Method for non-redundant library construction
First Claim
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1. A method for constructing a nucleic acid library comprising:
- a) obtaining a population of end-labeled double-stranded cDNA molecules;
b) dividing said population into a first portion and a second portion;
c) digesting said first portion with at least one sequence-specific endonuclease wherein said first portion is divided into one pool per endonuclease;
d) digesting said second portion with at least one (Y) endonuclease having a degenerate recognition sequence and fractionating the digested cDNA into YXz pools where Y is the number of degenerate endonucleases, X is the the extent of degeneracy and z is the number of bases;
e) isolating nucleic acid fragments from said endonuclease digestions of said first and second portions using said end-labels;
f) digesting the fragments of said first portion with said at least one endonuclease of d) sequence and fractionating the digested cDNA into YXz pools where Y is the number of degenerate endonucleases, X is the the extent of degeneracy and z is the number of bases;
g) digesting the fragments of said second portion with said at least one endonuclease of c) wherein the second portion pools are divided into one pool per endonuclease;
h) removing labeled nucleic acid fragments from said first and second portions while retaining unlabeled fragments;
i) adding a population of adapters to each of the pools, said population containing adapters specific for the endonucleases used, wherein each adapter comprises a first region specific to a particular endonuclease used and a second region containing a primer binding site;
j) hybridizing and ligating said adapters to said unlabeled fragments;
k) amplifying the fragments using the adapters; and
l) separating the amplified fragments by size.
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Abstract
Provided are novel methods for the production of nucleic acid libraries having reduced redundancy. Also provided are methods for determination of changes in RNA expression associated with pathological conditions, and physiological or developmental state. Additional aspects provided non-redundant tags or probes produced by the disclosed methods and microarrays incorporating such tags.
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Citations
43 Claims
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1. A method for constructing a nucleic acid library comprising:
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a) obtaining a population of end-labeled double-stranded cDNA molecules;
b) dividing said population into a first portion and a second portion;
c) digesting said first portion with at least one sequence-specific endonuclease wherein said first portion is divided into one pool per endonuclease;
d) digesting said second portion with at least one (Y) endonuclease having a degenerate recognition sequence and fractionating the digested cDNA into YXz pools where Y is the number of degenerate endonucleases, X is the the extent of degeneracy and z is the number of bases;
e) isolating nucleic acid fragments from said endonuclease digestions of said first and second portions using said end-labels;
f) digesting the fragments of said first portion with said at least one endonuclease of d) sequence and fractionating the digested cDNA into YXz pools where Y is the number of degenerate endonucleases, X is the the extent of degeneracy and z is the number of bases;
g) digesting the fragments of said second portion with said at least one endonuclease of c) wherein the second portion pools are divided into one pool per endonuclease;
h) removing labeled nucleic acid fragments from said first and second portions while retaining unlabeled fragments;
i) adding a population of adapters to each of the pools, said population containing adapters specific for the endonucleases used, wherein each adapter comprises a first region specific to a particular endonuclease used and a second region containing a primer binding site;
j) hybridizing and ligating said adapters to said unlabeled fragments;
k) amplifying the fragments using the adapters; and
l) separating the amplified fragments by size. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27)
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28. A method for constructing a nucleic acid library comprising:
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a) obtaining a population of 3′
end-labeled double-stranded cDNA molecules by a method comprising, isolating polyA mRNA from a cell;
hybridizing a 5′
end labeled primer containing an oligo dT tail to said polyA mRNA;
synthesizing a first cDNA strand by extension of said primer; and
synthesizing a second cDNA strand by nick translation to produce a double stranded cDNA;
b) dividing said labeled population into a first portion and a second portion;
c) digesting said first portion with at least one sequence-specific endonuclease selected from the group consisting of at least one endonuclease having a 4 base recognition sequence, at least one endonuclease having a 5 base recognition sequence and at least one endonuclease having a six base recognition sequence wherein said first portion is divided into one pool per endonuclease;
d) digesting said second portion with at least one endonuclease having a degenerate recognition sequence wherein said endonuclease produces fragments comprising unpaired overhangs containing Nm unique sequences where N is an integer between 2 and 4, m is an integer between 2 and 6, and Nm equals at least 64 and fractionating the digested cDNA into YXz pools where Y is the number of degenerate endonucleases, X is the extent of degeneracy and z is the number of bases;
e) isolating nucleic acid fragments from said endonuclease digestions of said first and second portions using said end-labels;
f) digesting the fragments of said first portion with said at least one endonuclease of d) and fractionating the digested cDNA into YXz pools where Y is the number of degenerate endonucleases, X is the extent of degeneracy and z is the number of bases;
g) digesting the fragments of said second portion with said at least one endonuclease of c) wherein said first portion is divided into one pool per endonuclease;
h) removing labeled nucleic acid fragments from said first and second portions while retaining unlabeled fragments;
i) adding a population of adapters to each of the pools, said population containing adapters specific for at least some of the endonucleases used, wherein each adapter comprises a first region specific to a particular endonuclease used and a second region containing a primer binding site, said primer binding sites comprising no more than 10 different sequences, said sequences lacking significant homology to sequences known to be in said population of nucleic acid molecules;
j) hybridizing and ligating said adapters to said unlabeled fragments;
k) amplifying said unlabeled fragments using the adapters; and
l) separating the amplified fragments on the basis of size. - View Dependent Claims (29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39)
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40. A method for constructing a nucleic acid library comprising:
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a) obtaining a population of double stranded cDNA wherein cDNA molecules contained in said population contain a detectable label on their 3′
end;
b) digesting said double-stranded cDNA with at least one restriction endonuclease having a degenerate recognition sequence comprising at least one degenerate base, wherein said digestion creates a single-stranded portion or overhang containing a region having the formula Nm, where N is the extent of degeneracy and m is the number of degenerate bases in said single stranded portion or overhang to produce digestion fragments and fractionating the digested cDNA into YXz pools where Y is the number of degenerate endonucleases, X is the extent of degeneracy and z is the number of bases;
c) adding a population of adapters to each of the pools, said adapters specific for the at least one endonuclease used;
d) hybridizing and ligating said adapters to the 5′
end of said digestions fragments;
e) separating said 3′
end digestion fragments using said detectable label;
f) amplifying said 3′
end digestion fragments;
g) separating said amplified digestion fragments on the basis of size. - View Dependent Claims (41, 42, 43)
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Specification