# US 7,407,773 B2 · Method for characterizing a carbohydrate polymer

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- Number: US 7,407,773 B2
- Document ID: US7407773B2
- Status: Granted
- Kind: B2
- Application number: 11/402,646
- Filed: 2006-04-11
- Published: 2007-04-26
- Granted: 2008-08-05
- Earliest claimed: 2006-04-11
- Assignees: Procognia, Ltd.
- Inventors: Ofer Markman; Assaf (Assaph) Peretz Oron; Chana Rothmann-Schertz
- Web page: https://patentgrep.com/patent/US7407773B2

## CPC

- G01N 33/5308: {for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites}
- G01N 2400/00: Assays, e.g. immunoassays or enzyme assays, involving carbohydrates
- 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)

## Abstract

Disclosed is a method for characterizing carbohydrate polymer by identifying at least two binding agents that bind to the carbohydrate polymer. Binding is preferably determined by contacting the carbohydrate polymer with substrate that contains a plurality of first saccharide-binding agents affixed at predetermined locations on the substrate. The carbohydrate polymer is allowed to contact the substrate under conditions that allow for formation of a first complex between the first saccharide-binding agent and the carbohydrate polymer. A second saccharide-binding agent, which preferably includes a label, is also contacted with the carbohydrate polymer under conditions that allow for formation of a second complex between the second binding agent and the first complex. Identification of the first and second binding agent allows for characterization of the polysaccharide.

## Claims

### Claim 1

A method for characterizing a carbohydrate polymer, the method comprising:
a) providing a surface comprising a plurality of different essentially sequence- and/or site-specific binding agents having different binding specificities attached to a plurality of predetermined locations on said surface;
b) contacting said surface with a carbohydrate polymer sample;
c) contacting said surface with at least one saccharide-binding agent, wherein at least one of the carbohydrate polymer sample or saccharide-binding agent comprise a detectable label;
d) detecting said label; and
e) identifying said saccharide-binding agent if bound in a complex with said carbohydrate polymer and if said carbohydrate polymer is bound in a complex with at least one of a plurality of different essentially sequence- and/or site-specific binding agents,
thereby characterizing said carbohydrate polymer.

### Claim 2 (depends on 1)

The method of claim 1, wherein said at least one of said plurality of different essentially sequence- and/or site-specific binding agents is identified by determining the location of the detected label on the substrate.

### Claim 3 (depends on 2)

The method of claim 2, wherein said detectable label is selected from the group consisting of a chromogenic labels, a radiolabel, a fluorescent label, and a biotinylated label.

### Claim 4 (depends on 1)

The method of claim 1, wherein said surface comprises at least five different essentially sequence- and/or site-specific binding agents affixed to said surface.

### Claim 5 (depends on 1)

The method of claim 1, wherein said surface comprises at least 15 different essentially sequence- and/or site-specific binding agents affixed to said surface.

### Claim 6 (depends on 1)

The method of claim 1, wherein said surface is contacted with at least 5 different saccharide-binding agents.

### Claim 7 (depends on 1)

The method of claim 1, wherein said surface is contacted with at least 15 different saccharide-binding agents.

### Claim 8 (depends on 4)

The method of claim 4, wherein said surface is contacted with at least five different saccharide-binding agents.

### Claim 9 (depends on 5)

The method of claim 5, wherein said surface is contacted with at least 15 different saccharide-binding agents.

### Claim 10 (depends on 6)

The method of claim 6, wherein said plurality of different essentially sequence- and/or site-specific binding agents is selected from the group consisting of a lectin, a saccharide-cleaving enzyme, and an antibody.

### Claim 11 (depends on 7)

The method of claim 7, wherein said saccharide binding agent is selected from the group consisting of a lectin, a polysaccharide-cleaving enzyme, a saccharide modifying enzyme, and an antibody to a saccharide.

### Claim 12 (depends on 10)

The method of claim 10, wherein said saccharide binding agent is selected from the group consisting of a lectin, a polysaccharide-cleaving or modifying enzyme, and an antibody to a saccharide.

### Claim 13 (depends on 11)

The method of claim 11, wherein said carbohydrate polymer is provided after digestion with a saccharide-cleaving agent.

### Claim 14 (depends on 1)

The method of claim 1, wherein said carbohydrate polymer is digested with a saccharide-cleaving agent prior to contacting said saccharide with said saccharide-binding agent.

### Claim 15 (depends on 1)

The method of claim 1, further comprising removing unbound plurality of different essentially sequence- and/or site-specific binding agents from said surface prior to contacting said surface with said saccharide-binding agent.

### Claim 16 (depends on 1)

The method of claim 1, wherein said method further comprises acquiring one or more images of said plurality of different essentially sequence- and/or site-specific binding agents and said saccharide-binding agent.

### Claim 17 (depends on 16)

The method of claim 16, wherein said image is stored.

### Claim 18 (depends on 17)

The method of claim 17, wherein said image is stored as a photograph or digitized image.

### Claim 19

A method of generating a fingerprint of a carbohydrate polymer, the method comprising
providing a carbohydrate polymer sample,
contacting said carbohydrate polymer with a plurality of different essentially sequence- and/or site-specific binding agents;
determining whether said carbohydrate polymer binds to at least one of said plurality of different essentially sequence- and/or site-specific binding agents;
contacting said carbohydrate polymer with a saccharide-binding agent, wherein at least one of the carbohydrate polymer sample or saccharide-binding agent comprise a detectable label;
detecting said label; and
determining whether said carbohydrate polymer binds to said saccharide-binding reagent,
thereby generating a fingerprint of said carbohydrate polymer.

### Claim 20 (depends on 19)

The method of claim 19, further comprising contacting said carbohydrate polymer with at least five different essentially sequence- and/or site-specific binding agents, and determining whether said carbohydrate polymer binds to each of said at least five different essentially sequence- and/or site-specific binding agents.

### Claim 21 (depends on 19)

The method of claim 19, further comprising contacting said carbohydrate polymer with at least 15 different essentially sequence- and/or site-specific binding agents, and determining whether said carbohydrate polymer binds to each of said at least 15 different essentially sequence- and/or site-specific binding agents.

### Claim 22 (depends on 19)

The method of claim 19, wherein said carbohydrate polymer is selected from the group consisting of a glycoprotein and a glycolipid.

### Claim 23 (depends on 19)

The method of claim 19, wherein said carbohydrate polymer is a polysaccharide.

### Claim 24 (depends on 19)

The method of claim 19, wherein binding of each of said plurality of different essentially sequence- and/or site-specific binding agents and said saccharide binding agent is determined by
a) providing a surface comprising a plurality of different essentially sequence- and/or site-specific binding agents having different binding specificities attached to a plurality of predetermined locations on said surface;
b) contacting said surface with a carbohydrate polymer sample;
c) contacting said surface with at least one saccharide-binding agent, wherein at least one of the carbohydrate polymer sample or saccharide-binding agent comprise a detectable label;
d) detecting said label; and
e) identifying said saccharide binding agent if bound in a complex with said carbohydrate polymer and if said carbohydrate polymer is bound in a complex with at least one of said plurality of different essentially sequence- and/or site-specific binding agents.

### Claim 25 (depends on 19)

The method of claim 19, wherein said at least one of said plurality of different essentially sequence and/or site-specific binding agent is identified by determining the location of the detected label on the substrate.

### Claim 26 (depends on 19)

The method of claim 19, wherein said detectable label is selected from the group consisting of a chromogenic label, a radiolabel, a fluorescent label, and a biotinylated label.

### Claim 27 (depends on 19)

The method of claim 19, wherein said surface comprises at least five different essentially sequence and/or site-specific binding agents affixed to said surface.

### Claim 28 (depends on 19)

The method of claim 19, wherein said surface comprises at least 15 different essentially sequence and/or site-specific binding agents affixed to said surface.

### Claim 29 (depends on 19)

The method of claim 19, wherein said surface is contacted with at least 5 different saccharide-binding agents.

### Claim 30 (depends on 19)

The method of claim 19, wherein said surface is contacted with at least 15 different saccharide-binding agents.

### Claim 31 (depends on 19)

The method of claim 19, wherein said surface is contacted with at least five saccharide-binding agents.

### Claim 32 (depends on 19)

The method of claim 19, wherein said surface is contacted with at least 15 different saccharide-binding agents.

### Claim 33 (depends on 19)

The method of claim 19, wherein said plurality of different essentially sequence and/or site-specific binding agents is selected from the group consisting of a lectin, a saccharide-cleaving enzyme, and an antibody.

### Claim 34 (depends on 33)

The method of claim 33, wherein said saccharide binding agent is selected from the group consisting of a lectin, a polysaccharide-cleaving or modifying enzyme, and an antibody to a saccharide.

### Claim 35 (depends on 19)

The method of claim 19, wherein said saccharide binding agent is selected from the group consisting of a lectin, a polysaccharide-modifying or cleaving enzyme, and an antibody to a saccharide.

### Claim 36 (depends on 19)

The method of claim 19, wherein said carbohydrate polymer is provided after digestion with a saccharide-cleaving agent.

### Claim 37 (depends on 19)

The method of claim 19, wherein said carbohydrate polymer is digested with a saccharide-cleaving agent prior to contacting said saccharide with said saccharide-binding agent.