Amplification of simple sequence repeats

• US 5,874,215 A
• Filed: 01/16/1996
• Issued: 02/23/1999
• Est. Priority Date: 01/16/1995
• Status: Expired due to Term

• Current Assignee: Keygene N.V.
• Original Assignee: Keygene N.V.
• Inventors: Vos, Picter, Zabeau, Marc, Kuiper, Martin T. R.
• Primary Examiner(s): Jones, W. Garn
• Assistant Examiner(s): WHISENANT, ETHAN C
• Application Number:
  US08/585,888
• Time in Patent Office: 1,134 Days
• Field of Search: 435/6, 536/24.3, 536/23.1, 935/76, 935/77, 935/78
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6855 Ligating adaptors

Abstract

The invention relates to a process for the selective amplification of restriction fragements comprising simple sequence repeats.

The process of the invention can be used in a range of fields including but not limited to plant and animal breeding, genetic identity testing in humans, plants and animals, disease identification and screening, forensic analysis and gene tagging and isolation.

Claims

1. Process for the selective amplification of restriction fragments comprising simple sequence repeats, comprising the following:

(a) digesting a starting target DNA with two or more different restriction enzymes, at least one of these enzymes cleaving at or near its recognition nucleotide sequence overlapping or flanking with the simple sequence repeat (referred to as first restriction enzyme) and at least one of these enzymes cleaving the restriction fragments into amplificable restriction fragments (referred to as second restriction enzyme) to obtain restriction fragments,

(b) ligating an appropriate double stranded oligonucleotide adaptor to each of the ends of the restriction fragments produced by said restriction enzymes,

(c) amplifying the restriction fragments of step b) using two or more different amplification primers with the following general structure;

one primer having a sequence at its 5'"'"' end matching the common sequence of the restriction fragments produced with the first restriction enzyme, and a sequence at its 3'"'"' end of at least 5 nucleotides matching the sequence of the simple sequence repeat (referred to as primer one);

one primer having a sequence at its 5'"'"' end matching the common sequence of the restriction fragments produced with the second restriction enzyme (referred to as primer two),

(d) recovering the amplified fragments.

2. Process for the selective amplification of restriction fragments according to claim 1 wherein the two or more different amplification primers have the following general design:

one primer having a sequence at its 5'"'"' end matching the sequence of the adaptor of the first restriction enzyme and its recognition site, and a sequence at its 3'"'"' end of at least 5 nucleotides matching the sequence of the simple sequence repeat (referred to as primer one);

one primer having a sequence at its 5'"'"' end matching the sequence of the adaptor of the second restriction enzyme and its recognition sequence, and a sequence at its 3'"'"' end ranging from 0 to 4 randomly chosen nucleotides (referred to as primer two).

3. Process according to claim 1 wherein said first restriction enzyme has a recognition sequence which comprises at least one nucleotide which does not overlap with the simple sequence repeat.

4. Process according to claim 1 wherein said first restriction enzyme has a recognition sequence which is located immediately adjacent to the simple sequence repeat.

5. Process according to claim 1 wherein said restriction fragments are amplified in two or more consecutive amplification steps, whereby

(i) in the first amplification step, two different PCR primers are used with the following general design:

primer one having a sequence at its 5'"'"' end matching the common sequence of the restriction fragments produced with the first restriction enzyme and a sequence at its 3'"'"' end ranging from 0 to 3 nucleotides, matching the sequence of the simple sequence repeat;

primer two having a sequence at its 5'"'"' end matching the common sequence of the restriction fragments produced with the second restriction enzyme and a sequence at its 3'"'"' end ranging from 0 to 3 randomly chosen nucleotides;

(ii) in each following amplification step two different PCR primers are used, whereby

primer one has the same nucleotide sequence as primer one in the first amplification step and a sequence at its 3'"'"' end of at least one additional nucleotide matching the sequence of the simple sequence repeat;

primer two is identical to primer two in the first amplification step or has the same nucleotide sequence as primer two in the first amplification step and a sequence at its 3'"'"' end of at least one additional randomly chosen nucleotide.

6. Process according to claim 1 wherein said first restriction enzyme is a type 2 restriction enzyme and wherein said primer one has a sequence at its 5'"'"' end matching the sequence of the adaptor of the first restriction enzyme, and a sequence at its 3'"'"' end of at least 5 nucleotides matching the sequence of the simple sequence repeat.

7. Process according to claim 1 wherein said starting DNA is genomic DNA.

8. Process according to claim 7 wherein said genomic DNA is from eukaryotic organisms.

9. Process according to claim 1 wherein the amplified fragments are recovered as DNA fingerprints.

10. Process for identifying the differences or similarities, between different target DNAs, said process comprising comparing the DNA fingerprints from each of said target DNAs obtained according to claim 9, and identifying the differences or similarities between the DNA fingerprints between the different target DNAs.

11. Process according to claim 1 wherein one of the restriction enzymes cleaves a four-base sequence.

12. Process according to claim 1 wherein primer two has a sequence at the 5'"'"' end matching part of the common sequence of the restriction fragments produced with the second restriction enzyme.

13. Process according to claim 1 wherein primer two further comprises at least one randomly chosen nucleotide at its 3'"'"' end.

14. Process according to claim 13 wherein primer two comprises a sequence at its 3'"'"' end of 1, 2, 3 or 4 randomly chosen nucleotides.

15. Process according to claim 8 wherein said eukaryotic organisms are selected from the group consisting of animals, plants and humans.