Compositions and Methods for Nucleic Acid Analysis of Sequences with Insertions or Deletions
First Claim
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1. A test kit comprising:
- a plurality of first single stranded nucleic acids, each having an unique tag sequence coupled to a targeting sequence, and each further having a discriminating sequence coupled to the targeting sequence, wherein the discriminating sequence is further coupled to a label; and
wherein each of the discriminating sequences has a sequence suitable for at least partial hydrolysis of the single stranded nucleic acid by a discriminating agent under a discriminating condition to thereby separate the label from the unique tag sequence.
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Abstract
Contemplated methods and kits include a plurality of single stranded oligonucleotides that comprise a discriminating sequence that is encompassed on one end by a label and on the other end by a unique tag sequence. In one preferred aspect, the discriminating sequence is an RNA repeat unit, forms a heteroduplex with a complementary DNA repeat unit of the target nucleic acid, and the discriminating agent is RNaseH. Using such systems, the number of repeat units can be simply identified by hydrolysis of the discriminating sequence where such sequence is adjacent to a predetermined number of DNA repeat units in the single stranded oligonucleotide.
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Citations
22 Claims
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1. A test kit comprising:
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a plurality of first single stranded nucleic acids, each having an unique tag sequence coupled to a targeting sequence, and each further having a discriminating sequence coupled to the targeting sequence, wherein the discriminating sequence is further coupled to a label; and wherein each of the discriminating sequences has a sequence suitable for at least partial hydrolysis of the single stranded nucleic acid by a discriminating agent under a discriminating condition to thereby separate the label from the unique tag sequence. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8)
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9. A method of determining a genotype of a nucleic acid, comprising:
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incubating a sample nucleic acid with a plurality of first single stranded nucleic acids to thereby form a test mixture; wherein each of the first single stranded nucleic acids has a unique tag sequence that is coupled to a targeting sequence and further has a discriminating sequence that is coupled to the targeting sequence, wherein the discriminating sequence is further coupled to a label; adding under a discriminating condition a discriminating agent to the test mixture to thereby separate the label from at least one of the first single stranded nucleic acids; determining separation of the label from the at least one of the first single stranded nucleic acids using the unique tag sequence; and deducing the genotype from the step of determining. - View Dependent Claims (10, 11, 12, 13, 14, 15)
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16. A method of determining a copy number of a repeat unit in a nucleic acid, comprising:
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combining a plurality of single stranded nucleic acids of the general formula A-T-Rn-R′
-L with the nucleic acid under hybridization conditions to form a duplex;wherein A is a unique tag DNA sequence, T is a targeting DNA sequence, R is a DNA repeat sequence, n is an integer between 1 and 500, inclusive, R′
is a RNA repeat sequence, and L is a label;hydrolyzing at least part of R′
using RNaseH in a duplex where R′ and
the repeat unit in the nucleic acid form a complementary double strand to thereby separate L from A;binding the single stranded nucleic acids onto a chip in predetermined positions using A; and measuring a signal from the predetermined positions. - View Dependent Claims (17, 18, 19)
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20. A chimeric oligonucleotide having the formula A-T-Rn-R′
- -L, wherein A is a unique tag DNA sequence, T is a targeting DNA sequence, R is a DNA repeat sequence, n is an integer between 1 and 500, inclusive, R′
is a RNA repeat sequence, and L is a label.
- -L, wherein A is a unique tag DNA sequence, T is a targeting DNA sequence, R is a DNA repeat sequence, n is an integer between 1 and 500, inclusive, R′
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21. A method of determining a copy number of a repeat unit in a nucleic acid, comprising:
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combining a plurality of single stranded nucleic acids of the general formula T-Rn-R′
-L* with the nucleic acid under hybridization conditions to form a duplex;wherein T is a targeting DNA sequence, R is a DNA repeat sequence, n is an integer between 1 and 500, inclusive, R′
is a RNA repeat sequence, and L* is an optional label, and wherein each of the single stranded nucleic acids has not a 3′
-OH terminus;hydrolyzing at least part of R′
using a discriminating agent when R′ and
the repeat unit in the nucleic acid form a complementary double strand to thereby generate a 3′
-OH terminus;(a) adding at least one optionally labeled nucleotide to the 3′
-OH terminus, or (b) adding a plurality of nucleotides to the 3′
-OH terminus and labeling the added nucleotides; anddetecting the label in solution. - View Dependent Claims (22)
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Specification