Novel methods for amplifying and detecting nucleic acid sequences
First Claim
1. A process for linearly amplifying a specific nucleic acid sequence comprising the steps of:
- providing;
said specific nucleic acid sequence, an initial primer or a nucleic acid construct comprising two segments, (A) a first segment (i) being substantially complementary to a first portion of said specific nucleic acid sequence and (ii) capable of template-dependent first extension, and (B) a second segment being (i) substantially non-identical to said first segment, (ii) substantially identical to a second portion of said specific nucleic acid sequence, (iii) capable of binding to a complementary sequence of said second segment and (iv) capable of providing for subsequent binding of a first segment of a second primer or nucleic acid construct to said first portion of said specific nucleic acid sequence under isostatic or limited cycling conditions, such that a second primer extension is produced and displaces a first primer extension; and
substrates, buffer and a template-dependent polymerizing enzyme; and
incubating said specific nucleic acid sequence and said novel primer or nucleic acid construct in the presence of said substrates, buffer and template-dependent polymerizing enzyme under isostatic or limited cycling conditions;
thereby linearly amplifying said specific nucleic acid sequence.
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Abstract
This invention provides novel processes for amplifying nucleic acid sequences of interest, including linear and non-linear amplification. In linear amplification, a single initial primer or nucleic acid construct is utilized to carry out the amplification process. In non-linear amplification, a first initial primer or nucleic acid construct is employed with a subsequent initial primer or nucleic acid construct. In other non-linear amplification processes provided by this invention, a first initial primer or nucleic acid construct is deployed with a second initial primer or nucleic acid construct to amplify the specific nucleic acid sequence of interest and its complement that are provided. A singular primer or a singular nucleic acid construct capable of non-linear amplification can also be used to carry out non-linear amplification in accordance with this invention. Post-termination labeling process for nucleic acid sequencing is also disclosed in this invention that is based upon the detection of tagged molecules that are covalently bound to chemically reactive groups provided for chain terminators. A process for producing nucleic acid sequences having decreased thermodynamic stability to complementary sequences is also provided and achieved by this invention. Unique nucleic acid polymers are also disclosed and provided in addition to other novel compositions, kits and the like.
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Citations
59 Claims
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1. A process for linearly amplifying a specific nucleic acid sequence comprising the steps of:
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providing;
said specific nucleic acid sequence, an initial primer or a nucleic acid construct comprising two segments, (A) a first segment (i) being substantially complementary to a first portion of said specific nucleic acid sequence and (ii) capable of template-dependent first extension, and (B) a second segment being (i) substantially non-identical to said first segment, (ii) substantially identical to a second portion of said specific nucleic acid sequence, (iii) capable of binding to a complementary sequence of said second segment and (iv) capable of providing for subsequent binding of a first segment of a second primer or nucleic acid construct to said first portion of said specific nucleic acid sequence under isostatic or limited cycling conditions, such that a second primer extension is produced and displaces a first primer extension; and
substrates, buffer and a template-dependent polymerizing enzyme; and
incubating said specific nucleic acid sequence and said novel primer or nucleic acid construct in the presence of said substrates, buffer and template-dependent polymerizing enzyme under isostatic or limited cycling conditions;
thereby linearly amplifying said specific nucleic acid sequence. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 39, 40, 41, 42, 43, 44)
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12. A process for non-linearly amplifying a specific nucleic acid sequence comprising the steps of:
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providing;
said specific nucleic acid sequence, a first initial primer or a nucleic acid construct for said specific nucleic acid sequence, said first initial primer or nucleic acid construct comprising two segments;
(A) a first segment (i) being substantially complementary to a first portion of said specific nucleic acid sequence and (ii) capable of template-dependent first extension, and (B) a second segment being (i) substantially non-identical to said first segment, (ii) substantially identical to a second portion of said specific nucleic acid sequence, (iii) capable of binding to a complementary sequence of said second segment and (iv) capable of providing for subsequent binding of a first segment of a second primer or nucleic acid construct to said first portion of said specific nucleic acid sequence under isostatic or limited cycling conditions, such that a second primer extension is produced to displace a first primer extension; and
a subsequent initial primer or a nucleic acid construct to the complement of said specific nucleic acid sequence, said subsequent initial primer or nucleic acid construct comprising two segments, (A) a first segment (i) being substantially complementary to a first portion of said specific nucleic acid sequence and (ii) capable of template-dependent first extension, and (B) a second segment being (i) substantially non-identical to said first segment, (ii) substantially identical to a second portion of said specific nucleic acid sequence, (iii) capable of binding to a complementary sequence of said second segment and (iv) capable of providing for subsequent binding of a first segment of a subsequent primer to said first portion of said specific nucleic acid sequence under isostatic or limited cycling conditions, such that a second primer extension is produced and displaces a first primer extension; and
substrates, buffer and a template-dependent polymerizing enzyme; and
incubating said specific nucleic acid sequence and said novel primer or nucleic acid construct in the presence of said substrates, buffer and template-dependent polymerizing enzyme under isostatic or limited cycling conditions;
thereby non-linearly amplifying said specific nucleic acid sequence. - View Dependent Claims (13, 14, 15, 16, 17, 18, 19, 20, 21, 22)
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23. A process for non-linearly amplifying a specific nucleic acid sequence comprising the steps of:
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providing;
said specific nucleic acid sequence and its complement;
a first initial primer or a nucleic acid construct for said specific nucleic acid sequence, said first initial primer or nucleic acid construct comprising two segments;
(A) a first segment (i) being substantially complementary to a first portion of said specific nucleic acid sequence and (ii) capable of template-dependent first extension, and (B) a second segment being (i) substantially non-identical to said first segment, (ii) substantially identical to a second portion of said specific nucleic acid sequence, (iii) capable of binding to a complementary sequence of said second segment and (iv) capable of providing for subsequent binding of a first segment of a subsequent first primer to said first portion of said specific nucleic acid sequence under isostatic or limited cycling conditions, such that a second primer extension is produced and displaces said first primer extension; and
a second initial primer or a nucleic acid construct complementary to said first primer extension, said second initial primer or nucleic acid construct comprising a segment characterized by capable of template-dependent extension under isostatic or limited cycling conditions; and
substrates, buffer and a template-dependent polymerizing enzyme;
incubating said specific nucleic acid sequence and said novel primer or nucleic acid construct in the presence of said substrates, buffer and template-dependent polymerizing enzyme under isostatic or limited cycling conditions;
thereby non-linearly amplifying said specific nucleic acid sequence. - View Dependent Claims (24, 25, 26, 27, 28, 29, 30, 31)
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32. A process for non-linearly amplifying a specific nucleic acid sequence comprising the steps of:
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providing;
said specific nucleic acid sequence;
a singular primer or a singular nucleic acid construct capable of non-linear amplification, comprising three segments;
(a) a first segment (i) being substantially complementary to a first portion of said specific nucleic acid sequence and (ii) capable of template-dependent first extension;
(b) a second segment substantially identical to a second portion of said specific nucleic acid sequence; and
(c) a third segment substantially identical to said first segment;
wherein said first primer extension is capable of producing sequences that are capable of hybridizing to said second segment and is capable of self-priming and self-extending to produce a complement to said third segment, and substrates, buffer and a template-dependent polymerizing enzyme; and
incubating said specific nucleic acid sequence and said primer or nucleic acid construct in the presence of said substrates, buffer and template-dependent polymerizing enzyme;
thereby non-linearly amplifying said specific nucleic acid sequence. - View Dependent Claims (33, 34, 35, 36, 37)
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45. A post-termination labeling process for nucleic acid sequencing comprising the steps of:
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producing, in the presence of untagged or unlabeled substrates, untagged or unlabeled primer, polymerizing enzyme, buffer and an appropriate untagged or unlabeled terminator for each nucleotide base, nucleic acid fragments corresponding to said nucleic acid sequence of interest, wherein each of said terminators comprise a chemically reactive group that covalently binds to a tagged molecule under conditions that internal sequences are substantially non-reactive to said tagged molecules and said chemical reactions do not substantially interfere with separation of said fragments in a medium or matrix;
separating the fragments produced in a medium or matrix; and
detecting said separated fragments by detecting said tagged molecule in said medium or matrix. - View Dependent Claims (46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57)
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58. A process for producing nucleic acid sequences that have decreased thermodynamic stability to complementary sequences, said process comprising the step of incorporating into the nucleic acid sequences produced at least one modified nucleotide or nucleotide analog having a negatively charged chemical moiety.
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59. A single-stranded or double-stranded nucleic acid polymer selected from the group consisting of a linear nucleic acid, branched nucleic acid, an inverted nucleic acid and a peptide-nucleic acid, or a combination of any of the foregoing, wherein said nucleic acid polymer comprises at least one purine or pyrimidine base comprising one negatively charged chemical moiety in one or both strands.
Specification