System and method for inhibiting the decryption of a nucleic acid probe sequence used for the detection of a specific nucleic acid
First Claim
1. A method of masking the identity of a detection sequence on a nucleic acid molecule comprising:
- (a) obtaining a detection nucleic acid molecule comprising a known detection sequence that hybridizes to a target nucleic acid sequence of interest in a sample during a hybridization assay;
(b) designing and making a first masking nucleic acid molecule comprising a first masking sequence, wherein the first masking nucleic acid molecule is the same length as the detection nucleic acid molecule and does not hybridize to a nucleic acid sequence in the sample during the hybridization assay, and wherein the masking sequence varies from the detection sequence at at least half of its nucleic acid positions,(c) masking the identity of the detection sequence on the detection nucleic acid molecule by combining the detection nucleic acid molecule and the first masking nucleic acid molecule on the same solid support or in the same solution if the detection nucleic acid molecule and the first masking nucleic acid molecule are not immobilized on solid supports, whereby upon nucleic acid sequence analysis the presence of both the detection nucleic acid molecule and the first masking nucleic acid molecule produce a nonsensical nucleotide sequence at at least half of the nucleic acid positions in the detection sequence.
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Abstract
Sequence-specific nucleic acid hybridization assays are used for the detection of specific genetic sequences as indicators of genetic anomalies, mutations, and disease propensity. In addition, they are used for the detection of various biological agents and infectious pathogens. Because a complementary probe or nucleic acid sequence is required to detect a sequence of interest in a hybridization-based assay, nucleic acid sequencing techniques can rapidly determine the specific probe sequence being used for detection. This allows reverse engineered assays to be produced rapidly. In addition, it enables the circumvention of hybridization-based assays for biological agent or infectious pathogen detection by providing the information necessary to create or alter nucleic acid sequences to produce false positives or false negatives. The present invention provides methods and compositions for inhibiting the identification of specific detection sequences. More specifically, the invention provides masking sequences that mask the identity of specific detection sequences.
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Citations
34 Claims
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1. A method of masking the identity of a detection sequence on a nucleic acid molecule comprising:
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(a) obtaining a detection nucleic acid molecule comprising a known detection sequence that hybridizes to a target nucleic acid sequence of interest in a sample during a hybridization assay; (b) designing and making a first masking nucleic acid molecule comprising a first masking sequence, wherein the first masking nucleic acid molecule is the same length as the detection nucleic acid molecule and does not hybridize to a nucleic acid sequence in the sample during the hybridization assay, and wherein the masking sequence varies from the detection sequence at at least half of its nucleic acid positions, (c) masking the identity of the detection sequence on the detection nucleic acid molecule by combining the detection nucleic acid molecule and the first masking nucleic acid molecule on the same solid support or in the same solution if the detection nucleic acid molecule and the first masking nucleic acid molecule are not immobilized on solid supports, whereby upon nucleic acid sequence analysis the presence of both the detection nucleic acid molecule and the first masking nucleic acid molecule produce a nonsensical nucleotide sequence at at least half of the nucleic acid positions in the detection sequence. - 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)
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24. A method of performing a hybridization reaction comprising the steps of:
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(a) providing a hybridization probe, which comprises a hybridization sequence designed to hybridize to a target sequence in a sample during a hybridization reaction; (b) providing a first masking nucleic acid molecule that comprises a first masking sequence, wherein the first masking nucleic acid molecule is the same length as the hybridization probe and does not hybridize to a nucleic acid sequence in the sample during the hybridization reaction, and wherein the masking sequence of the first masking nucleic acid molecule varies from the hybridization sequence at at least half of its nucleic acid positions, and further wherein the first masking nucleic acid molecule has a reduced ability or inability to hybridize to the target; (c) masking the identity of the hybridization sequence on the nucleic acid molecule by combining the hybridization probe and the first masking nucleic acid molecule on the same solid support or in the same solution if the hybridization probe and the first masking nucleic acid molecule are not immobilized on solid supports, whereby upon nucleic acid sequence analysis the presence of both the hybridization probe and the first masking nucleic acid molecule produce a nonsensical nucleotide sequence at at least half of the nucleic acid positions in the hybridization sequence; (d) performing the hybridization reaction comprising the hybridization probe and the first masking nucleic acid molecule in the presence of the target sequence under conditions permitting the selective hybridization of the hybridization probe to the target sequence. - View Dependent Claims (25, 26, 27, 28, 29, 30, 31, 32, 33, 34)
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Specification