Kits for Performing Amplification Reactions
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Accused Products
Abstract
The present invention is directed to novel methods of synthesizing multiple copies of a target nucleic acid sequence which are autocatalytic (i.e., able to cycle automatically without the need to modify reaction conditions such as temperature, pH, or ionic strength and using the product of one cycle in the next one). In particular, the present invention discloses a method of nucleic acid amplification which is robust and efficient, while reducing the appearance of side products. The method uses only one primer, the “priming oligonucleotide,” a 3'"'"'blocked promoter oligonucleotide and optionally, a means for terminating a primer extension reaction, to amplify RNA or DNA molecules in vitro, while reducing or eliminating the formation of side products. The method of the present invention minimizes or eliminates the emergence of side products, thus providing a high level of specificity. Furthermore, the appearance of side products can complicate the analysis of the amplification reaction by various molecular detection techniques. The present invention minimizes or eliminates this problem, thus providing an enhanced level of sensitivity.
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Citations
86 Claims
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1-13. -13. (canceled)
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14. A kit for use in synthesizing multiple copies of an RNA target sequence contained within a target nucleic acid, said kit comprising:
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a priming oligonucleotide which hybridizes to the 3′
-end of said RNA target sequence and primes the synthesis of a first DNA primer extension product complementary to said RNA target sequence, wherein said priming oligonucleotide is substantially comprised of deoxynucleotides;
a promoter oligonucleotide comprising a first region which hybridizes to a 3′
-region of said first DNA primer extension product and a second region which is a promoter for an RNA polymerase, said promoter oligonucleotide being modified to prevent the initiation of DNA synthesis therefrom; and
a binding molecule which binds to said target nucleic acid adjacent to or near the 5′
-end of said RNA target sequence. - View Dependent Claims (15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33)
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34. A kit for use in synthesizing multiple copies of a DNA target sequence contained within a target nucleic acid, said kit comprising:
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a promoter oligonucleotide comprising a first region which hybridizes to a 3′
-region of said DNA target sequence present in a target nucleic acid to form a promoter oligonucleotide;
target nucleic acid hybrid and a second region which is a promoter for an RNA polymerase, said promoter oligonucleotide being modified to prevent the initiation of DNA synthesis therefrom;
a priming oligonucleotide which hybridizes to the 3′
-end of an RNA product transcribed from said promoter oligonucleotide;
target nucleic acid hybrid and primes the synthesis of a first DNA primer extension product complementary to said RNA product, wherein said RNA product comprises a base region complementary to said DNA target sequence,provided that said kit does not include a priming oligonucleotide which hybridizes to said target nucleic acid and primes the synthesis of a primer extension product complementary to said DNA target sequence, and further provided that said kit does not include a restriction endonuclease capable of cleaving a double-stranded complex comprising said target nucleic acid. - View Dependent Claims (35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49)
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50. A kit for use in synthesizing multiple copies of an RNA target sequence, said kit comprising:
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a priming oligonucleotide which hybridizes to the 3′
-end of said RNA target sequence and primes the synthesis of a first DNA primer extension product complementary to said RNA target sequence;
a promoter oligonucleotide comprising a first region which hybridizes to a 3′
-region of said first DNA primer extension product and a second region which is a promoter for an RNA polymerase, said promoter oligonucleotide being modified to prevent the initiation of DNA synthesis therefrom; and
an extender oligonucleotide which hybridizes to said first DNA primer extension product 3′
to said promoter oligonucleotide. - View Dependent Claims (51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64)
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65. A kit for use in synthesizing multiple copies of an RNA target sequence, said kit comprising:
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a priming oligonucleotide which hybridizes to the 3′
-end of said RNA target sequence and primes the synthesis of a first DNA primer extension product complementary to said RNA target sequence; and
a cap which hybridizes to a region at the 3′
-end of said priming oligonucleotide, wherein the 5′
-terminal base of said cap is complementary to the 3′
-terminal base of said priming oligonucleotide, and wherein said cap is modified to prevent the initiation of DNA synthesis therefrom. - View Dependent Claims (66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79)
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80. A composition comprising:
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a promoter oligonucleotide having first and second regions, said first region comprising a 3′
-portion containing a contiguous arrangement of ribonucleotides and a portion 5′
thereto that is capable of hybridizing to a DNA template, and said second region being a promoter for an RNA polymerase, wherein said first region is situated 3′
to said second region, and wherein said promoter oligonucleotide is modified to prevent the initiation of DNA synthesis therefrom; and
an oligodeoxynucleotide hybridized to said 3′
-portion of said first region, thereby forming an RNA;
DNA duplex. - View Dependent Claims (81)
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82. A method for making available a priming oligonucleotide for extension in the presence of a target nucleic acid, said method comprising the steps of:
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(a) providing said priming oligonucleotide to a reaction mixture containing said target nucleic acid, said priming oligonucleotide having a cap hybridized to a region at the 3′
-end thereof, wherein the 5′
-terminal base of said cap is complementary to the 3′
-terminal base of said priming oligonucleotide, and wherein said cap is modified to prevent the initiation of DNA synthesis therefrom;
(b) hybridizing said priming oligonucleotide to a target sequence contained within said target nucleic acid, thereby displacing said cap from said priming oligonucleotide; and
(c) extending said priming oligonucleotide in a primer extension reaction with a DNA polymerase to give a DNA primer extension product complementary to said target sequence.
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83. A method of synthesizing multiple copies of a target sequence, said method comprising the steps of:
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(a) treating a target nucleic acid comprising an RNA target sequence with;
(i) a priming oligonucleotide which hybridizes to the 3′
-end of said target sequence such that a primer extension reaction can be initiated therefrom; and
(ii) a binding molecule which binds to said target nucleic acid adjacent to or near the 5′
-end of said target sequence;
(b) extending said priming oligonucleotide in a primer extension reaction with a DNA polymerase to give a DNA primer extension product complementary to said target sequence, said DNA primer extension product having a 3′
-end which is determined by said binding molecule and which is complementary to the 5′
-end of said target sequence;
(c) separating said DNA primer extension product from said target sequence using an enzyme which selectively degrades said target sequence;
(d) treating said DNA primer extension product with a promoter oligonucleotide comprising first and second regions, said first region hybridizing to a 3′
-region of said DNA primer extension product to form a promoter oligonucleotide;
DNA primer extension product hybrid, and said second region being a promoter for an RNA polymerase and situated 5′
to said first region, wherein any oligonucleotide provided in said method which comprises a promoter for an RNA polymerase is modified to prevent the initiation of DNA synthesis therefrom;
(e) treating said DNA primer extension product with an extender oligonucleotide, said extender oligonucleotide hybridizing to a region of said DNA primer extension product 3′
to said promoter oligonucleotide of said promoter oligonucleotide;
DNA primer extension product hybrid, such that an extender oligonucleotide;
DNA primer extension product hybrid is formed;
(f) extending the 3′
-end of said DNA primer extension product in said promoter oligonucleotide;
DNA primer extension product hybrid to add a sequence complementary to said second region of said promoter oligonucleotide; and
(g) transcribing from said promoter oligonucleotide;
DNA primer extension product hybrid multiple RNA products complementary to said DNA primer extension product using an RNA polymerase which recognizes said promoter and initiates transcription therefrom, wherein the base sequences of said RNA products are substantially identical to the base sequence of said target sequence.
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84. A method of synthesizing multiple copies of a target sequence, said method comprising the steps of:
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(a) treating a target nucleic acid comprising an RNA target sequence with a priming oligonucleotide which hybridizes to the 3′
-end of said target sequence, such that a primer extension reaction can be initiated therefrom;
(b) extending said priming oligonucleotide in a primer extension reaction with a DNA polymerase to give a first DNA primer extension product having an undefined 3′
-end and comprising a base region complementary to said target sequence;
(c) separating said first DNA primer extension product from said target nucleic acid using an enzyme which selectively degrades that portion of said target nucleic acid which is complementary to said first DNA primer extension product;
(d) treating said first DNA primer extension product with a promoter oligonucleotide comprising first and second regions, said first region hybridizing to a 3′
-region of said first DNA primer extension product to form a promoter oligonucleotide;
first DNA primer extension product hybrid, and said second region being a promoter for an RNA polymerase and situated 5′
to said first region, wherein any oligonucleotide provided in said method which comprises a promoter for an RNA polymerase is modified to prevent the initiation of DNA synthesis therefrom(e) treating said first DNA primer extension product with an extender oligonucleotide, said extender oligonucleotide hybridizing to a region of said first DNA primer extension product 3′
to said promoter oligonucleotide of said promoter oligonucleotide;
first DNA primer extension product hybrid, such that an extender oligonucleotide;
first DNA primer extension product hybrid is formed; and
(f) transcribing from said promoter oligonucleotide;
first DNA primer extension product hybrid multiple first RNA products complementary to at least a portion of said first DNA primer extension product using an RNA polymerase which recognizes said promoter and initiates transcription therefrom, wherein the base sequences of said first RNA products are substantially identical to the base sequence of said target sequence.
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85. A method of synthesizing multiple copies of a target sequence, said method comprising the steps of:
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(a) treating a target nucleic acid comprising a DNA target sequence with a promoter oligonucleotide comprising first and second regions, said first region hybridizing to the 3′
-end of said target sequence to form a promoter oligonucleotide;
target nucleic acid hybrid, and said second region being a promoter for an RNA polymerase and situated 5′
to said first region, wherein any oligonucleotide provided in said method which comprises a promoter for an RNA polymerase is modified to prevent the initiation of DNA synthesis therefrom, and wherein said target nucleic acid is not treated with a restriction endonuclease prior to step (a);
(b) treating said target nucleic acid with an extender oligonucleotide, said extender oligonucleotide hybridizing to a region of said target nucleic acid 3′
to said promoter oligonucleotide of said promoter oligonucleotide;
target nucleic acid hybrid such that an extender oligonucleotide;
target nucleic acid hybrid is formed;
(c) transcribing from said promoter oligonucleotide;
target nucleic acid hybrid multiple first RNA products comprising a base region complementary to said target sequence using an RNA polymerase which recognizes said promoter and initiates transcription therefrom;
(d) treating one of said first RNA products with a priming oligonucleotide which hybridizes to a 3′
-region of said first RNA product such that a primer extension reaction can be initiated therefrom;
(e) extending said priming oligonucleotide in a primer extension reaction with a DNA polymerase to give a DNA primer extension product complementary to at least a portion of said first RNA product, said DNA primer extension product having a 3′
-end which is complementary to the 5′
-end of said first RNA product;
(f) separating said DNA primer extension product from said first RNA product using an enzyme which selectively degrades said first RNA product;
(g) treating said DNA primer extension product with said promoter oligonucleotide to form a promoter oligonucleotide;
DNA primer extension product hybrid;
(h) treating said DNA primer extension product with an extender oligonucleotide, said extender oligonucleotide hybridizing to a region of said DNA primer extension product 3′
to said promoter oligonucleotide of said promoter oligonucleotide;
DNA primer extension product hybrid such that an extender oligonucleotide;
DNA primer extension product hybrid is formed; and
(i) transcribing from said promoter oligonucleotide;
DNA primer extension product hybrid multiple second RNA products complementary to said DNA primer extension product using said RNA polymerase, wherein the base sequences of said second RNA products are substantially complementary to the base sequence of said target sequence.
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86. An oligonucleotide up to 50 bases in length and comprising at least 10 contiguous bases of a base sequence selected from the group consisting of SEQ ID NO:
- 4, SEQ ID NO;
6, SEQ ID NO;
7, the complement of SEQ ID NO;
7, SEQ ID NO;
8, the complement of SEQ ID NO;
8, SEQ ID NO;
9, SEQ ID NO;
11, SEQ ID NO;
12, the complement of SEQ ID NO;
12, SEQ ID NO;
13, SEQ ID NO;
15, SEQ ID NO;
16, the complement of SEQ ID NO;
16, SEQ ID NO;
17, SEQ ID NO;
19, SEQ ID NO;
20, the complement of SEQ ID NO;
20, SEQ ID NO;
21, SEQ ID NO;
23, SEQ ID NO;
24, the complement of SEQ ID NO;
24, SEQ ID NO;
25, SEQ ID NO;
27, SEQ ID NO;
29, SEQ ID NO;
30, the complement of SEQ ID NO;
30, SEQ ID NO;
31, the complement of SEQ ID NO;
31, SEQ ID NO;
32, the complement of SEQ ID NO;
32, and equivalent sequences thereof containing thymine bases substituted for uracil bases.
- 4, SEQ ID NO;
Specification