US4876187A — Nucleic acid compositions with scissile linkage u…

Claim 1

Independent Claim 134 words

A synthetic, non-naturally occurring composition comprising the structure: --NA.sub.1 --S--NA.sub.2 ].sub.n wherein NA 1 and NA 2 are different noncomplementary nucleic acid sequences; wherein --S-- is a scissile linkage which is capable of being cleaved or disrupted without cleaving or disrupting the nucleic acid sequences of NA 1 or NA 2 or of a target nucleic acid sequence capable of hybridizing to the NA 1 and NA 2 sequences, or to the NA 1 and NA 2 sequences and the scissile linkage of said composition, wherein if the scissile linkage is a nucleic acid sequence it is RNA when both NA 1 and NA 2 are DNA sequences, or the scissile linkage is DNA when both NA 1 and NA 2 are RNA sequences; and wherein n is an integer from 1 to 4.

Claim 2

Dependent Claim 134 words

A synthetic, non-naturally occurring composition comprising the structure: --NA.sub.1 --S--NA.sub.2 ].sub.n wherein NA 1 and NA 2 are different noncomplementary nucleic acid sequences; wherein --S-- is a scissile linkage which is capable of being cleaved or disrupted without cleaving or disrupting the nucleic acid sequences of NA 1 or NA 2 or of a target nucleic acid sequence capable of hybridizing to the NA 1 and NA 2 sequences, or to the NA 1 and NA 2 sequences and the scissile linkage of said composition, wherein if the scissile linkage is a nucleic acid sequence it is RNA when both NA 1 and NA 2 are DNA sequences, or the scissile linkage is DNA when both NA 1 and NA 2 are RNA sequences; and wherein n is an integer from 1 to 4.

Claim 3

Dependent Claim 12 words

The composition of claim 1, wherein the dashed lines represent chemical bonds.

Claim 4

Dependent Claim 12 words

The composition of claim 2, wherein the chemical bonds are covalent bonds.

Claim 5

Dependent Claim 30 words

The composition of claim 1, wherein the scissile linkage is selected from the group consisting of RNA sequences, DNA sequences, amino acid sequences, abasic nucleic acid sequences or carbohydrate polymers.

Claim 6

Dependent Claim 14 words

The composition of claim 1, wherein the scissile linkage is a nucleic acid sequence.

Claim 7

Dependent Claim 10 words

The composition of claim 1 immobilized on a solid support.

Claim 8

Dependent Claim 14 words

The composition of claim 1, wherein NA 1 and NA 2 are DNA sequences.

Claim 9

Dependent Claim 14 words

The composition of claim 1, wherein NA 1 and NA 2 are RNA sequences.

Claim 10

Dependent Claim 36 words

The composition of claim 1, wherein when the scissile linkage is other than a nucleic acid sequence NA 1 is either an RNA or DNA sequence and NA 2 is either an RNA or DNA sequence.

Claim 11

Dependent Claim 23 words

The molecule of claim 1, wherein NA 1 or NA 2 comprises a sequence which is not a naturally occurring nucleic acid sequence.

Claim 12

Dependent Claim 18 words

The composition of claim 1, wherein NA 1 or NA 2 is a naturally occurring nucleic acid sequence.

Claim 13

Dependent Claim 26 words

The composition of claim 1, wherein in each -NA 1 --S--NA 2 ] a marker is attached to one of NA 1 or NA 2 .

Claim 14

Dependent Claim 10 words

The composition of claim 12 immobilized on a solid support.

Claim 15

Dependent Claim 23 words

The composition of claim 12, wherein the marker is a radioisotope, a radiolabelled molecule, a fluorescent molecule, biotin, an enzyme, or a ligand.

Claim 16

Dependent Claim 19 words

The composition of claim 1, wherein NA 1 and NA 2 each comprise between 8 nucleotides and 10,000 nucleotides.

Claim 17

Dependent Claim 22 words

The composition of claim 1, wherein n is greater than 1 and each [NA 1 --S--NA 2 ] unit is the same.

Claim 18

Dependent Claim 21 words

The composition of claim 1, wherein n is greater than 1 and each [NA 1 --S--NA 2 ] unit is different.

Claim 19

Dependent Claim 132 words

A synthetic, non-naturally occurring composition comprising the structure: --NA.sub.1 --S--NA.sub.2 ].sub.n wherein NA 1 and NA 2 are nucleic acid sequences; wherein --S-- is a scissile linkage which is capable of being cleaved or disrupted without cleaving or disrupting the nucleic acid sequences of NA 1 or NA 2 or of a target nucleic acid sequence capable of hybridizing to the NA 1 and NA 2 sequences, or to the NA 1 and NA 2 sequences and the scissile linkage of said composition, wherein if the scissile linkage is a nucleic acid sequence it is RNA when both NA 1 and NA 2 are DNA sequences, or the scissile linkage is DNA when both NA 1 and NA 2 are RNA sequences; and wherein n is an integer from 2 to 4.

Claim 20

Dependent Claim 132 words

A synthetic, non-naturally occurring composition comprising the structure: --NA.sub.1 --S--NA.sub.2 ].sub.n wherein NA 1 and NA 2 are nucleic acid sequences; wherein --S-- is a scissile linkage which is capable of being cleaved or disrupted without cleaving or disrupting the nucleic acid sequences of NA 1 or NA 2 or of a target nucleic acid sequence capable of hybridizing to the NA 1 and NA 2 sequences, or to the NA 1 and NA 2 sequences and the scissile linkage of said composition, wherein if the scissile linkage is a nucleic acid sequence it is RNA when both NA 1 and NA 2 are DNA sequences, or the scissile linkage is DNA when both NA 1 and NA 2 are RNA sequences; and wherein n is an integer from 2 to 4.

Claim 21

Dependent Claim 19 words

The composition of claim 18, wherein a marker is attached to one of NA 1 or NA 2 .

Claim 22

Dependent Claim 10 words

The composition of claim 18 immobilized on a solid support.

Claim 23

Dependent Claim 162 words

A composition comprising the structure: S--L[NA.sub.1 --S--NA.sub.2 ].sub.n M wherein NA 1 and NA 2 are nucleic acid sequences; wherein --S-- is a scissile linkage which is capable of being cleaved or disrupted without cleaving or disrupting the nucleic acid sequences of NA 1 or NA 2 or of a target nucleic acid sequence capable of hybridizing to the NA 1 and NA 2 sequences, or to the NA 1 and NA 2 sequences and the scissile linkage of said composition, wherein if the scissile linkage is a nucleic acid sequence it is RNA when both NA 1 and NA 2 are DNA sequences, or the scissile linkage is DNA when both NA 1 and NA 2 are RNA sequences; wherein n is an integer from 1 to 4; wherein the solid lines represent chemical bonds; wherein X is a solid support; wherein L is a chemical entity which links NA 1 to the solid support; and wherein M is a marker.

Claim 24

Dependent Claim 162 words

A composition comprising the structure: S--L[NA.sub.1 --S--NA.sub.2 ].sub.n M wherein NA 1 and NA 2 are nucleic acid sequences; wherein --S-- is a scissile linkage which is capable of being cleaved or disrupted without cleaving or disrupting the nucleic acid sequences of NA 1 or NA 2 or of a target nucleic acid sequence capable of hybridizing to the NA 1 and NA 2 sequences, or to the NA 1 and NA 2 sequences and the scissile linkage of said composition, wherein if the scissile linkage is a nucleic acid sequence it is RNA when both NA 1 and NA 2 are DNA sequences, or the scissile linkage is DNA when both NA 1 and NA 2 are RNA sequences; wherein n is an integer from 1 to 4; wherein the solid lines represent chemical bonds; wherein X is a solid support; wherein L is a chemical entity which links NA 1 to the solid support; and wherein M is a marker.

Claim 25

Dependent Claim 18 words

The composition of claim 21, wherein X is a silicaceous, cellulosic, or plastic material or controlled pore glass.

Claim 26

Dependent Claim 12 words

The composition of claim 21, wherein the chemical bonds are covalent bonds.

Claim 27

Dependent Claim 14 words

The composition of claim 21, wherein the chemical bonds are hydrogen or covalent bonds.

Claim 28

Dependent Claim 19 words

The composition of claim 21, wherein M is a radioisotope, a radiolabelled molecule, a fluorescent molecule, or a ligand.

Claim 29

Dependent Claim 12 words

The composition of claim 21, wherein the dashed lines represent chemical bonds.

Claim 30

Dependent Claim 17 words

The composition of claim 26, wherein the chemical bonds represented by the dashed lines are covalent bonds.

Claim 31

Dependent Claim 29 words

The composition of claim 21, wherein the scissile linkage is selected from the group consisting of RNA sequences, DNA sequences, amino acid sequences, abasic nucleotide sequences or carbohydrate polymers.

Claim 32

Dependent Claim 19 words

The composition of claim 21, wherein NA 1 and NA 2 each comprise between 8 nucleotides and 10,000 nucleotides.

Claim 33

Dependent Claim 22 words

The composition of claim 21, wherein n is greater than 1 and each [NA 1 --S--NA 2 ] unit is the same.

Claim 34

Dependent Claim 21 words

The composition of claim 21, wherein n is greater than 1 and each [NA 1 --S--NA 2 ] unit is different.

Claim 35

Dependent Claim 166 words

A composition comprising the structure: Y--NA.sub.1 --S--NA.sub.2 ].sub.n Z wherein NA 1 and NA 2 are nucleic acid sequences; wherein --S-- is a scissile linkage which is capable of being cleaved or disrupted without cleaving or disrupting the nucleic acid sequences of NA 1 or NA 2 or of a target nucleic acid sequence capable of hybridizing to the NA 1 and NA 2 sequences, or to the NA 1 and NA 2 sequences and the scissile linkage of said composition, wherein if the scissile linkage is a nucleic acid sequence it is RNA when both NA 1 and NA 2 are DNA sequences, or the scissile linkage is DNA when both NA 1 and NA 2 are RNA sequences; wherein the solid lines represent chemical bonds; wherein n is an integer from 1 to 4; wherein Y is absent or is a chemical entity which confers an identifying characteristic; and wherein Z is absent or is a chemical entity which confers a different identifying characteristic.

Claim 36

Dependent Claim 166 words

A composition comprising the structure: Y--NA.sub.1 --S--NA.sub.2 ].sub.n Z wherein NA 1 and NA 2 are nucleic acid sequences; wherein --S-- is a scissile linkage which is capable of being cleaved or disrupted without cleaving or disrupting the nucleic acid sequences of NA 1 or NA 2 or of a target nucleic acid sequence capable of hybridizing to the NA 1 and NA 2 sequences, or to the NA 1 and NA 2 sequences and the scissile linkage of said composition, wherein if the scissile linkage is a nucleic acid sequence it is RNA when both NA 1 and NA 2 are DNA sequences, or the scissile linkage is DNA when both NA 1 and NA 2 are RNA sequences; wherein the solid lines represent chemical bonds; wherein n is an integer from 1 to 4; wherein Y is absent or is a chemical entity which confers an identifying characteristic; and wherein Z is absent or is a chemical entity which confers a different identifying characteristic.

Claim 37

Dependent Claim 12 words

The composition of claim 32, wherein the chemical bonds are covalent bonds.

Claim 38

Dependent Claim 25 words

The composition of claim 32, wherein the identifying characteristic of Y is hydrophobicity or hydrophilicity and the identifying characteristic of Z is hydrophilicity or hydrophobicity.

Claim 39

Dependent Claim 18 words

The composition of claim 32, wherein when one of Y or Z is absent, the other is hydrophobic.

Claim 40

Dependent Claim 12 words

The composition of claim 32, wherein the dashed lines represent chemical bonds.

Claim 41

Dependent Claim 16 words

The composition of claim 36, wherein the chemical bonds represented by dashed lines are covalent bonds.

Claim 42

Dependent Claim 29 words

The composition of claim 32, wherein the scissile linkage is selected from the group consisting of RNA sequences, DNA sequences, amino acid sequences, abasic nucleotide sequences or carbohydrate polymers.

Claim 43

Dependent Claim 19 words

The composition of claim 32, wherein one of Y or Z is a marker and the other is hydrophobic.

Claim 44

Dependent Claim 19 words

The composition of claim 32, wherein a marker is attached to one of NA 1 or NA 2 .

Claim 45

Dependent Claim 14 words

The compositiion of claim 32, wherein NA 1 and NA 2 are DNA sequences.

Claim 46

Dependent Claim 14 words

The composition of claim 32, wherein NA 1 and NA 2 are RNA sequences.

Claim 47

Dependent Claim 36 words

The composition of claim 32, wherein when the scissile linkage is other than a nucleic acid sequence NA 1 is either an RNA or DNA sequence and NA 2 is either an RNA or DNA sequence.

Claim 48

Dependent Claim 23 words

The composition of claim 32, wherein NA 1 and NA 2 comprises a sequence which is not a naturally occurring nucleic acid sequence.

Claim 49

Dependent Claim 18 words

The composition of claim 32, wherein NA 1 or NA 2 is a naturally occurring nucleic acid sequence.

Claim 50

Dependent Claim 99 words

A method of detecting in a sample the presence of a target nucleic acid sequence of interest comprising: (a) contacting the sample with a composition of claim 12 which comprises a nucleic acid sequence substantially complementary to the target nucleic acid sequence of interest, under hybridizing conditions to form a hybridized complex; (b) immobilizing said complex on a solid support; (c) treating the immobilized complex so as to cleave the scissile linkage; (d) separately recovering the immobilized complex; and (e) detecting the presence of the marker on the immobilized complex and thereby the target nucleic acid sequence of interest.

Claim 51

Dependent Claim 90 words

A method of detecting in a sample the presence of a target nucleic acid sequence of interest comprising: (a) contacting the sample with a composition of claim 21 which comprises a nucleic acid sequence substantially complementary to the target nucleic acid sequence of interest, under hybridizing conditions to form a hybridized complex; (b) treating said complex so as to cleave the scissile linkage; (c) separately recovering the immobilized complex; and (d) detecting the presence of the marker on the immobilized complex and thereby the target nucleic acid sequence of interest.

Claim 52

Dependent Claim 141 words

A method of detecting in a sample a target nucleic acid sequence of interest comprising: (a) contacting under hybridizing conditions the sample with an aqueous solution comprising a composition of claim 40 which comprises a nucleic acid sequence complementary to the target nucleic acid sequence of interest to form a hybridized complex, wherein Y is a hydrophobic entity and Z is a hydrophilic entity; (b) mixing the resulting solution with a nonpolar solvent to form a biphasic solution in which the complex is present at the phase interface of the biphasic solution, Y being oriented in one phase and Z being oriented in the other phase; (c) treating the complex so as to cleave the scissile linkage; (d) recovering the complex so treated; and (e) detecting the presence of the marker and thereby detecting the target nucleic acid sequence of interest.

Claim 53

Dependent Claim 33 words

A diagnostic method for detecting the presence of a foreign pathogen in a sample which comprises detecting a nucleic acid sequence characteristic of the pathogen using the method of any of claims 46-48.

Claim 54

Dependent Claim 107 words

A method for quantitatively determining in a sample the amount of a target nucleic acid sequence of interest comprising: (a) contacting the sample with a predetermined amount of a composition of claim 12, which comprises a nucleic acid sequence substantially complementary to the target nucleic acid sequence of interest, under hybridizing conditions to form a hybridized complex; (b) immobilizing said complex on a solid support; (c) treating the immobilized complex so as to cleave the scissile linkage; (d) separately recovering the immobilized complex; and (e) quantitatively determining the amount of marker present on the immobilized complex and thereby the amount of target nucleic acid sequence of interest.

Claim 55

Dependent Claim 99 words

A method for quantitatively determining in a sample the amount of a target nucleic acid sequence of interest comprising: (a) contacting the sample with a predetermined amount of a composition of claim 21, which comprises a nucleic acid sequence substantially complementary to the target nucleic acid sequence of interest, under hybridizing conditions to form a hybridized complex; (b) treating the immobilized complex so as to cleave the scissile linkage; (c) separately recovering the immobilized complex; and (d) quantitatively determining the amount of marker present on the immobilized complex and thereby the amount of target nucleic acid sequence of interest.

Claim 56

Dependent Claim 145 words

A method for quantitatively determining in a sample the amount of a target nucleic acid sequence of interest comprising: (a) contacting under hybridizing conditions the sample with an aqueous solution comprising a composition of claim 40 which comprises a nulceic acid sequence complementary to the target nucleic acid sequence of interest to form a hybridized complex, wherein Y is a hydrophobic entity and Z is a hydrophilic entity; (b) mixing the resulting solution with a nonpolar solvent to form a biphasic solution in which the complex is present at the phase interface of the biphasic solution, Y being oriented in one phase and Z being oriented in the other phase; (c) treating the complex so as to cleave the scissile linkage; (d) recovering the complex so treated; and (e) quantitatively determining the amount of a marker and thereby the target nucleic acid sequence of interest.

Claim 57

Dependent Claim 31 words

A diagnostic method for measuring the amount of a foreign pathogen in a sample which comprises detecting a nucleic acid of the pathogen using the method of any of claims 50-52.

Annuity Stage	Window Opens	Payment Deadline	Surcharge Period Until	Estimated Fee	Status
3.5 Years (Year 4)	1992-10-23	1993-04-24	1993-10-24	$2000.00	Window Closed / Lapsed
7.5 Years (Year 8)	1996-10-23	1997-04-24	1997-10-24	$3760.00	Window Closed / Lapsed
11.5 Years (Year 12)	2000-10-23	2001-04-24	2001-10-24	$7700.00	Window Closed / Lapsed

Nucleic acid compositions with scissile linkage useful for detecting nucleic acid sequences

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