Nucleic acid affinity columns

• US 6,013,440 A
• Filed: 03/10/1997
• Issued: 01/11/2000
• Est. Priority Date: 03/11/1996
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Lipshutz, Robert J., Chee, Mark S., Gingeras, Thomas R., Morris, MacDonald S.
• Primary Examiner(s): Horlick, Kenneth R.
• Application Number:
  US08/815,395
• Time in Patent Office: 1,037 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 435/183, 435/270, 536/23.1, 536/24.3, 536/24.33, 536/25.3, 536/25.4, 935/8, 935/76, 935/77, 935/78
• US Class Current: 506/7
• 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 2219/00619 using hydrophilic or hydrophobic regions
• 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 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2565/107 Alteration in the property of hybridised versus free label oligonucleotides
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof

Abstract

This invention provides nucleic acid affinity matrices that bear a large number of different nucleic acid affinity ligands allowing the simultaneous selection and removal of a large number of preselected nucleic acids from the sample. Methods of producing such affinity matrices are also provided. In general the methods involve the steps of a) providing a nucleic acid amplification template array comprising a surface to which are attached at least 50 oligonucleotides having different nucleic acid sequences, and wherein each different oligonucleotide is localized in a predetermined region of said surface, the density of said oligonucleotides is greater than about 60 different oligonucleotides per 1 cm², and all of said different oligonucleotides have an identical terminal 3'"'"' nucleic acid sequence and an identical terminal 5'"'"' nucleic acid sequence. b) amplifying said multiplicity of oligonucleotides to provide a pool of amplified nucleic acids; and c) attaching the pool of nucleic acids to a solid support.

Claims

1. A method of making a nucleic acid affinity matrix for removing known nucleic acid molecules in a sample, said method comprising the steps of:

i) providing a multiplicity of nucleic acid probes selected such that for each of said known nucleic acid molecules there exists in said multiplicity a probe sufficiently complementary to said nucleic molecule or a subsequence thereof to hybridize thereto under stringent conditions, and wherein said multiplicity of probes does not include every possible probe having the same length as said probe;

ii) attaching said probes to a solid support;

iii) contacting the multiplicity of probes with the sample, whereby the known nucleic acid molecules hybridize to the multiplicity of probes; and

iv) analyzing a nucleic acid molecule remaining in the sample.

2. The method of claim 1, wherein said providing comprises synthesizing a multiplicity of probes having nucleotide sequences determined by the steps of:

i) determining an allowable Tm interval;

ii) determining a mismatch Tm threshold;

iii) identifying all nucleic acid sequences of a preselected length complementary to a known nucleic acid molecule whose Tm to said molecule is within said allowable Tm interval;

iv) determining the likelihood of each of said nucleic acid sequences complementary to said known molecule also occurring in an unknown nucleic acid molecule;

v) sorting said sequences in order of likelihood with the least likely sequence first;

vi) selecting the first nucleic acid sequence whose Tm to all other known nucleic acid molecules in said sample is below said mismatch Tm;

vii) repeating step vi) until a desired number of nucleic acids that specifically hybridize, under stringent conditions, to said known nucleic acid molecule are obtained;

viii) repeating steps iii) through vii) until at least one nucleic acid sequence that hybridizes specifically under stringent conditions to each known nucleic acid molecule is selected, and

ix) synthesizing probes comprising the nucleic acid sequences determined in step viii), these being the probes attached to the support in step (ii) of claim 1.

3. The method of claim 2, wherein step (vi) further comprises selecting the probe that additionally has a T_m to all already selected nucleic acids below said mismatch T_m.

4. The method of claim 2, wherein said allowable T_m interval ranges from about 30°

C. to about 80°

C.

5. The method of claim 2, wherein said mismatch T_m is at least 5°

C. lower than said allowable T_m interval.

6. The method of claim 2, wherein said likelihood is determined by calculating the probability of occurrence of each of said nucleic acid sequences of step (iii) in a calculated nucleic acid probability distribution.

7. The method of claim 2, wherein said synthesizing comprises amplifying said multiplicity of nucleic acids from a nucleic acid amplification template array.

8. The method of claim 7, wherein said nucleic acid template array is synthesized using light-directed polymer synthesis methods.

9. A method of making an affinity matrix that binds to previously unknown nucleic acid molecules, said method comprising

i) providing a multiplicity of different nucleic acid probes, each probe being sufficiently complementary to an unknown nucleic acid molecule predicted to be present in a nucleic acid sample or a subsequence of said unknown nucleic acid molecule to hybridize thereto under stringent conditions, wherein said multiplicity of probes does not include every possible probe having the same length as said multiciplicity of different probes;

and

ii) attaching said probes to the solid support to produce an affinity matrix.

10. The method of claim 9, wherein said providing comprises the steps of:

(i) calculating a probability of occurrence in a nucleic acid distribution of a collection of all probes of length k minus probes that hybridize to known nucleic acid molecules;

(ii) sorting said collection from highest probability to lowest probability;

(iii) selecting the highest probability probe for inclusion in said affinity matrix;

(iv) repeating steps i through ii until the different probes are selected.

11. The method of claim 10, wherein said select step iii further comprises recalculating said probability on the condition that said probability distribution contains no nucleic acids sufficiently complementary to those probes already selected to hybridize thereto under stringent conditions.

12. The method of claim 10, wherein step iii further comprises selecting an allowable Tm interval and selecting said highest probability probe whose Tm lies within said allowable Tm interval.

13. The method of claim 10, wherein said selected probes are amplified from a nucleic acid amplification template array.

14. The method of claim 10, wherein said nucleic acid template array is synthesized using light-directed polymer synthesis methods.

15. The method of claim 10, wherein said probes are attached to a said solid support by attachment to a biotin which is attached to a streptavidin bound to said solid support.

16. A method to enrich a nucleic acid sample for previously unknown expressed RNA sequences, said method comprising the steps of:

i) providing an affinity matrix having at least one nucleic acid probe sufficiently complementary to each known expressed RNA present in a sample to hybridize thereto under stringent conditions, wherein said affinity matrix does not include every possible probe having the same length as said at least one probe;

ii) hybridizing RNA from an undifferentiated control cell and differentiated or activated test cell respectively to said affinity matrix thereby removing known expressed RNAs from said control cell and said differentiated or activated test cell;

iii) reverse transcribing the RNA from each of said control cell and said differentiated or activated test cell to produce a cDNA, wherein said reverse transcription adds a polymerase chain reaction primer binding region to the cDNAs from said differentiated or activated test cell;

iv) combining said cDNAs from said differentiated or activated test cell with the cDNA from said control cell such that there is at least about a 5 to 1 ratio of cDNA from the control cell to cDNA from the differentiated or activated test cell;

v) amplifying said mixture of cDNAs using primers complementary to said primer binding regions whereby said amplification results in an enrichment of nucleic acid sequences transcribed in said differentiated or activated test cell at a significantly higher level than in said control cell.