Methods for identifying differentially expressed genes and differences between genomic nucleic acid sequences
First Claim
1. A method for identifying a differentially expressed gene, comprising:
- (a) providing a tester DNA molecule with an amplification tag at the 5'"'"' and 3'"'"' ends of the molecule and a driver DNA or RNA molecule lacking said amplification tag;
(b) hybridizing said tester and said driver molecules to form a reaction mixture, wherein said reaction mixture comprises a tester--tester homoduplex, a tester-driver heteroduplex, a driver--driver homoduplex, a single stranded driver DNA molecule and a single stranded tester DNA molecule;
(c) treating said reaction mixture to reduce the number of single stranded molecules in said mixture;
(d) treating said reaction mixture to remove said amplification tag from said tester-driver heteroduplex; and
(e) amplifying said tester--tester homoduplex from said reaction mixture to form an amplification product, wherein steps (c) and (d) occur before step (e).
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Abstract
Methods for identifying differentially expresses genes and differences between genomic nucleic acid sequences are described. These methods typically include: (a) providing a tester DNA molecule with an amplification tag at the 5'"'"' and 3'"'"' ends of the molecule and a driver DNA or RNA molecule lacking said amplification tag; (b) hybridizing said tester and said driver molecules to form a reaction mixture, wherein said reaction mixture comprises a tester--tester homoduplex, a tester-driver heteroduplex, a driver--driver homoduplex, a single stranded driver DNA molecule and a single stranded tester DNA molecule; (c) treating said reaction mixture to reduce the number of single stranded molecules in said mixture; (d) treating said reaction mixture to remove said amplification tag from said tester-driver heteroduplex; and (e) amplifying said tester--tester homoduplex from said reaction mixture to form an amplification product, wherein steps (c) and (d) occur before step (e).
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Citations
34 Claims
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1. A method for identifying a differentially expressed gene, comprising:
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(a) providing a tester DNA molecule with an amplification tag at the 5'"'"' and 3'"'"' ends of the molecule and a driver DNA or RNA molecule lacking said amplification tag; (b) hybridizing said tester and said driver molecules to form a reaction mixture, wherein said reaction mixture comprises a tester--tester homoduplex, a tester-driver heteroduplex, a driver--driver homoduplex, a single stranded driver DNA molecule and a single stranded tester DNA molecule; (c) treating said reaction mixture to reduce the number of single stranded molecules in said mixture; (d) treating said reaction mixture to remove said amplification tag from said tester-driver heteroduplex; and (e) amplifying said tester--tester homoduplex from said reaction mixture to form an amplification product, wherein steps (c) and (d) occur before step (e). - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13)
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14. A method for identifying a differentially expressed gene, comprising:
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(a) providing a tester DNA molecule with an amplification tag at the 5'"'"' and 3'"'"' ends of the molecule and a driver DNA or RNA molecule lacking said amplification tag; (b) hybridizing said tester and said driver molecules to form a reaction mixture, wherein said reaction mixture comprises a tester--tester homoduplex, a tester-driver heteroduplex, a driver--driver homoduplex, a single stranded driver DNA molecule and a single stranded tester DNA molecule; (c) treating said reaction mixture with a DNA nuclease which digests single stranded DNA molecules to reduce the number of said single stranded molecules in said mixture and to remove said amplification tag from said tester-driver heteroduplexes; and (d) amplifying said tester--tester homoduplex from said reaction mixture to form an amplification product, wherein step (c) occurs before step (d). - View Dependent Claims (15, 16, 17, 18, 19, 20, 21, 22, 23, 24)
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25. A method for constructing a subtraction library containing a differentially expressed gene, comprising:
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(a) providing a tester DNA molecule with an amplification tag at both 5'"'"' and 3'"'"' ends of the molecule and a driver DNA or RNA molecule lacking said amplification tag; (b) hybridizing said tester and said driver molecules to form a reaction mixture, wherein said reaction mixture comprises a tester--tester homoduplex, a tester-driver heteroduplex, a driver--driver homoduplex, a single stranded driver DNA molecule and a single stranded tester DNA molecule; (c) treating said reaction mixture with a DNA nuclease which digests single stranded DNA molecules to reduce the number of said single stranded molecules in said mixture and to remove said amplification tag from said tester-driver heteroduplexes; (d) amplifying said tester--tester homoduplex from said reaction mixture to form an amplification product, wherein step (c) occurs before step (d); (e) repeating steps (b) through (d) at least one additional time; (f) inserting an amplification product from step (e) into a vector; and (g) constructing a subtraction library. - View Dependent Claims (26, 27, 28, 29, 30)
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- 31. A reaction mixture comprising a tester--tester homoduplex, wherein said homoduplex includes an amplification tag at both 5'"'"' and 3'"'"' ends of the homoduplex molecule, a tester-driver heteroduplex lacking the amplification tags, and a driver--driver homoduplex lacking the amplification tags.
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33. A method for identifying a difference between genomic DNA sequences, comprising:
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(a) providing a tester DNA molecule with an amplification tag at the 5'"'"' and 3'"'"' ends of the molecule and a driver DNA molecule lacking said amplification tag; (b) hybridizing said tester and said driver molecules to form a reaction mixture, wherein said reaction mixture comprises a tester--tester homoduplex, a tester-driver heteroduplex, a driver--driver homoduplex, a single stranded driver DNA molecule and a single stranded tester DNA molecule; (c) treating said reaction mixture to reduce the number of single stranded molecules in the mixture and to remove said amplification tag from the tester-driver heteroduplex; and (d) amplifying said tester--tester homoduplex from said reaction mixture to form an amplification product, wherein step (c) occurs before step (d).
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34. A kit comprising an amplification tag, wherein said tag is a double-stranded oligodeoxynucleotide sequence having two restriction enzyme sites, and a DNA nuclease which digests single-stranded DNA molecules.
Specification