# US 7,745,126 B2 · Methods, kits and compositions pertaining to combination oligomers and libraries for their preparation

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- Number: US 7,745,126 B2
- Document ID: US7745126B2
- Status: Granted
- Kind: B2
- Application number: 11/616,141
- Filed: 2006-12-26
- Published: 2008-04-10
- Granted: 2010-06-29
- Earliest claimed: 2001-03-09
- Assignees: Boston Probes, Inc.
- Inventors: James M. Coull; Mark J. Fiandaca; Mark D. Kristjanson; Jens J. Hyldig-Nielsen; Theresa S. Creasey
- Web page: https://patentgrep.com/patent/US7745126B2

## CPC

- C12Q 1/6816: characterised by the detection means (C12Q1/6804 takes precedence)
- C40B 20/04: Identifying library members by means of a tag, label, or other readable or detectable entity associated with the library members, e.g. decoding processes
- C40B 30/04: by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
- C40B 40/06: Libraries containing nucleotides or polynucleotides, or derivatives thereof
- C07B 2200/11: Compounds covalently bound to a solid support
- C40B 40/00: Libraries per se, e.g. arrays, mixtures
- Y10S 435/81: Packaged device or kit
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C40B: COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES (in silico combinatorial libraries of nucleic acids, proteins or peptides G16B35/00; in silico combinatorial chemistry G16C20/60)
- C07B: GENERAL METHODS OF ORGANIC CHEMISTRY; APPARATUS THEREFOR (preparation of carboxylic acid esters by telomerisation C07C67/47; telomerisation C08F)
- Y10S: TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS

## Abstract

This invention pertains to the field of combination oligomers, including the block synthesis of combination oligomers in the absence of a template, as well as related methods, kits, libraries and other compositions.

## Claims

### Claim 1

An array of at least two oligomers, wherein at least one of the oligomers is a combination oligomer that comprises a segment having the formula:
A-B-C
wherein:
each of A and C is an oligomer block independently selected from the group consisting of a peptide nucleic acid, a PNA chimera and a PNA combination oligomer and each of A and C is optionally linked to other moieties; and
B is a linker of at least three atoms in length that covalently links oligomer block A to oligomer block C;
wherein:
oligomer blocks A and C taken together encode a probing nucleobase sequence that is designed to sequence specifically hybridize juxtaposed to a target sequence of contiguous nucleobases, such that there is no gap or gap base, to thereby form a double stranded target sequence/combination oligomer complex.

### Claim 2

The away of clam 1, wherein the linker is not part of a nucleobase containing backbone subunit of the polymer.

### Claim 3 (depends on 1)

The array of claim 1, wherein the linker is selected from the group consisting of one amino acid residue, two amino acid residues, three amino acid residues, one E-linker residue, two E-Linker residues, one O-linker residue, two O-linker residues, one X-linker residue and two X-linker residues.

### Claim 4 (depends on 3)

The array of claim 3, wherein the linker is selected from the group consisting of the amino acid glycine, the amino acid dimer gly-gly, the amino acid dimer gly-lys, the amino acid dimer lys-gly, the amino acid dimer glu-gly, the amino acid dimer gly-cys, the amino acid dimer cys-gly and the amino acid dimer asp-gly.

### Claim 5 (depends on 1)

The array of claim 1, wherein at least one of the at least two oligomers comprises a third oligomer block that is linked covalently to the first or second oligomer block by a second linker that is at least three atoms in length, such that the second linker is the same or different in kind from the first said linker.

### Claim 6 (depends on 1)

The array of claim 1, wherein the first and second oligomer blocks are peptide nucleic acids.

### Claim 7 (depends on 1)

The array of claim 1, wherein at least one of the at least two oligomers further comprises at least one energy transfer set of labels such that at least one acceptor moiety of the energy transfer set is linked to one of the linked oligomer blocks of the combination oligomer whilst at least one donor moiety of the energy transfer set is linked to another of the linked oligomer blocks of the combination oligomer, wherein the labels of the set are linked to the oligomer blocks at positions that facilitate a change in detectable signal of at least one label when the combination oligomer is hybridized to the target sequence as compared to when the combination oligomer is in a non-hybridized state.

### Claim 8 (depends on 7)

The array of claim 7, wherein the labels of the energy transfer set are linked to the distal-most termini of the oligomer blocks or to sites within the oligomer blocks.

### Claim 9 (depends on 8)

The array of claim 8, wherein the energy transfer set of each combination oligomer comprises a single donor moiety and a single acceptor moiety.

### Claim 10 (depends on 9)

The array of claim 9, wherein both the donor and acceptor moieties are fluorophores.

### Claim 11 (depends on 9)

The array of claim 9, wherein the donor moiety is a donor fluorophore and the acceptor moiety is a non-fluorescent quencher moiety.

### Claim 12 (depends on 1)

The array of claim 1, wherein each combination oligomer further comprises one or more reporter moieties.

### Claim 13 (depends on 1)

The array of claim 1, wherein each combination oligomer is unlabeled.

### Claim 14

A method comprising:
(a) reacting, at a site on a solid surface, a first oligomer block, a second oligomer block, and optionally a condensation reagent or reagents under condensation conditions to thereby form a combination oligomer having a linker of at least three atoms in length that covalently links the first oligomer block to the second oligomer block;
wherein:
(i) one of said two oligomer blocks is support bound;
(ii) each of the first and second oligomer blocks independently selected from the group consisting of a peptide nucleic acid, a PNA chimera and a PNA combination oligomer;
(iii) one or both oligomer blocks do not comprise nucleobase protecting groups; and
(iv) the combination oligomer forms in the absence of a template; and
(b) repeating step (a) at one or more sites until the array of combination oligomers is constructed,
with the further proviso that the first and second oligomer blocks taken together encode a probing nucleobase sequence that is designed to sequence specifically hybridize juxtaposed to a target sequence of contiguous nucleobases, such that there is no gap or gap base, to thereby form a double stranded target sequence/combination oligomer complex.

### Claim 15 (depends on 14)

The method of claim 14, wherein the linker is not part of a nucleobase containing backbone subunit of the polymer.

### Claim 16

A method comprising:
(a) reacting, at a site on a solid surface, a combination oligomer having a linker of at least three atoms in length that covalently links the first oligomer block to the second oligomer block with a surface functional group to thereby attached the combination oligomer to the surface of the array, wherein:
(i) each of the first and second oligomer blocks independently selected from the group consisting of a peptide nucleic acid, a PNA chimera and a PNA combination oligomer;
(ii) one or both oligomer blocks do not comprise nucleobase protecting groups; and
(b) repeating step (a) at one or more sites until the array of combination oligomers is constructed,
with the further proviso that the combination oligomer hybridizes juxtaposed to a target sequence of contiguous nucleobases, with no gap or gap base.

### Claim 17 (depends on 16)

The method of claim 16, wherein the linker is not part of a nucleobase containing backbone subunit of the polymer.

### Claim 18

An array of at least two oligomers, wherein at least one of the oligomers is a combination oligomer that comprises a segment having the formula:
A-B-C
wherein:
each of A and C is an oligomer block independently selected from the group consisting of a peptide nucleic acid, a PNA chimera and a PNA combination oligomer and each of A and C is optionally linked to other moieties; and
B is a linker of at least three atoms in length that covalently links oligomer block A to oligomer block C;
wherein:
oligomer blocks A and C taken together encode a probing nucleobase sequence that is designed to sequence specifically hybridize juxtaposed to a target sequence of contiguous nucleobases, such that there is no gap or gap base, to thereby form a double stranded target sequence/combination oligomer complex,
with the further proviso that the linker is not part of a nucleobase containing backbone subunit of the polymer.

### Claim 19

An array of at least two oligomers, wherein at least one of the oligomers is a combination oligomer that comprises a segment having the formula:
A-B-C
wherein:
each of A and C is an oligomer block independently selected from the group consisting of a peptide nucleic acid, a PNA chimera and a PNA combination oligomer and each of A and C is optionally linked to other moieties; and
B is a linker of at least three atoms in length that covalently links oligomer block A to oligomer block C;
wherein:
oligomer blocks A and C taken together encode a probing nucleobase sequence that is designed to sequence specifically hybridize juxtaposed to a target sequence of contiguous nucleobases, such that there is no gap or gap base, to thereby form a double stranded target sequence/combination oligomer complex, and
wherein at least one of the at least two oligomers further comprises at least one energy transfer set of labels such that at least one acceptor moiety of the energy transfer set is linked to one of the linked oligomer blocks of the combination oligomer whilst at least one donor moiety of the energy transfer set is linked to another of the linked oligomer blocks of the combination oligomer, wherein the labels of the set are linked to the oligomer blocks at positions that facilitate a change in detectable signal of at least one label when the combination oligomer is hybridized to the target sequence as compared to when the combination oligomer is in a non-hybridized state.

### Claim 20 (depends on 19)

The array of claim 19, wherein the labels of the energy transfer set are linked to the distal-most termini of the oligomer blocks or to sites within the oligomer blocks.

### Claim 21 (depends on 20)

The array of claim 20, wherein the energy transfer set of each combination oligomer comprises a single donor moiety and a single acceptor moiety.

### Claim 22 (depends on 21)

The array of claim 21, wherein both the donor and acceptor moieties are fluorophores.

### Claim 23 (depends on 21)

The array of claim 21, wherein the donor moiety is a donor fluorophore and the acceptor moiety is a non-fluorescent quencher moiety.

### Claim 24

A method comprising:
(a) reacting, at a site on a solid surface, a first oligomer block, a second oligomer block, and optionally a condensation reagent or reagents under condensation conditions to thereby form a combination oligomer having a linker of at least three atoms in length that covalently links the first oligomer block to the second oligomer block, wherein:
(i) one of said two oligomer blocks is support bound;
(ii) each of the first and second oligomer blocks independently selected from the group consisting of a peptide nucleic acid, a PNA chimera and a PNA combination oligomer;
(iii) one or both oligomer blocks do not comprise nucleobase protecting groups; and
(iv) the combination oligomer forms in the absence of a template; and
(b) repeating step (a) at one or more sites until the array of combination oligomers is constructed,
with the further proviso that the linker is not part of a nucleobase containing backbone subunit of the polymer.

### Claim 25 (depends on 24)

The method of claim 24, wherein the first and second oligomer blocks taken together encode a probing nucleobase sequence that is designed to sequence specifically hybridize juxtaposed to a target sequence of contiguous nucleobases, such that there is no gap or gap base, to thereby form a double stranded target sequence/combination oligomer complex.

### Claim 26

A method comprising:
(a) reacting, at a site on a solid surface, a combination oligomer having a linker of at least three atoms in length that covalently links the first oligomer block to the second oligomer block with a surface functional group to thereby attached the combination oligomer to the surface of the array, wherein:
(i) each of the first and second oligomer blocks independently selected from the group consisting of a peptide nucleic acid, a PNA chimera and a PNA combination oligomer;
(ii) one or both oligomer blocks do not comprise nucleobase protecting groups; and
(b) repeating step (a) at one or more sites until the array of combination oligomers is constructed,
with the further proviso that the linker is not part of a nucleobase containing backbone subunit of the polymer.

### Claim 27 (depends on 26)

The method of claim 26, wherein the first and second oligomer blocks taken together encode a probing nucleobase sequence that is designed to sequence specifically hybridize juxtaposed to a target sequence of contiguous nucleobases, such that there is no gap or gap base, to thereby form a double stranded target sequence/combination oligomer complex.