Method and Kit for enhanced differential display

• US 5,580,726 A
• Filed: 04/29/1994
• Issued: 12/03/1996
• Est. Priority Date: 04/29/1994
• Status: Expired due to Fees

• Current Assignee: Geron Corporation
• Original Assignee: Geron Corporation
• Inventors: Funk, Walter, Feng, Junli, Villeponteau, Bryant, Linskens, Maarten H. K.
• Primary Examiner(s): Jones, W. Gary
• Assistant Examiner(s): CAMPBELL, EGGERTON A
• Application Number:
  US08/235,180
• Time in Patent Office: 949 Days
• Field of Search: 435/6, 435/92.1, 935/77, 935/78
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6881 for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
• CPC Class Codes: C12Q 2521/107 RNA dependent DNA polymerase,(i.e. reverse transcriptase)
• CPC Class Codes: C12Q 2600/158 Expression markers

Abstract

An improved method for detecting and isolating differentially expressed mRNAs which comprises using first oligonucleotide primers for reverse transcription of mRNAs and both the first oligonucleotide primers and second oligonucleotide primers for amplification of the resultant cDNAs. The improvement of this method comprises providing first and second oligonucleotide primers with a length of at least 21 oligonucleotides. The method further comprises using a two-step PCR amplification, wherein non-stringent conditions are used for the first 1 to 4 cycles, and stringent conditions are used for the next 16 to 22 cycles. This highly reproducible method will permit the preparation of comprehensive catalogs of gene expression for any given cell type.

Claims

1. Method for detecting different stages of cell development or detecting differences in gene expression comprising the steps of:

a) contacting mRNA from each of said cell populations in separate reaction vessels with a first oligonucleotide primer, wherein said first oligonucleotide primer has a hybridizing sequence sufficiently complementary to a region of said mRNA to hybridize therewith,

b) extending said first oligonucleotide primer in an extension reaction using the mRNA as a template to give a first DNA primer extension product complementary to the mRNA,

c) contacting said first DNA primer extension product with a second oligonucleotide primer, wherein said second oligonucleotide primer has a hybridizing sequence sufficiently complementary to said first DNA primer extension product to hybridize therewith,

d) extending said second oligonucleotide primer in an extension reaction using the first DNA primer extension product as a template to give a second DNA primer extension product complementary to the first DNA primer extension product,

e) amplifying said first and second DNA primer extension products in a polymerase chain reaction comprising cycles of primer annealing, extension and denaturation, at an annealing temperature of between 35° and

45°

for at least two and not more than four cycles, then

f) amplifying said first and second DNA primer extension products at an annealing temperature of between 55° and

70°

for at least 16 cycles, to provide amplified gene sequences

g) separating said amplified gens sequences by size and/or charge; and

h) comparing amplified gens sequences separated in step (g) to detect an amplified gene sequence from one of said cell populations that is present at a different level in the other of said cell populations;

wherein said first and second oligonucleotide primers comprise at least 21 nucleotides.

2. The method of claim 1 wherein a mixture of two or more first primers is used.

3. The method of claim 1 wherein a mixture of two or more second primers is used.

4. The method of claim 1 wherein a mixture of two or more first primers and a mixture of two or more second primers are used.

5. The method of claim 1 wherein said first and second oligonucleotide primers consist of from 21 to 50 oligonucleotides.

6. The method of claim 1 wherein said first oligonucleotide primer contains a restriction site.

7. The method of claim 1 wherein said second oligonucleotide primer contains a restriction site.

8. The method of claim 4 wherein said first oligonucleotide primer hybridizes to a region of mRNA comprising a portion of a 3'"'"' polyadenosine tail of said mRNA and at least one nucleotide 5'"'"' to said 3'"'"'polyadenosine tail.

9. The method of claim 4 wherein said first primers are selected from the group consisting of

5'"'"'-GCG CAA GCT TTT TTT TTT TTC T-3'"'"' (SEQ ID NO. 19);

5'"'"'-GCG CAA GCT TTT TTT TTT TTC C-3'"'"' (SEQ ID NO-

     20);

5'"'"'-GCG CAA GCT TTT TTT TTT TTC G-3'"'"' (SEQ ID NO.

     21);

5'"'"'-GCG CAA GCT TTT TTT TTT TTG T-3'"'"' (SEQ ID NO-

     22);

5'"'"'-GCG CAA GCT TTT TTT TTT TTG G-3'"'"' (SEQ ID NO.

     23);

5'"'"'-GCG CAA GCT TTT TTT TTT TTG A-3'"'"' (SEQ ID NO-

     24);

5'"'"'-GCG CAA GCT TTT TTT TTT TTA T-3'"'"' (SEQ ID NO.

     25);

5'"'"'-GCG CAA GCT TTT TTT TTT TTA C-3'"'"' (SEQ ID NO,

     26);

5'"'"'-GCG CAA GCT TTT TTT TTT TTA G-3'"'"' (SEQ ID NO.

     27);

5'"'"'-GCG CAA GCT TTT TTT TTT TTA A-3'"'"' (SEQ ID NO.

     28);

5'"'"'-GCG CAA GCT TTT TTT TTT TTC A-3'"'"' (SEQ ID NO.

     29); and

,

5'"'"'-GCG CAA GCT TTT TTT TTT TTG C-3'"'"' (SEQ ID NO.

     30).

10. The method of claim 4 wherein said first primers are selected from the group consisting of

5'"'"'-GCG CAA GCT TTT TTT TTT TTC C-3'"'"' (SEQ ID NO. 20);

5'"'"'-GCG CAA GCT TTT TTT TTT TTC G-3'"'"' (SEQ ID NO-

     21);

5'"'"'-GCG CAA GCT TTT TTT TTT TTG T-3'"'"' (SEQ ID NO.

     22);

'"'"' -GCG CAA GCT TTT TTT TTT TTG G-3'"'"' (SEQ ID NO.

     23);

5'"'"'-GCG CAA GCT TTT TTT TTT TTG A-3'"'"' (SEQ ID NO.

     24) ;

,

5'"'"'-GCG CAA GCT TTT TTT TTT TTA C-3'"'"' (SEQ ID NO,

     26);

5'"'"'-GCG CAA GCT TTT TTT TTT TTA G-3'"'"' (SEQ ID NO.

     27);

5'"'"'-GCG CAA GCT TTT TTT TTT TTA A-3'"'"' (SEQ ID NO.

     28);

5'"'"'-GCG CAA GCT TTT TTT TTT TTC A-3'"'"' (SEQ ID NO.

     29); and

,

5'"'"'-GCG CAA GCT TTT TTT TTT TTG C-3'"'"' (SEQ ID NO.

     30).

11. The method of claim 4 wherein said first primers are selected, from the group consisting of

5'"'"'-GCG CAA GCT TTT TTT TTT TTC C-3'"'"' (SEQ ID NO. 20);

5'"'"'-GCG CAA GCT TTT TTT TTT TTC G-3'"'"' (SEQ ID NO.

     21);

5'"'"'-GCG CAA GCT TTT TTT TTT TTG T-3'"'"' (SEQ ID NO.

     22);

5'"'"'-GCG CAA GCT TTT TTT TTT TTG G-3'"'"' (SEQ ID NO.

     23);

5'"'"'-GCG CAA GCT TTT TTT TTT TTG A-3'"'"' (SEQ ID NO.

     24);

5'"'"'-GCG CAA GCT TTT TTT TTT TTC A-3'"'"' (SEQ ID NO.

     29); and

,

5'"'"'-GCG CAA GCT TTT TTT TTT TTG C-3'"'"' (SEQ ID NO.

     30).

12. The method of claim 4 wherein each of said second primers comprises a region of randomly selected nucleotides.

13. The method of claim 12 wherein said second primers differ from each other in the region of randomly selected nucleotides.

14. The method of claim 4 wherein said second primers are selected from the group consisting of:

5'"'"'-CGG GAA GCT TAT CGA CTC CAA G -3'"'"' ( SEQ ID NO. 7 );

5'"'"'-CGG GAA GCT TTA GCT AGC ATG G-3'"'"' (SEQ ID NO.

     8);

5'"'"'-CGG GAA GCT TGC TAA GAC TAG C-3'"'"' (SEQ ID NO.

     9);

5'"'"'-CGG GAA GCT TTG CAG TGT GTG A-3'"'"' (SEQ ID NO.

     10);

'"'"' -CGG GAA GCT TGT GAC CAT TGC A-3'"'"' (SEQ ID NO.

     11);

5'"'"'-CGG GAA GCT TGT CTG CTA GGT A-3'"'"' (SEQ ID NO.

     12);

5'"'"'-CGG GAA GCT TGC ATG GTA GTC T-3'"'"' (SEQ ID NO. 13 );

5'"'"'-CGG GAA GCT TGT GTT GCA CCA T-3'"'"' (SEQ ID NO.

     14);

5'"'"'-CGG GAA GCT TAG ACG CTA GTG T-3'"'"' (SEQ ID NO.

     15);

5'"'"'-CGG GAA GCT TTA GCT AGC AGA C-3'"'"' (SEQ ID NO.

     16);

5'"'"'-CGG GAA GCT TCA TGA TGC TAC C-3'"'"' (SEQ ID NO.

     17); and

,

5'"'"'-CGG GAA GCT TAC TCC ATG ACT C - 3'"'"' (SEQ ID NO.

     18).