Reagents for detecting and assaying nucleic acid sequences
First Claim
Patent Images
1. A dendritic polynucleotide having a plurality of single stranded hybridization arms;
- said dendritic polynucleotide being comprised of a plurality of matrix polynucleotide monomers bonded together by hybridization;
each matrix polynucleotide monomer, prior to being hybridization bonded to other matrix polynucleotide monomers, having at least three single stranded hybridization regions; and
in said dendritic polynucleotide each matrix polynucleotide monomer is hybridization bonded to at least one other matrix polynucleotide monomer at at least one such hybridization region and when hybridization bonded to more than one such hybridization region of the same matrix polynucleotide monomer, there is an intermediate region where the two monomers are not hybridization bonded;
wherein each matrix polynucleotide monomer, prior to hybridization bonding, has a linear, double stranded waist region having a first end and a second end, said first end terminating with two single stranded hybridization regions, each from a strand of the waist region, and said second end terminating with one or two single stranded hybridization region(s), each from a strand of the waist region; and
, the plurality of matrix polynucleotide monomers present does not exceed saturation of the dendritic polynucleotide.
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Abstract
A novel class of reagents for assaying nucleic acid sequences comprise successive layers of polynucleotides of a specific structure, including a double-stranded waist and single-stranded, free arms at the molecule ends, formed by hybridization of the arms to adjacent molecule arms. The reagent is used to assay for specific nucleic acid sequences. The outer layer of polynucleotides are specific for the sequence to be assayed through their non-annealed, free, single-stranded arms. The reagents are useful in the assay of a wide variety of nucleic acid sequences including those associated with pathogens such as pathogenic bacteria and virus.
152 Citations
51 Claims
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1. A dendritic polynucleotide having a plurality of single stranded hybridization arms;
- said dendritic polynucleotide being comprised of a plurality of matrix polynucleotide monomers bonded together by hybridization;
each matrix polynucleotide monomer, prior to being hybridization bonded to other matrix polynucleotide monomers, having at least three single stranded hybridization regions; and
in said dendritic polynucleotide each matrix polynucleotide monomer is hybridization bonded to at least one other matrix polynucleotide monomer at at least one such hybridization region and when hybridization bonded to more than one such hybridization region of the same matrix polynucleotide monomer, there is an intermediate region where the two monomers are not hybridization bonded;
wherein each matrix polynucleotide monomer, prior to hybridization bonding, has a linear, double stranded waist region having a first end and a second end, said first end terminating with two single stranded hybridization regions, each from a strand of the waist region, and said second end terminating with one or two single stranded hybridization region(s), each from a strand of the waist region; and
, the plurality of matrix polynucleotide monomers present does not exceed saturation of the dendritic polynucleotide. - View Dependent Claims (2, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29)
- said dendritic polynucleotide being comprised of a plurality of matrix polynucleotide monomers bonded together by hybridization;
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3. A composition for use as a hybridization reagent for detection of a nucleic acid sequence, said composition comprising a dendritic polynucleotide having a plurality of single stranded hybridization arms;
- said dendritic polynucleotide being comprised of a plurality of matrix polynucleotide monomers bonded together by hybridization;
each matrix polynucleotide monomer, prior to be hybridization bonded to other matrix polynucleotide monomers, having at least three single stranded hybridization regions; and
in said dendritic polynucleotide each matrix polynucleotide monomer is hybridization bonded to at least one other matrix polynucleotide monomer at at least one such hybridization region and when hybridization bonded to more than one such hybridization region of the same matrix polynucleotide monomer, there is an intermediate region where the two monomers are not hybridization bonded;
wherein the plurality of single stranded hybridization arms includes at least one sequence complementary to the nucleic acid sequence to be detected; and
, wherein the plurality of single stranded hybridization arms comprises from at least 108 single stranded arms, up to and including, but not exceeding, that which saturates the dendritic polynucleotide. - View Dependent Claims (13)
- said dendritic polynucleotide being comprised of a plurality of matrix polynucleotide monomers bonded together by hybridization;
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4. A composition for use as a hybridization reagent for detection of a nucleic acid sequence, said composition comprising a dendritic polynucleotide having a plurality of single stranded hybridization arms;
- said dendritic polynucleotide being comprised of a plurality of matrix polynucleotide monomers bonded together by hybridization;
each matrix polynucleotide monomer, prior to being hybridization bonded to other matrix polynucleotide monomers, having at least three single stranded hybridization regions; and
in said dendritic polynucleotide each matrix polynucleotide monomer is hybridization bonded to at least one other matrix polynucleotide monomer at at least one such hybridization region and when hybridization bonded to more than one such hybridization region of the same matrix polynucleotide monomer, there is an intermediate region where the two monomers are not hybridization bonded;
wherein said composition has a sphere volume in a range of 1.6×
106 (nm)3 to 7.5×
108 (nm)3, but the sphere volume does not exceed saturation; and
wherein the plurality of single stranded hybridization arms includes at least one sequence complementary to the nucleic acid sequence to be detected.
- said dendritic polynucleotide being comprised of a plurality of matrix polynucleotide monomers bonded together by hybridization;
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5. A composition for use as a hybridization reagent for detection of a nucleic acid sequence, said composition comprising a dendritic polynucleotide having a plurality of single stranded hybridization arms;
- said dendritic polynucleotide being comprised of a plurality of matrix polynucleotide monomers bonded together by hybridization;
each matrix polynucleotide monomer, prior to being hybridization bonded to other matrix polynucleotide monomers, having at least three single stranded hybridization regions; and
in said dendritic polynucleotide each matrix polynucleotide monomer is hybridization bonded to at least one other matrix polynucleotide monomer at at least one such hybridization region and when hybridization bonded to more than one such hybridization region of the same matrix polynucleotide monomer, there is an intermediate region where the two monomers are not hybridization bonded;
wherein the composition has a shell volume in a range of 1.2×
106 (nm)3 to 1.0×
108 (nm)3, but does not exceed saturation; and
, wherein the plurality of single stranded hybridization arms includes at least one sequence complementary to the nucleic acid sequence to be detected.
- said dendritic polynucleotide being comprised of a plurality of matrix polynucleotide monomers bonded together by hybridization;
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6. A composition for use as a hybridization reagent for detection of a nucleic acid sequence, said composition comprising a dendritic polynucleotide having a plurality of single stranded hybridization arms;
- said dendritic polynucleotide being comprises of a plurality of matrix polynucleotide monomers bonded together by hybridization;
each matrix polynucleotide monomer, prior to being hybridization bonded to other matrix polynucleotide monomers, having at least three single stranded hybridization regions; and
in said dendritic polynucleotide each matrix polynucleotide monomer is hybridization bonded to at least one other matrix polynucleotide monomer at at least one such hybridization region and when hybridization bonded to more than one such hybridization region of the same matrix polynucleotide monomer, there is an intermediate region where the two monomers are not hybridization bonded;
wherein said dendritic polynucleotide comprises DNA and the composition has a total DNA volume in a range of 5.0×
102 (nm)3 to 2.0×
1011 (nm)3, but does not exceed saturation; and
, wherein the plurality of single stranded hybridization arms includes at least one sequence complementary to the nucleic acid sequence to be detected.
- said dendritic polynucleotide being comprises of a plurality of matrix polynucleotide monomers bonded together by hybridization;
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7. A composition for use as a hybridization reagent for detection of a nucleic acid sequence, said composition comprising a dendritic polynucleotide having a plurality of single stranded hybridization arms;
- said dendritic polynucleotide being comprises of a plurality of matrix polynucleotide monomers bonded together by hybridization;
each matrix polynucleotide monomer, prior to being hybridization bonded to other matrix polynucleotide monomers, having at least three single stranded hybridization regions; and
in said dendritic polynucleotide each matrix polynucleotide monomer is hybridization bonded to at least one other matrix polynucleotide monomer at at least one such hybridization region and when hybridization bonded to more than one such hybridization region of the same matrix polynucleotide monomer, there is an intermediate region where the two monomers are not hybridization bonded;
wherein said dendritic polynucleotide comprises DNA and the composition has a total DNA concentration in a range of 1 mg/ml to 744 mg/ml, but does not exceed saturation; and
, wherein the plurality of single stranded hybridization arms includes at least one sequence complementary to the nucleic acid sequence to be detected.
- said dendritic polynucleotide being comprises of a plurality of matrix polynucleotide monomers bonded together by hybridization;
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8. A composition for use as a hybridization reagent for detection of a nucleic acid sequence, said composition comprising a dendritic polynucleotide having a plurality of single stranded hybridization arms;
- said dendritic polynucleotide being comprised of a plurality of matrix polynucleotide monomers bonded together by hybridization;
each matrix polynucleotide monomer, prior to being hybridization bonded to other matrix polynucleotide monomers, having at least three single stranded hybridization regions; and
in said dendritic polynucleotide each matrix polynucleotide monomer is hybridization bonded to at least one other matrix polynucleotide monomer at at least one such hybridization region and when hybridization bonded to more than one such hybridization region of the same matrix polynucleotide monomer, there is an intermediate region where the two monomers are not hybridization bonded;
wherein said composition has a shell concentration in a range of 1 mg/ml to 899 mg/ml, but does not exceed saturation; and
, wherein the plurality of single stranded hybridization arms includes at least one sequence complementary to the nucleic acid sequence to be detected.
- said dendritic polynucleotide being comprised of a plurality of matrix polynucleotide monomers bonded together by hybridization;
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30. A saturated composition comprising a dendritic polynucleotide comprised of a plurality of matrix polynucleotide monomers bonded together by hybridization;
- each matrix polynucleotide monomer, prior to being hybridization bonded to other matrix polynucleotide monomers, having at least three single stranded hybridization regions; and
in said dendritic polynucleotide each matrix polynucleotide monomer is hybridization bonded to at least one other matrix polynucleotide monomer at at least one such hybridization region and when hybridization bonded to more than one such hybridization region of the same matrix polynucleotide monomer, there is an intermediate region where the two monomers are not hybridization bonded;
wherein the number of non-bonded single stranded hybridization arms multiplied by the volume of one matrix polynucleotide monomer is greater than the space available for bonding of the matrix polynucleotide monomers to the non-bonded single stranded hybridization arms; and
, wherein each matrix polynucleotide monomer, prior to hybridization bonding, has a linear double stranded waist region having a first end and a second end, said first end terminating with two single stranded hybridization regions, each from a strand of the waist region, and said second end terminating with one or two single stranded hybridization region(s), each from a strand of the waist region; and
the plurality of matrix polynucleotide monomers present does not exceed saturation of the dendritic polynucleotide. - View Dependent Claims (31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51)
- each matrix polynucleotide monomer, prior to being hybridization bonded to other matrix polynucleotide monomers, having at least three single stranded hybridization regions; and
Specification