# US 12,595,281 B2 · Indodicarbocyanine phosphoramidites with bathochromically shifted absorption and emission, and tunable hydrophobicity

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- Number: US 12,595,281 B2
- Document ID: US12595281B2
- Status: Granted
- Kind: B2
- Application number: 18/160,925
- Filed: 2023-01-27
- Published: 2023-08-10
- Granted: 2026-04-07
- Earliest claimed: 2022-02-07
- Assignees: The Government of the United States of America, as represented by the Secretary of the Navy
- Applicants: The Government of the United States of America, as represented by the Secretary of the Navy
- Inventors: Igor L. Medintz; Joseph Melinger; William B. Knowlton; Bernard Yurke; Kimihiro Susumu; Sang Ho Lee; Adam Meares; Divita Mathur; Olga A. Mass; Jeunghoon Lee; Ryan D. Pensack
- Web page: https://patentgrep.com/patent/US12595281B2

## CPC

- C07H 21/00: Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
- C07H 21/04: with deoxyribosyl as saccharide radical
- C07H: SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS (derivatives of aldonic or saccharic acids C07C, C07D; aldonic acids, saccharic acids C07C59/105, C07C59/285; cyanohydrins C07C255/16; glycals C07D; compounds of unknown constitution C07G; polysaccharides, derivatives thereof C08B; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification C12N15/00; sugar industry C13)

## Abstract

New phosphoramidite Cy5 derivatives can be used in automated DNA synthesis, allowing the labeling of DNA sequences with a wider array of chromophores than are presently commercially available. In addition to varying dye hydrophobicity/hydrophilicity, the 5,5′-substituents (including hexyloxy, triethyleneglycol monomethyl ether, tert-butyl, and chloro groups) can modulate electron donating/withdrawing character while also tuning resulting absorption and emission properties. Modification of the Cy5 periphery enables the tuning of photophysical properties, such as absorption and emission maxima, fluorescence quantum yield, and fluorescence lifetime.

## Claims

### Claim 1

A Cy5 derivative comprising a compound having the structure:
wherein MMTr is 4-monomethoxytrityl and R is selected from the group consisting of —O(CH2)5CH3, —O(CH2CH2O)3CH3), —C(CH3)3, and —Cl, and
wherein the Cy5 derivative includes a suitable counterion for the compound.

### Claim 2 (depends on 1)

A Cy5 derivative according to claim 1, wherein said counterion is iodide.

### Claim 3 (depends on 1)

A nucleic acid in a state of having been synthesized to incorporate a Cy5 derivative according to claim 1.

### Claim 4 (depends on 1)

The Cy5 derivative of claim 1, wherein R is —O(CH2)5CH3.

### Claim 5 (depends on 1)

The Cy5 derivative of claim 1, wherein R is —O(CH2CH2O)3CH3).

### Claim 6 (depends on 1)

The Cy5 derivative of claim 1, wherein R is —C(CH3)3.

### Claim 7 (depends on 1)

The Cy5 derivative of claim 1, wherein R is —Cl.

### Claim 8

A Cy5 derivative comprising a compound having the structure:
wherein MMTr is 4-monomethoxytrityl and R is selected from the group consisting of consisting of —CF3 and —CN, and
wherein the Cy5 derivative includes a suitable counterion for the compound.

### Claim 9 (depends on 8)

The Cy5 derivative of claim 8, wherein said counterion is iodide.

### Claim 10 (depends on 1)

A method of synthesizing a Cy5 derivative according to claim 1, comprising, in order:
preparing an N-alkyl indolinium iodide salt precursor;
coupling the iodide salt precursor with malonaldehyde dianilide hydrocholoride; and
conducting a substitution reaction with 4-monomethoxytrityl chloride (MMTr-Cl).

### Claim 11 (depends on 10)

The method of claim 10, wherein said Cy 5 derivative is purified by iterative powderization.

### Claim 12 (depends on 10)

The method of claim 10, wherein R is —O(CH2)5CH3.

### Claim 13 (depends on 10)

The method of claim 10, wherein R is —O(CH2CH2O)3CH3).

### Claim 14 (depends on 10)

The method of claim 10, wherein R is —C(CH3)3.

### Claim 15 (depends on 10)

The method of claim 10, wherein R —Cl.