# US 7,611,888 B2 · Rotaxane compound, rotaxane-bonded solid substrate, and biochip using the same

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- Number: US 7,611,888 B2
- Document ID: US7611888B2
- Status: Granted
- Kind: B2
- Application number: 10/563,477
- Filed: 2004-07-05
- Published: 2006-07-13
- Granted: 2009-11-03
- Earliest claimed: 2003-07-05
- Assignees: Postech Foundation
- Inventors: Kimoon Kim; Jin Koo Kang; Woo Seong Jeon; Miran Noh; Dongwoo Kim; Kangkyun Baek
- Web page: https://patentgrep.com/patent/US7611888B2

## CPC

- C07D 487/22: in which the condensed system contains four or more hetero rings
- G01N 33/545: Synthetic resin
- C07B 2200/11: Compounds covalently bound to a solid support
- G01N 2035/00158: {Elements containing microarrays, i.e. "biochip"}
- C07D: HETEROCYCLIC COMPOUNDS (macromolecular compounds C08)
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)
- C07B: GENERAL METHODS OF ORGANIC CHEMISTRY; APPARATUS THEREFOR (preparation of carboxylic acid esters by telomerisation C07C67/47; telomerisation C08F)

## Abstract

The present disclosure provides a rotaxane compound that can be used to separate molecules within a linkage layer formed on a solid substrate of a biochip by a predetermined distance. The compound is represented by Formula 1, in which a compound of Formula 3 vertically passes through a cavity of cucurbituril or its derivative of Formula 2. It further provides gene chips, protein chips and sensors for biomaterial assays which use the rotaxane molecules to allow biomaterials to be immobilized on a linkage layer such that they are regularly spaced apart from each other by a predetermined distance.

## Claims

### Claim 1

A solid substrate for a biochip comprising a compound represented by Formula 1 below:
wherein R1, R2, and R3 are each independently saturated or unsaturated linear C2-C10 alkylene, ethyleneglycol oligomer, 1,4-substituted benzene, or 1,4-substituted pyridine; R4 and R5 are each independently hydrogen, an alkenyloxy group with an unsaturated bond end and a substituted or unsubstituted alkyl moiety of C1-C20, a carboxyalkylsulfinyloxy group with a substituted or unsubstituted alkyl moiety of C1-C20, a carboxyalkyloxy group with a substituted or unsubstituted alkyl moiety of C2-C8, an aminoalkyloxy group with a substituted or unsubstituted alkyl moiety of C2-C8, or a hydroxyalkyloxy group with a substituted or unsubstituted alkyl moiety of C2-C8; X1 and X2 are each independently a positively charged functional group for ion-dipole interaction with an oxygen atom of cucurbituril or its derivative of represented by Formula 2; Y1 is a functional group for a linkage with a biomaterial comprising a gene or a protein; and Y2 is a functional group capable of binding to the solid substrate, wherein the compound of Formula 1 bonded to the solid substrate provides a linkage layer with a predetermined spacing in the biochip; and
wherein a compound of Formula 3
Y1—R1—X1—R2—X2—R3—Y2 (3)
(wherein R1, R2, R3, X1, X2, Y1, and Y2 are as defined in Formula 1 above)
vertically passes through a cavity of cucurbituril or its derivative represented by Formula 2
(wherein n is an integer of 4 to 20; and R4 and R5 are as defined in Formula 1 above).

### Claim 2 (depends on 1)

The solid substrate of claim 1, wherein X1 and
X2 are each independently secondary ammonium, 1,4-substituted pyridinum, or benzyl ammonium; and Y1 and Y2 are each independently a primary amine group, an amide group, an acrylamine group, an alkylester group, an aldehyde group, a carboxyl group, an alkoxysilane group, a halogenated acyl group, a hydroxyl group, a thiol group, a halogen group, a cyan group, an isocyan group, or an isothiocyan group.

### Claim 3 (depends on 1)

The solid substrate of claim 1, wherein the compound of Formula 1 is selected from the group consisting of compounds represented by Formulae 5 through 13:

### Claim 4 (depends on 1)

The solid substrate of claim 1, wherein the compound of Formula 1 is present in a density of 0.05 to 0.6 compounds/nm2.

### Claim 5 (depends on 1)

The solid substrate of claim 1, which is a glass, a silicon wafer, an indium tin oxide (ITO) glass, an aluminum oxide substrate, or a titanium dioxide substrate.

### Claim 6 (depends on 1)

A gene chip comprising the solid substrate of claim 1 and a DNA capable of selectively interacting with a DNA to be assayed.

### Claim 7 (depends on 1)

A protein chip comprising the solid substrate of claim 1 and a protein capable of selectively interacting with a protein to be assayed.

### Claim 8 (depends on 1)

A sensor for biomaterial assay comprising the solid substrate of claim 1, wherein the biomaterial is a DNA or protein.

### Claim 9 (depends on 1)

The solid substrate of claim 1, wherein the biochip is selected from the group consisting of a gene chip, a protein chip and a sensor for biomaterial assay.

### Claim 10 (depends on 1)

The solid substrate of claim 1, wherein the compound of Formula 1 is bonded to the solid substrate via a covalent bond or a non-covalent bond.