CA2582809A1 - Replica amplification of nucleic acid arrays - Google Patents

Replica amplification of nucleic acid arrays Download PDF

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CA2582809A1
CA2582809A1 CA002582809A CA2582809A CA2582809A1 CA 2582809 A1 CA2582809 A1 CA 2582809A1 CA 002582809 A CA002582809 A CA 002582809A CA 2582809 A CA2582809 A CA 2582809A CA 2582809 A1 CA2582809 A1 CA 2582809A1
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nucleic acid
features
array
primer
mixture
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George M. Church
Rob D. Mitra
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Harvard College
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Abstract

Disclosed are improved methods of making and using immobilized arrays of nucleic acids, particularly methods for producing replicas of such arrays. Included are methods for producing high density arrays of nucleic acids and replicas of such arrays, as well as methods for preserving the resolution of arrays through rounds of replication. Also included are methods which take advantage of the availability of replicas of arrays for increased sensitivity in detection of sequences on arrays.
Improved methods of sequencing nucleic acids immobilized on arrays utilizing single copies of arrays and methods taking further advantage of the availability of replicas of arrays are disclosed. The improvements lead to higher fidelity and longer read lengths of sequences immobilized on arrays. Methods are also disclosed which improve the efficiency of multiplex PCR
using arrays of immobilized nucleic acids.

Description

SEQUENCE LISTING
<110> President and Fellows of Harvard College <120> Replica Amplification of Nucleic Acid Arrays <130> 10498.87039 <140> PCT/USOO/06390 <141> 2000-03-10 <150> US 09/267,496 <151> 1999-03-12 <160> 24 <170> PatentIn Ver. 2.1 <210> 1 <211> 17 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:T7 RNA
polymerase binding sequence <400> 1 taatacgact cactata 17 <210> 2 <211> 10 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:hypothetical sequence <400> 2 tgcatgctat 10 <210> 3 <211> 25 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:hypothetical sequence <400> 3 atagcatgca atgcatttac gtagc 25 <210> 4 <211> 32 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:hypothetical sequence <220>
<221> unsure <222> (27) . . (32) <223> N can be a, c, g or t <400> 4 gcagcagtac gactagcata tccgacnnnn nn 32 <210> 5 <211> 32 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:hypothetical sequence <220>
<221> unsure <222> (27) . . (32) <223> N can be a, c, g or t <400> 5 cgatagcagt agcatgcagg tccgacnnnn nn 32 <210> 6 <211> 66 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:hypothetical sequence <400> 6 tcggctcatc tgcatgctgc cagcagtcgg actacgtacc ccggtacgtg cgctacacgc 60 agcttt 66 <210> 7 <211> 88 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:hypothetical sequence <400> 7 gcagcagtac gactagcata tccgacctgc gtgtagcgca cgtaccgggg tacgtagtcc 60 gactgctggc agcatgcaga tgagccga 88 <210> 8 <211> 94 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:hypothetical sequence <400> 8 cgatagcagt agcatgcagg tccgaccagc agtcggacta cgtaccccgg tacgtgcgct 60 acacgcaggt cggatatgct agtcgtactg ctgc 94 <210> 9 <211> 94 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:hypothetical sequence <400> 9 gcagcagtac gactagcata tccgacctgc gtgtagcgca cgtaccgggg tacgtagtcc 60 gactgctggt cggacctgca tgctactgct atcg 94 <210> 10 <211> 24 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:primer used for solid phase amplification <400> 10 ccactacgcc tccgctttcc tctc 24 <210> 11 <211> 23 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:primer used for solid phase amplification <400> 11 ctgccccggg ttcctcattc tct 23 <210> 12 <211> 24 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:primer used for solid phase amplification <220>
<221> miscfeature <222> (1) <223> Primer is modified to include ACRYDITE linker moiety at the 5' end <400> 12 CcactaCgcc tCCgctttCC tctc 24 <210> 13 <211> 24 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:primer used for solid phase amplification <400> 13 gggcggaagc ttgaaggagg tatt 24 <210> 14 <211> 23 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:primer used for solid phase amplification <400> 14 gcccggtctc gagcgtctgt tta 23 <210> 15 <211> 24 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:primer used for solid phase amplification <220>
<221> misc_feature <222> (1) <223> Primer is modified to include ACRYDITE linker moiety at the 5' end <400> 15 gggcggaagc ttgaaggagg tatt 24 <210> 16 <211> 47 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:primer used for solid phase amplification <400> 16 gggcggaagc ttgaaggagg tatttaagga gaaaataccg catcagg 47 <210> 17 <211> 44 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:primer used for solid phase amplification <400> 17 gcccggtctc gagcgtctgt ttacaccgat cgcccttccc aaca 44 <210> 18 <211> 47 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:primer used for solid phase amplification <400> 18 gcccggtctc gagcgtctgt ttaaattcac tggccgtcgt tttacaa 47 <210> 19 <211> 45 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:primer used for solid phase amplification <400> 19 gcccggtctc gagcgtctgt ttaccaatac gcaaaccgcc tctcc 45 <210> 20 <211> 48 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:primer used for solid phase amplification <400> 20 ccactacgcc tccgctttcc tctcgggcgg aagcttgaag gaggtatt 48 <210> 21 <211> 46 <212> DNA
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence:primer used for solid phase amplification <400> 21 .ctgccccggg ttcctcattc tctgcccggt ctcgagcgtc tgttta 46 <210> 22 <211> 23 <212> DNA
<213> Artificial Sequence <220>

<223> Description of Artificial Sequence:sequencing primer <400> 22 gcccggtctc gagcgtctgt tta 23 <210> 23 <211> 60 <212> DNA
<213> Artificial Sequence <220>
<221> miscfeature <222> (1) <223> Primer is modified to include ACRYDITE linker moiety at the 5' end <220>
<223> Description of Artificial Sequence:sequencing template <400> 23 tcggccaacg cgcggggaga ggcggtttgc gtatcagtaa acagacgctc gagaccgggc 60 <210> 24 <211> 60 <212> DNA
<213> Artificial Sequence r = 4-<220>
<221> misc_feature <222> (1) <223> Primer is modified to include ACRYDITE linker moiety at the 5' end <220>
<223> Description of Artificial Sequence:sequencing template <400> 24 cccagtcacg acgttgtaaa acgacggcca gtgtcgataa acagacgctc gagaccgggc 60

Claims (36)

1. A method for determining the nucleotide sequence of the features of an immobilized nucleic acid array, said method comprising the steps of:

a) ligating a first double-stranded nucleic acid probe to one end of a nucleic acid of a feature of said array, said first double stranded nucleic acid probe having a restriction endonuclease recognition site for a restriction endonuclease whose cleavage site is separate from its recognition site and which generates a protruding strand upon cleavage;

b) identifying one or more nucleotides at the end of said polynucleotide by the identity of the first double stranded nucleic acid probe ligated thereto or by extending a strand of the polynucleotide or probe;

c) amplifying the features of said array using a primer complementary to said first double stranded nucleic acid probe, such that only molecules which have been successfully ligated with said first double stranded nucleic acid probe are amplified to yield an amplified array;

d) contacting said amplified array with support such that at least a subset of nucleic acid molecules produced by said amplifying are transferred to said support;

e) covalently attaching said subset of nucleic acid molecules transferred in step (d) to said support to form a replica of said amplified array;

f) cleaving the nucleic acid features of the array with a nuclease recognizing said nuclease recognition site of said probe such that the nucleic acid of the features is shortened by one or more nucleotides; and g) repeating steps (a)-(f) until the nucleotide sequences of the features of said array are determined.
2. The method of claim 1 wherein said nucleic acid probe comprises four components, each component being capable of indicating the presence of a different nucleotide in said protruding strand upon ligation.
3. The method of claim 2 wherein each of said components of said probe is labeled with a different fluorescent dye and the different fluorescent dyes are spectrally resolvable.
4. The method of claim 1 wherein after said step (e) and before said step (f), the features of said array are amplified.
5. The method of claim 1 wherein amplification is performed by PCR.
6. The method of claim 1 wherein:

i) after one or more cycles using said first double stranded nucleic acid probe in step (a), a distinct nucleic acid probe is used, in place of said first double stranded nucleic probe in step (a), said distinct nucleic acid probe comprising a restriction endonuclease recognition site for a restriction endonuclease whose cleavage site is separated from its recognition site, said distinct nucleic acid probe also comprising sequences such that a primer complementary to said distinct nucleic acid probe will not hybridize with said first double stranded nucleic acid probe; and ii) a primer complementary to said distinct nucleic acid probe is used in place of said primer complementary to said first double stranded nucleic acid probe in step (c), so that selective amplification of those features which successfully completed the previous cycle of restriction and ligation occurs.
7. The method of claim 6 wherein a new distinct nucleic acid probe is used after each cycle of restriction and ligation, said new distinct nucleic acid probe comprising a sequence such that a primer complementary to that sequence will not hybridize to any probe used in previous cycles.
8. A method of determining the nucleotide sequence of the features of an array of immobilized nucleic acids comprising the steps of:

a) adding a mixture comprising an oligonucleotide primer and a template-dependent polymerase to an array of immobilized nucleic acid features under conditions permitting hybridization of the primer to the immobilized nucleic acids;

b) adding a single, fluorescently labeled deoxynucleoside triphosphate to the mixture under conditions which permit incorporation of the labeled deoxynucleotide onto the 3' end of the primer if it is complementary to the next adjacent base in the sequence to be determined;

c) detecting incorporated label by monitoring fluorescence;

d) repeating steps (b)-(c) with each of the remaining three labeled deoxynucleoside triphosphates in turn; and e) repeating steps (b)-(d) until the nucleotide sequence is determined.
9. The method of claim 8 wherein the primer, buffer and polymerase are cast into a polyacrylamide gel bearing the array of immobilized nucleic acids.
10. The method of claim 9 wherein said polyacrylamide gel is macroporous.
11. The method of claim 10 wherein said polyacrylamide gel comprises up to about 25% PEG, about 3% to about 12%
total acrylamide and about 1% to about 30% cross linker.
12. The method of claim 11 wherein the percentage of said PEG is about 2.5%.
13. The method of claim 10 wherein said polyacrylamide gel comprises DATD.
14. The method of claim 8 wherein single-stranded binding protein is present during step (b).
15. The method of claim 8 wherein said single fluorescently labeled deoxynucleotide further comprises a mixture of the single deoxynucleoside triphosphate in labeled and unlabeled forms.
16. The method of claim 8 wherein after step (d) and before step (e) the additional step of photobleaching said array is performed.
17. The method of claim 8 wherein said fluorescently labeled deoxynucleoside triphosphates are labeled with a cleavable linkage to the fluorophore.
18. The method of claim 17 wherein after step (d) and before step (e) the additional step of cleaving said linkage to the fluorophore is performed.
19. The method of claim 18 wherein said step of cleaving comprises contacting said linkage with a reducing agent.
20. The method of claim 19 wherein said reducing agent is dithiothreitol.
21. The method of claim 8 wherein said oligonucleotide primer comprises sequences permitting formation of a hairpin loop.
22. The method of claim 8 wherein after a predetermined number of cycles of steps (b)-(d), a defined regimen of deoxynucleotide and chain-terminating deoxynucleotide analog addition is performed, such that out-of-phase molecules are blocked from further extension cycles, said regimen followed by continued cycles of steps (b)-(d) until said nucleotide sequence is determined.
23. A method of determining the nucleotide sequence of the features of an array of immobilized nucleic acids comprising the steps of:

a) adding a mixture comprising an oligonucleotide primer and a template-dependent polymerase to an array of immobilized nucleic acid features under conditions permitting hybridization of the primer to the immobilized nucleic acids;

b) adding a first mixture of three unlabeled deoxynucleoside triphosphates under conditions which permit incorporation of deoxynucleotides to the end of the primer if they are complementary to the next adjacent base in the sequence to be determined;

c) adding a second mixture of three unlabeled deoxynucleoside triphosphates, said second mixture comprising the deoxynucleoside triphosphate not included in the mixture of step (b), under conditions which permit incorporation of deoxynucleotides to the end of the primer if they are complementary to the next adjacent base in the sequence to be determined;

d) repeating steps (b)-(c) for a predetermined number of cycles;

e) adding a single, fluorescently labeled deoxynucleoside triphosphate to the mixture under conditions which permit incorporation of the labeled deoxynucleotide onto the 3' terminus of the primer if it is complementary to the next adjacent base in the sequence to be determined;

f) detecting incorporated label by monitoring fluorescence;

g) repeating steps (e)-(f), with each of the remaining three labeled deoxynucleoside triphosphates in turn; and h) repeating steps (e)-(g) until the nucleotide sequence is determined.
24. The method of claim 23 wherein for said first or second mixtures of three unlabeled deoxynucleoside triphosphates, a mixture which comprises deoxyguanosine triphosphate further comprises deoxyadenosine triphosphate.
25. The method of claim 23 wherein the primer and polymerase are cast into a polyacrylamide gel bearing the array of immobilized nucleic acids.
26. The method of claim 23 wherein said single fluorescently labeled deoxynucleotide further comprises a mixture of the single deoxynucleoside triphosphate in labeled and unlabeled forms.
27. The method of claim 23 wherein after step (g) and before step (h) the additional step of photobleaching said array is performed.
28. The method of claim 23 wherein said fluorescently labeled deoxynucleoside triphosphates are labeled with a cleavable linkage to the fluorophore.
29. The method of claim 28 wherein after step (g) and before step (h) the additional step of cleaving said linkage to the fluorophore is performed.
30. The method of claim 23 wherein said oligonucleotide primer comprises sequences permitting formation of a hairpin loop.
31. The method of claim 23 wherein after a predetermined number of cycles of steps (e)-(g), a defined regimen of deoxynucleotide and chain-terminating deoxynucleotide analog addition is performed, such that out-of-phase molecules are blocked from further extension cycles, said regimen followed by continued cycles of steps (e)-(g) until said nucleotide sequence of the features of the array is determined.
32. A method of determining the nucleotide sequence of the features of a microarray of nucleic acid molecules, said method comprising the following steps:

a) creating a microarray of nucleic acid features in a linear arrangement within and along one side of a polyacrylamide gel, said gel further comprising one or more oligonucleotide primers, and a template-dependent polymerizing activity;

b) amplifying the microarray of step (a);
c) adding a mixture of deoxynucleoside triphosphates, said mixture comprising each of the four deoxynucleoside triphosphates dATP, dGTP, dCTP and dTTP, said mixture further comprising chain-terminating analogs of each of the deoxynucleoside triphosphates dATP, dGTP, dCTP
and dTTP, and said chain-terminating analogs each distinguishably labeled with a spectrally distinguishable fluorescent moiety;

d) incubating said mixture with said microarray under conditions permitting extension of said one or more oligonucleotide primers;

e) electrophoretically separating the products of said extension within said polyacrylamide gel; and f) determining the nucleotide sequence of the features of said microarray by detecting the fluorescence of the extended, terminated and separated reaction products within the gel.
33. The method of claim 32 wherein said amplifying is performed by PCR.
34. The method of claim 32 wherein said amplifying is performed by an isothermal method.
35. The method of claim 32 wherein said microarray of nucleic acid features in a linear arrangement is derived as a replica of features arranged on a chromosome.
36. The method of claim 32 wherein said microarray of nucleic acid features in a linear arrangement is derived as a replica of one linear subset of features on a separate, non-linear microarray of nucleic acid features.
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