Replica amplification of nucleic acid arrays

• US 6,511,803 B1
• Filed: 03/10/2000
• Issued: 01/28/2003
• Est. Priority Date: 10/10/1997
• Status: Expired due to Term

• Current Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Original Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Inventors: Church, George M., Mitra, Robi D.
• Primary Examiner(s): Siew, Jeffrey
• Application Number:
  US09/522,732
• Time in Patent Office: 1,054 Days
• Field of Search: 435/6, 435/7.1, 435/91.1, 435/91.2, 536/22.1, 536/23.1, 536/24-- 2
• US Class Current: 506/4
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00657 One-dimensional arrays
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C07K 1/047 Simultaneous synthesis of different peptide species; Peptide libraries
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2565/515 characterised by the interaction between or sequential use of two or more arrays

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.

Claims

1. A method of determining the nucleotide sequence of the features of a micro-array of nucleic acid molecules, said method comprising the following steps:

a) creating a micro-array 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 micro-array 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 micro-array by detecting the fluorescence of the extended, terminated and separated reaction products within the gel.

2. The method of claim 1 wherein said amplifying is performed by PCR.

3. The method of claim 1 wherein said amplifying is performed by an isothermal method.

4. The method of claim 1 wherein said microarray of nucleic acid features in a linear arrangement is derived as a replica of features arranged on a chromosome.

5. The method of claim 1 wherein said micro-array of nucleic acid features in a linear arrangement is derived as a replica of one linear subset of features on a separate, non-linear micro-array of nucleic acid features.

6. The method of claim 1 wherein said polyacrylamide gel is macroporous.

7. The method of claim 6 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.

8. The method of claim 7 wherein the percentage of said PEG is about 2.5%.

9. The method of claim 6 wherein said polyacrylamide gel comprises DATD.

10. The method of claim 1 wherein said oligonucleotide primer comprises sequences permitting formation of a hairpin loop.

11. 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;

e) photobleaching said array; and

f) repeating steps (b)-(e) until the nucleotide sequence is determined.

12. 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;

h) photobleaching said array; and

i) repeating steps (e)-(h) until the nucleotide sequence is determined.