Selecting tag nucleic acids

• US 6,458,530 B1
• Filed: 04/04/1996
• Issued: 10/01/2002
• Est. Priority Date: 04/04/1996
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Shoemaker, Daniel D., Morris, Macdonald S., Davis, Ronald W., Mittmann, Michael P.
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US08/626,285
• Time in Patent Office: 2,371 Days
• Field of Search: 435/6, 435/810, 436/501, 536/23.1, 536/24.1, 536/24.2, 536/24-- 2, 536/25.3, 935/77, 935/78
• US Class Current: 435/6.13
• 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 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/0054 Means for coding or tagging the apparatus or the reagents
• CPC Class Codes: B01J 2219/00542 Alphanumeric characters
• 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 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 Covalent
• 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 2219/00695 Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 70/00 Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes

Abstract

Methods of selecting tag nucleic acids and VLSIPS™ arrays and the arrays made by the methods are used to label and track compositions, including cells and viruses, e.g., in libraries of cells or viruses. In addition to providing a way of tracking compositions in mixtures, the tags facilitate analysis of cell and viral phenotypes.

Claims

1. A method for selecting a set of tag nucleic acids, said method comprising:

(a) providing a plurality of candidate tag nucleic acid sequences, wherein the total number of nucleotides in each tag nucleic acid sequence is identical, the number of G+C nucleotides in each tag nucleic acid sequence is identical and the overall number of A+G nucleotides in each of the tag nucleic acids sequences is even;

(b) aligning a first candidate tag with each of the other candidate tags in the plurality;

(c) excluding the first candidate tag from the plurality if it can be aligned with less than two errors to another candidate tag, wherein an error is either a mismatch hybridization or an overlapping nucleotide,

(d) repeating (b) and (c) for each of the remaining candidate tags in the plurality, thereby providing a set of nucleic acid tags; and

(e) synthesizing at least 100 members of the set of nucleic acid tags.

2. A method for selecting a set of tag nucleic acids, wherein each tag nucleic acid sequence comprises a constant region and a variable region, said method comprising:

(a) providing a plurality of candidate tag nucleic acid sequences;

(b) aligning a selected candidate tag with each of the other candidate tags in the plurality;

(c) excluding the selected candidate tag if it can be aligned with less than two errors in the variable region to another candidate tag, wherein an error is either a mismatch hybridization or an overlapping nucleotide;

(d) repeating (b) and (c) for each of the remaining candidate tags in the plurality, thereby providing a set of nucleic acid tags; and

(e) synthesizing members of the set of nucleic acid tags.

3. A composition comprising a set of tag nucleic acids to individually detect members of a plurality of tagged components in a mixture of tagged components, which set of tag nucleic acid sequences comprises a plurality of at least 100 different tag nucleic acid sequences, which tag nucleic acid sequences comprise a variable region and a constant region;

which variable region for each tag nucleic acid sequence in the set of tag nucleic acid sequences has the same T_m, the same G+C to A+T ratio, the same length, does not cross-hybridize under stringent conditions to any other tag nucleic acid sequence variable region, and does not cross-hybridize under stringent conditions to the complement of any other tag nucleic acid sequence variable region;

wherein the variable regions of the tag nucleic acid sequence in the set of tag nucleic acid sequences cannot be aligned with less than two differences between any two of the tag nucleic acid sequences in the set of tag nucleic acid sequences, and

further wherein each member of the set of nucleic acid tags is comprised of a single nucleic acid sequence from the set of nucleic acid tags.

4. The composition of claim 3, wherein the variable region of each of the tag nucleic acid sequences in the tag nucleic acid sequence set comprises less than two C nucleotides.

5. The composition of claim 3, wherein the variable region of the tag nucleic acid sequence from the set of tag nucleic acid sequences comprises an even number of A+G nucleotides.

6. A set of at least 100 different tag nucleic acids selected according to the mothod of 104.

7. A set of at least 100 different tag nucleic acids wherein each member of the set:

(a) does not have a region of complementarity with any other member of the set greater than four nucleotides;

(b) does not have a selected length of contiguous nucleotides in common with any other tag nucleic acid sequence in the set, wherein the length is selected from the following;

5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15;

(c) has greater than 5 differences out of 20 nucleotides when aligned for maximal sequence correspondence with any other tag nucleic acid sequence in the set, and

(d) does not have four contiguous nucleotides selected from the group consisting of four X residues, four Y residues and four Z residues, wherein X is G or C, Y is G or A, and Z is A or T, and

(e) each member of the set of tag nucleic acids is comprised of a single nucleic acid sequence from the set of nucleic acid tags.

8. A set of at least 100 different tag nucleic acids wherein:

(a) no two members of the set can be aligned with less than two errors, wherein an error is either a mismatch hybridization or an overhanging nucleotide;

(b) the total number of nucleotides in each tag nucleic acid sequence is identical;

(c) the number of G+C nucleotides in each tag nucleic acid sequence is identical;

(d) the overall number of A+G nucleotides in each of the of the tag nucleic acid sequences is even; and

(e) each member of the set of tag nucleic acids is comprised of a single nucleic acid sequence from the set of nucleic acid tags.

9. A set of tag nucleic acids according to claim 8, wherein each tag nucleic acid sequence comprises a constant region and a variable region, wherein no two members of the set can be aligned with less than two errors in the variable region, wherein an error is either a mismatch hybridization or an overhanging nucleotide and each member of the set of tag nucleic acids is comprised of a single nucleic acid sequence from the set of nucleic acid tags.

10. The set of tag nucleic acids of claim 9, wherein:

(a) the total number of nucleotides in each tag nucleic acid sequence is identical;

(b) the number of G+C nucleotides in each tag nucleic acid sequence is identical; and

,

(c) the overall number of A+G nucleotides in each of the variable regions of the tag nucleic acid sequences is even, and

(d) each member of the set of tag nucleic acids is comprised of a single nucleic acid sequence from the set of nucleic acid tags.