Method to produce single stranded DNA of defined length and sequence and DNA probes produced thereby

• US 7,897,747 B2
• Filed: 05/24/2007
• Issued: 03/01/2011
• Est. Priority Date: 05/25/2006
• Status: Active Grant

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Inventors: Davis, Ronald W., Krishnakumar, Sujatha, Mindrinos, Michael
• Primary Examiner(s): Horlick; Kenneth R
• Assistant Examiner(s): Thomas; David C
• Application Number:
  US11/805,676
• Publication Number:
  US 20080026393A1
• Time in Patent Office: 1,377 Days
• Field of Search: None
• US Class Current: 536/24.3
• CPC Class Codes: C12N 15/10 Processes for the isolation, preparation or purification of DNA or RNA chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

A method for producing a single stranded DNA (ssDNA) molecule of a defined length and sequence is disclosed. This method enables the preparation of, inter alia, probes of greater length than can be chemically synthesized. The method starts with a double stranded molecule, such as genomic, double stranded DNA (dsDNA) from any organism. A fragment of the starting molecule (dsDNA) is amplified by specific primers engineered to introduce cleavage sites on either side of the desired sequence. Cleavage steps on the amplified, engineered fragment are combined with a phosphate removal step, thereby creating a construct that can be digested with an exonuclease without damage to the desired ssDNA. Probes, which hybridize with large gaps between the ends of the probes, are also disclosed.

Claims

1. A polynucleic acid probe, having a defined sequence, for hybridization to a target polynucleic acid sequence, comprising the following sub-sequences:

(a) a first target sequence, at one end of the probe, complementary to a first target region of the target polynucleic acid, for specifically binding thereto;

(b) a second target sequence, at an opposite end of the probe, complementary to a second target region of the target polynucleic acid for specifically binding thereto,

where said first and second target regions are separated on the target polynucleic acid, when hybridized thereto, by a gap of at least 250 nt of target sequence, said gap adapted to be filled by at least 250 nt of added gap filling nucleotides;

(c) at least one amplification primer site, on the probe, adjacent the target sequence, and connected to a spacer backbone sequence, for specifically binding a PCR primer, said primer oriented in a direction for amplification of target sequences and gap filling nucleotides only when nucleotides are joined to the target sequences as complementary to the target polynucleic acid and further oriented to not amplify the backbone sequence; and

(d) said spacer backbone sequence, of at least 125 nt, chosen to be non-complementary to the target polynucleic acid, and being a random nucleic acid sequence having a length permitting a length of said gap of at least 250 nt, said spacer backbone sequence having a length of at least 50% of the length of said gap.

2. The probe of claim 1 wherein the polynucleic acid molecule is DNA.

3. The probe of claim 1 comprising two amplification primer sites, one adjacent the first target sequence and one adjacent the second target sequence, oriented towards each other for amplification of a sequence comprising a sequence complementary to the gap sequence.

4. The probe of claim 1 which has been circularized with at least 25 nt complementary to said target polynucleic acid.

5. The probe of claim 1 wherein the spacer backbone sequence is from a non-human organism and the target sequences hybridize to human genetic sequences.

6. The probe of claim 1 wherein the target sequences are sequences which hybridize, respectively, adjacent to a 5′

end and adjacent to a 3′

end of an exon of a eukaryotic gene.

7. The probe of claim 1 wherein the target sequences are separated on the target polynucleic acid by between 250 and 1000 nt.

9. A method for preparing a single stranded DNA molecule according to claim 1, of defined sequence and length, having a predefined 5′

end and 3′

end, using a portion of a first strand of a double stranded precursor molecule, comprising the steps of;

(a) amplifying the double stranded precursor with primers containing a sequence homologous to the desired 5′

and 3′

ends, said primers further containing restriction enzyme cleavage sites to obtain an amplified double stranded molecule having cleavage sites at the desired 3′ and

5′

ends;

(b) cleaving the amplified double stranded molecule with a restriction enzyme which leaves a 5′

overhang or blunt end on the first strand at the desired 5′

end;

(c) removing a 5′

terminal phosphate on the first strand;

(d) cleaving the amplified double stranded molecule at the desired 3′

end to create a 3′

blunt end or no 5′

overhang; and

(e) digesting the second strand to leave the single stranded DNA molecule of defined sequence and length.

10. The method of claim 9 wherein the cleaving is done with a type IIs restriction enzyme.

11. The method of claim 9 further comprising the steps of digesting with Bsal to generate a 5′

overhang outside of BsaI'"'"'s recognition site.

12. The method of claim 9 wherein multiple probes, having different sequences, are prepared using single cleaving, removing and digesting steps.

13. A collection of probes according to claim 1, wherein each probe comprises a different first and second target sequence, and similar amplification sites for simultaneous amplification of individual probes, each individual probe comprising two amplification sites.

14. The collection of probes of claim 13 wherein the probes are targeted to human genomic DNA.

15. The collection of probes of claim 13 comprising at least 500 probes.

8. A pre-probe for making a probe for hybridization to a target polynucleic acid sequence, comprising a polynucleic acid molecule comprising the following sequences:

(a) a first target sequence, at a 5′

end of the probe, complementary to a first region of the target polynucleic acid, for specifically binding thereto,

(b) a second target sequence, at a 3′

end of the probe, complementary to a second region of target polynucleic acid for specifically binding thereto, said first and second regions of target polynucleic acid separated on the target polynucleic acid by a gap, said gap having a length of at least 250 nt,

(c) at least one amplification primer site, adjacent a target sequence, and connected to a spacer backbone sequence, for specifically binding PCR primers, said primers oriented in a direction for amplification of target sequences only when nucleic acids are joined to the target sequences as complementary to the target polynucleic acid and further oriented to not amplify the spacer backbone sequence;

(d) said spacer backbone sequence being of at least 250 nt. wherein said backbone sequence is a random nucleic acid sequence chosen to be non-complementary to any target polynucleic acid, said spacer backbone sequence having a length of at least 50% of the length of said gap; and

(e) restriction endonuclease recognition sites 5′

of the desired 5′

target sequence and 3′

of the desired 3′

target sequence, further defining cut sites at the desired final 5′

nucleotide and desired final 3′

nucleotide, said restriction endonuclease recognition sites being comprised in a sequence extending 5′

of said desired final 5′

nucleotide and in a sequence extending 3′

of said desired final 3′

nucleotide.

16. A method for specifically detecting a target polynucleic acid sequence, comprising:

(a) hybridizing the target polynucleic acid sequence with a probe comprising the following sequences;

(i) a first target sequence, at one end of the probe, complementary to a first region of the target polynucleic acid, for specifically binding thereto,

(ii) a second target sequence. at an opposite end of the probe, complementary to a second region of target polynucleic acid for specifically binding thereto, said first and second regions of target polynucleic acid separated on the target polynucleic acid by a gap, said gap having a length of at least 250 nt,

(iii) at least one amplification primer site, adjacent the target sequence, and connected to a backbone sequence, for specifically binding PCR primers, said primers oriented in a direction for amplification of target sequences only when nucleic acids are joined to the target sequences as complementary to the target polynucleic acid and further oriented to not amplify the backbone sequence; and

(iv) a backbone sequence which is at least 125 nt long to permit hybridization of the first target sequence and the second target sequence with said gap, said spacer backbone sequence being at least 50% of the length of said gap and wherein said spacer backbone sequence is a random nucleic acid sequence from a nonhuman organism and does not hybridize to target sequences;

(b) filling in said gap of at least 250 nt with gap filling nucleotides to form a circular probe; and

(c) amplifying said circular probe without cleaving the probe using said amplification primer site, whereby amplification only occurs if said first target sequence and said second target sequence hybridize to the target polynucleotide, and said gap is filled.