaging, comprising: a base stage comprising a top surface, wherein the base stage is rotatable about a z-axis relative to an optical system of a sequencing system; one or more top stages positioned on the top surface of the base stage, wherein each of the one or more top stages are configured to receive and secure one or more flow cell devices thereon, and wherein said each of the one or more top stages are movable relative to the base stage; a first motor configured to actuate the base stage to rotate with a first resolution.The sample stage of any one of the preceding claims, Wherein the top surface is of a circular shape.
88. The sample stage of any one of the preceding claims, wherein the first resolution is angular resolution and less than 0.1 degrees, 0.2 degrees 0.5 degrees, 1 degree, 2 degrees, 3 degrees, 4 degrees, 5 degrees, 10 degrees, 20 degrees, 30 degrees, or 50 degrees.
89. The sample stage of any one of the preceding claims, wherein each of the flow cell devices comprises one or more samples immobilized thereon to be sequenced.
90. The sample stage of any one of the preceding claims, wherein at least one of the flow cell devices comprises an in situ sample immobilized thereon.
91. The sample stage of any one of the preceding claims, wherein the sample stage further comprises one or more second motors configured to actuate the one or more top stages relative to the base stage at a second resolution individually.
92. The sample stage of any one of the preceding claims, wherein the sample stage further comprises a second motor configured to acuate the one or more top stages relative to the base stage at a second resolution simultaneously.
93. The sample stage of any one of the preceding claims, wherein the second resolution is less than 0.01 mm, 0.015 mm, 0.02 mm, 0.03 mm, 0.04 mm, 0.05 mm, 0.08 mm, 0.1 mm, 0.2 mm, or 1 mm.
94. The sample stage of any one of the preceding claims, wherein the sequencing system comprises a fluidic control device in fluidic communication with the flow cell devices positioned on the sample stage.
95. The sample stage of any one of the preceding claims, wherein said each of the one or more top stages are movable within a sample plane relative to the base stage.
96. The sample stage of any one of the preceding claims, wherein a first top stage of the one or more top stages is movable independently relative to a second top stage of the one or more top stages.
97. The sample stage of any one of the preceding claims, wherein a first top stage of the one or more top stages is movable simultaneously with a second top stage of the one or more top stages relative to the base stage.
98. The sample stage of any one of the preceding claims, wherein said each of the one or more top stages are movable along a radius of the top surface of the base stage relative to the base stage.
99. The sample stage of any one of the preceding claims, wherein said each of the one or more top stages are movable orthogonal to a radius of the top surface of the base stage relative to the base stage.
100. A method of sequencing multiple DNA samples positioned on a rotary sample stage, comprising: obtaining a sample stage comprising a base stage and one or more top stages positioned on a top surface of the base stage, wherein the base stage is rotatable about a z-axis relative to an optical system of a sequencing system; positioning and securing a first flow cell device relative to a first top stage of the one or more top stages;positioning and securing a second flow cell device relative to a second top stage of the one or more top stages; dispensing, by a first fluidic control device, one or more sequencing reagents to the first flow cell device; imaging a first sample region of the first flow cell device using the optical system of the sequencing system; moving the first top stage within the x-y plane relative to the optical system while preventing the second flow cell device from moving relative to the optical system; imaging a second sample region of the first flow cell device using the optical system of the sequencing system; rotating the sample stage with a predetermined angular resolution to position the second flow cell device in a predetermined position relative to the optical system; and imaging a first sample region of the second flow cell device using the optical system of the sequencing system.
101. The method of any one of the preceding claims, Wherein moving the first top stage within the x-y plane relative to the optical system while preventing the second flow cell device from moving relative to the optical system comprises: moving the first top stage along a radius of the top surface of the base stage with a predetermined distance relative to the optical system independently while preventing the second flow cell device from moving relative to the optical system.
102. The method of any one of the preceding claims, wherein moving the first top stage within the x-y plane relative to the optical system while preventing the second flow cell device from moving relative to the optical system comprises: moving the first top stage along a direction orthogonal to a radius of the top surface of the base stage with a predetermined distance relative to the optical system independently while preventing the second flow cell device from moving relative to the optical system.
103. The method of any one of the preceding claims, wherein the method further comprises: moving the first fluidic control device or a second fluidic control device to position the second fluidic cell device in a predetermined position relative to the first fluidic control device or the second fluidic control device.
104. The method of any one of the preceding claims, wherein the first sample region or the second sample region comprises a tile.
105. The method of any one of the preceding claims, wherein each of the one or more top stages comprises a motion range of greater than 15 mm and less than 80 mm, along a radius or orthogonal to the radius of the top surface of the base stage.
106. The method of any one of the preceding claims, wherein each of the one or more top stages comprises a motion range of greater than 25 mm and less than 100 mm, along a radius or orthogonal to the radius of the top surface of the base stage.