# US 5,705,333 A · Peptide-based nucleic acid mimics(PENAMS)

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- Number: US 5,705,333 A
- Document ID: US5705333A
- Status: Granted
- Kind: A
- Application number: 08/286,875
- Filed: 1994-08-05
- Granted: 1998-01-06
- Earliest claimed: 1994-08-05
- Assignees: The Regents of the University of California
- Inventors: Vibhakar J. Shah; George L. Kenyon; Irwin D. Kuntz
- Web page: https://patentgrep.com/patent/US5705333A

## CPC

- C12Q 1/6811: Selection methods for production or design of target specific oligonucleotides or binding molecules
- C07K 14/003: {Peptide-nucleic acids (PNAs)}
- C12Q 1/6813: Hybridisation assays
- Y10T 436/143333: Saccharide [e.g., DNA, etc.]
- 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
- C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00)
- Y10T: TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION

## Abstract

The present invention provides novel nucleic acid mimics (termed "PENAMs") comprising a peptidic backbone and nucleotidic sidechains; the sidechains being oriented in such a way that the PENAM is homomorphous to target nucleic acids with which it can effectively hydrogen bond. Homomorphism is achieved by the incorporation of unusual sterochemical centers, including D-chiral centers and quasi-chiral centers, into the peptidic backbone. The PENAMs are useful for targeting nucleic acid sequences in order to modulate their activity in an "antisense" manner. Targeting can also be used to detect, isolate or modify target nucleic acids.

## Claims

### Claim 1

A composition useful in targeting a nucleic acid comprising a stereochemically-selected population of peptide-based nucleic acid mimics (PENAMs) each member of which comprises a sequence of at least about 4 NuAA monomers,
wherein said NuAA monomers are each of the following formula: ##STR7## wherein: E is carbon (C) or nitrogen (N);
W is hydrogen or a spacer group;
Y is hydrogen or a spacer group (when E is carbon), or Y is a lone pair of electrons (when E is nitrogen);
S 1 is a bond or a first spacer group;
S2 is a bond or a second spacer group;
S3 is a bond or a third spacer group;
X is oxygen (O) or sulfur (S);
B is a base segment comprising a nucleotidic base or an analog thereof; and
N is nitrogen,
and wherein at least one of said PENAMs is a homomorphicaily-preferred PENAM comprising a D-chiral center and wherein said homomorphically-preferred PENAM makes up at least about 10% of the stereochemically-selected population of PENAMs wherein said D-chiral center is located within a NuAA at position E wherein E is carbon.

### Claim 2 (depends on 1)

A PENAM composition of claim 1, wherein the NuAA monomers in said homomorphically-preferred PENAM are joined directly to each other via peptide bonds and at least one of S1 and S2 in each of the adjacent NuAA monomers is a spacer group.

### Claim 3 (depends on 1)

A PENAM composition of claim 1, wherein the NuAA monomers in said homomorphically-preferred PENAM are joined via intervening aminoacyl residues and S2 in each of the NuAA monomers is a bond.

### Claim 4 (depends on 1)

A PENAM composition of claim 1, wherein said D-chiral center is located between two NuAA monomers at a chiral carbon in an intervening amino acid residue.

### Claim 5 (depends on 1)

A PENAM composition of claim 1, wherein at least about 50% of the chiral centers in said homomorphically-preferred PENAM are D-chiral centers.

### Claim 6 (depends on 1)

A PENAM composition of claim 1, wherein about 50% of the chiral centers in said homomorphically-preferred PENAM are D-chiral centers, and 50% of the chiral centers are L-chiral centers, and wherein at least about 80% of L-chiral centers are flanked by D-chiral centers.

### Claim 7 (depends on 1)

A PENAM composition of claim 1, wherein at least about 80% of the chiral centers in said homomorphically-preferred PENAM are D-chiral centers.

### Claim 8 (depends on 1)

A PENAM composition of claim 1, wherein at least one of S1 and S2 is a spacer group having a backbone of two to three atoms, S3 is a spacer group having a backbone of two to three atoms, W is hydrogen, E is carbon, and Y is hydrogen.

### Claim 9 (depends on 1)

A PENAM composition of claim 1, wherein said homomorphically-preferred PENAM comprises a quasi-chiral center and said quasi-chiral center is located within a NuAA monomer at position E wherein E is nitrogen.

### Claim 10 (depends on 1)

A PENAM composition of claim 1, wherein said homomorphically-preferred PENAM comprises a quasi-chiral center and said quasi-chiral center is located between two NuAA monomers in an intervening aza-amino acid residue.

### Claim 11 (depends on 1)

A PENAM composition of claim 1, wherein said homomorphically-preferred PENAM further comprises a target modifying group.

### Claim 12 (depends on 11)

A PENAM composition of claim 11, wherein said target modifying group is located within a NuAA monomer.

### Claim 13 (depends on 11)

A PENAM composition of claim 11, wherein said target modifying group is located between NuAA monomers or outside of a string of NuAA monomers.

### Claim 14

A free NuAA monomer that is a precursor of a NuAA monomeric subunit comprising a D-chiral center wherein said NuAA monomeric subunit comprising a D-chiral center is of the following formula: ##STR8## wherein: E is said D-chiral center and is carbon (C);
W is hydrogen or a spacer group;
Y is hydrogen or a spacer group;
S1 is a bond or a first spacer group;
S2 is a bond or a second spacer group;
S3 is a third spacer group with a backbone of at least two atoms;
X is oxygen (O) or sulfur (S);
B is a base segment comprising a nucleotidic base or an analog thereof; and
N is nitrogen;
and wherein at least one of S1 and S2 is a spacer group, and wherein S3 is a spacer group with a backbone of at least two atoms;
wherein said free NuAA monomer is of the same formula except that the N-terminus is in the form of an amine group or a protected amine group and the C-terminus is in the form of a carboxyl group or a protected carboxyl group.

### Claim 15 (depends on 1)

A method of preparing a PENAM composition of claim 1 for targeting a target nucleic acid comprising:
(a) providing at least about 4 NuAA monomers wherein at least one of said NuAA monomers comprises a D-chiral center at portion E wherein E is carbon; and
(b) synthesizing an oligomer of the monomers such that the arrangement of bases in the oligomer is substantially complementary to a sequence of nucleotidic bases in a portion of the target nucleic acid.

### Claim 16 (depends on 15)

A method of claim 15, wherein said NuAA monomers are linked to each other directly via peptide bonds.

### Claim 17 (depends on 15)

A method of claim 15, wherein said NuAA monomers are linked to each other indirectly via intervening aminoacyl monomers.

### Claim 18 (depends on 15)

A method of claim 15, further comprising the step of synthesizing a NuAA monomer having a D-chiral center at position E wherein E is carbon wherein said NuAA monomer having a D-chiral center at position E wherein E is carbon is present at a purity of at least about 90% enantiomeric excess relative to its enantiomeric NuAA monomer having an L-chiral center.

### Claim 19 (depends on 15)

A method of claim 15, further comprising the step of synthesizing a NuAA monomer having a quasi-chiral center.

### Claim 20 (depends on 1)

A method of targeting a target nucleic acid comprising:
(a) providing a PENAM composition according to claim 1; and
(b) contacting said PENAM composition with the target nucleic acid.

### Claim 21 (depends on 1)

A method of modulating a target nucleic acid in an antisense manner comprising:
(a) providing a PENAM composition according to claim 1 wherein the sequence of bases in said NuAA monomers is substantially complementary to a sequence of bases in the target nucleic acid; and
(b) contacting said PENAM composition with the target nucleic acid.

### Claim 22 (depends on 1)

A method of modifying a target nucleic acid comprising:
(a) providing a PENAM composition of claim 1 wherein said homomorphically-preferred PENAM further comprises a target modifying group; and
(b) contacting said PENAM composition with the target nucleic acid.

### Claim 23 (depends on 1)

A method of detecting a target nucleic acid comprising:
(a) providing a PENAM composition according to claim 1 wherein the sequence of bases in said NuAA monomers is substantially complementary to a sequence of bases in the target nucleic acid; and
(b) contacting said PENAM composition with the target nucleic acid; and
(c) detecting a target complex comprising said nucleic acid mimic and said target nucleic acid or detecting a modification in the target nucleic acid.

### Claim 24 (depends on 1)

A method of isolating a target nucleic acid comprising:
(a) providing a PENAM composition according to claim 1 wherein the sequence of bases in said NuAA monomers is substantially complementary to a sequence of bases in the target nucleic acid; and
(b) contacting said PENAM composition with the target nucleic acid; and
(c) isolating PENAMs bound to said target nucleic acid or isolating a modified target nucleic acid.