Apparatus for treatment of light-sensitive biopolymers

• US 20110065611A1
• Filed: 07/08/2010
• Published: 03/17/2011
• Est. Priority Date: 08/25/2004
• Status: Abandoned Application

• Current Assignee: Flexgen Technologies B.V. (Piculet Biosciences BV)
• Original Assignee: Flexgen Technologies B.V. (Piculet Biosciences BV)
• Inventors: Van Helvoort, Johannes Martinus Lambertus Maria, Heemskerk, Cornelis Jacobus Maria, Matysiak, Stefan Matthias
• Application Number:
  US12/803,860
• Publication Number:
  US 20110065611A1
• Time in Patent Office: Days
• US Class Current: 506/30
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00439 using micromirror arrays
• CPC Class Codes: B01J 2219/00441 using lasers
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00639 the compounds being trapped in or bound to a porous medium
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 for creating libraries

Abstract

A method of fabricating a device comprising an array of test locations defined on a substrate with each test location comprising one or more identical oligonucleotides affixed to the substrate. The method comprises the steps of:

• • (1) identifying a nucleotide type to be attached at a particular test location in order to construct the one or more identical oligonucleotides at that test location and determining one or both of an illumination intensity and an illumination duration for a laser light source;
  • (2) directing a laser beam generated by the laser light source and having the determined intensity and/or duration at a mirror, the position of the mirror having been set so as to redirect the laser beam towards said test location, such that removal of a protective group or groups at the test location is achieved;
  • (3) attaching a nucleotide or nucleotides of said nucleotide type at the test location; and
  • (4) repeating said steps (1) to (3) at a plurality of test locations across the array in order to construct the required oligonucleotide(s) at each test location.

Claims

1. A method of fabricating a device comprising an array of test locations defined on a substrate with each test location comprising one or more identical oligonucleotides affixed to the substrate, the method comprising:

(1) identifying a nucleotide type to be attached at a particular test location in order to construct the one or more identical oligonucleotides at that test location and determining one or both of an illumination intensity and an illumination duration for a laser light source;

(2) directing a laser beam generated by the laser light source and having the determined intensity and/or duration at a mirror, the position of the mirror having been set so as to redirect the laser beam towards said test location, such that removal of a protective group or groups at the test location is achieved;

(3) attaching a nucleotide or nucleotides of said nucleotide type at the test location; and

(4) repeating said steps (1) to (3) at a plurality of test locations across the array in order to construct the required oligonucleotide(s) at each test location.

2. A method according to claim 1, wherein said step of determining one or both of an illumination intensity and an illumination duration for that nucleotide type takes into account the nucleotide type to be attached.

3. A method according to claim 1, wherein said step of determining one or both of an illumination intensity and an illumination duration for that nucleotide type takes into account a relative location of the test location on the substrate.

4. A method according to claim 1, wherein said step of determining one or both of an illumination intensity and an illumination duration for that nucleotide type takes into account an identity of a nucleotide previously attached at said test location.

5. A method according to claim 1 and comprising a further step of selecting one of two or more available lasers for generating said laser beam, the lasers being configured to generate laser beams having different wavelengths.

6. A method according to claim 1, wherein the orientation of said mirror is adjusted in order to step the laser beam across the substrate, the movement of the mirror being synchronised with steps (1) and (2).

7. A method according to claim 1, wherein said protective group(s) is(are) a photolabile group or groups.

8. Apparatus for fabricating a device comprising an array of test locations defined on a substrate with each test location comprising one or more identical oligonucleotides affixed to the substrate, the apparatus comprising:

a laser light source for generating a laser beam;

an illumination controller for determining one or both of an illumination intensity and an illumination duration for a given test location, and for controlling the laser light source accordingly to generate a laser beam;

a mirror; and

a scan controller for setting the position of the mirror so as to redirect the laser beam towards said test location.

9. Apparatus according to claim 8, said illumination controller being further configured to identify a nucleotide type to be attached at said given test location in order to construct the one or more identical oligonucleotides at that test location, and to determine one or both of said illumination intensity and said illumination duration taking into account the identity of the nucleotide type.

10. Apparatus according to claim 8 and comprising at least two laser light sources configured to operate at respective different wavelengths, said illumination controller being configured to select one of the available laser light sources to illuminate a given test location.

11. A method of fabricating a device comprising an array of test locations defined on a substrate with each test location comprising two or more different oligonucleotide types affixed to the substrate, the method comprising, for a given test location:

(1) identifying an oligonucleotide type for which a nucleotide addition is to be made;

(2) selecting a laser light source from a set of two or more available laser light sources in dependence upon the identified oligonucleotide type;

(3) activating the selected laser light source and directing a laser beam at a mirror, the position of the mirror having been set so as to redirect the laser beam towards said test location, such that removal of a protective group or groups at the test location is achieved;

(4) attaching a nucleotide or nucleotides at the test location; and

(5) repeating steps (1) to (4) in respect of a further oligonucleotide type, step (2) comprising selecting a second of the available laser light sources;

repeating said steps (1) to (5) at a plurality of test locations across the array in order to construct the required different oligonucleotide(s) types at each test location.

12. A method according to claim 11 and comprising, for each test location and for each identified oligonucleotide type, identifying one or both of an illumination intensity and an illumination duration, and activating the selected laser light source accordingly.

13. Apparatus for fabricating a device comprising an array of test locations defined on a substrate with each test location comprising two or more different oligonucleotide types affixed to the substrate, the apparatus comprising:

two or more laser light sources for generating a laser beam;

an illumination controller for identifying an oligonucleotide type for which a nucleotide addition is to be made at a given test location, for selecting a laser light source from said two or more available lasers in dependence upon the identified oligonucleotide type, and for controlling the laser light source accordingly to generate a laser beam;

a mirror; and

a scan controller for setting the position of the mirror so as to redirect the laser beam towards said test location.

14. Apparatus according to claim 13 and comprising a process chamber for receiving a substrate on which said oligonucleotides are to be formed, and one or more conduits for introducing nucleotides into the process chamber.