Nucleic acid affinity columns

• US 6,280,950 B1
• Filed: 10/28/1999
• Issued: 08/28/2001
• 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: Morris, MacDonald S., Lipshutz, Robert J., Chee, Mark S., Gingeras, Thomas R.
• Primary Examiner(s): Horlick, Kenneth R.
• Application Number:
  US09/429,521
• Time in Patent Office: 670 Days
• Field of Search: 435/6, 435/91.2, 536/24.3, 536/24.31, 536/24.32
• US Class Current: 435/5
• 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 sequences; 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 nucleic acid amplification template array comprising a surface to which are attached at least 50 nucleic acid probes having different predetermined nucleic acid sequences and wherein:

i) each different probe is localized in a known location of said surface;

ii) the density of said probes is greater than about 60 different probes per 1 cm^2;

and

iii) said different probes have an identical terminal 3′

nucleic acid sequence and an identical terminal 5′

nucleic acid sequence, said identical terminal 3′ and

5′

nucleic acid sequence capable of serving as primer binding sites.

2. The template array of claim 1, wherein said 3′

terminal nucleic acid sequence and said 5′

terminal nucleic acid sequence each range in length from about 4 to about 30 nucleotides.

3. The template array of claim 1, wherein said 3′

terminal nucleic acid sequence and said 5′

terminal nucleic acid sequence are identical to each other.

4. The template array of claim 1, wherein said 3′

terminal nucleic acid sequence and said 5′

terminal nucleic acid sequence include a recognition site for a restriction endonuclease.

5. The template array of claim 1, wherein the different probes also each comprise a non-identical region, different probes having non-identical regions that differ in nucleotide sequence, and wherein non-identical regions of said probes range in length from about 10 to about 50 nucleotides.

6. The template array of claim 1, wherein the range of thermal melting points (T_m) of non-identical regions of said probes with sequences complementary to said non-identical regions is less than about 20°

C.

7. A nucleic acid affinity matrix that reduces known nucleic acid molecules in a sample, said affinity matrix comprising a multiplicity of at least 20 different predetermined nucleic acid probes, wherein:

there exists in said affinity matrix a probe complementary to each of said nucleic acid molecules or a subsequence thereof;

said at least 20 different predetermined probes do not include every possible probe having the same length as said predetermined probes; and

wherein the probes comprising said multiplicity of probes are preselected by the steps of;

i) determining an allowable T_m interval;

ii) determining a mismatch T_m threshold;

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

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

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

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

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.

8. The affinity matrix of claim 7, wherein said probes range in length from about 6 nucleotides to about 50 nucleotides.

9. The affinity matrix of claim 7, wherein said probes are present in approximately equimolar amounts.

10. The affinity matrix of claim 7, 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.

11. A nucleic acid affinity matrix that reduces known nucleic acid molecules in a sample, said affinity matrix comprising a multiplicity of at least 20 different predetermined nucleic acid probes, wherein:

there exists in said affinity matrix a probe complementary to each of said nucleic acid molecules or a subsequence thereof; and

said at least 20 different probes do not include every possible probe having the same length as said predetermined probes; and

wherein said affinity matrix is prepared according to a method that comprises

providing a nucleic acid amplification template array comprising a surface to which are attached at least 20 template nucleic acid probes having different predetermined nucleic acid sequences, wherein;

i) each different template probe is localized in a known location of said surface;

ii) the density of said template probes is greater than about 60 different template probes per 1 cm²; and

iii) said different template probes have an identical terminal 3′

nucleic acid sequence and an identical terminal 5′

nucleic acid sequence; and

amplifying said multiplicity of oligonucleotides at least about 10 fold to provide a nucleic acid pool from which the at least 20 different predetermined nucleic acid probes are obtained.